diff --git a/Bio/AlignIO/MafIO.py b/Bio/AlignIO/MafIO.py index bacff77a1..b1e851367 100644 --- a/Bio/AlignIO/MafIO.py +++ b/Bio/AlignIO/MafIO.py @@ -35,14 +35,7 @@ A 1-column wide alignment would have ``start == end``. import os from itertools import islice -try: - from sqlite3 import dbapi2 as _sqlite -except ImportError: - # Not present on Jython, but should be included in Python 2.5 - # or later (unless compiled from source without its dependencies) - # Still want to offer simple parsing/output - _sqlite = None - +from sqlite3 import dbapi2 from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio.Align import MultipleSeqAlignment @@ -275,10 +268,10 @@ class MafIndex: # if sqlite_file exists, use the existing db, otherwise index the file if os.path.isfile(sqlite_file): - self._con = _sqlite.connect(sqlite_file) + self._con = dbapi2.connect(sqlite_file) self._record_count = self.__check_existing_db() else: - self._con = _sqlite.connect(sqlite_file) + self._con = dbapi2.connect(sqlite_file) self._record_count = self.__make_new_index() # lastly, setup a MafIterator pointing at the open maf_file @@ -352,7 +345,7 @@ class MafIndex: return records_found - except (_sqlite.OperationalError, _sqlite.DatabaseError) as err: + except (dbapi2.OperationalError, dbapi2.DatabaseError) as err: raise ValueError("Problem with SQLite database: %s" % err) from None def __make_new_index(self): diff --git a/Bio/Blast/NCBIXML.py b/Bio/Blast/NCBIXML.py index c7aaee8fd..90e91a9bd 100644 --- a/Bio/Blast/NCBIXML.py +++ b/Bio/Blast/NCBIXML.py @@ -852,11 +852,6 @@ def parse(handle, debug=0): text, pending = pending, NULL break - # this was added because it seems that the Jython expat parser - # was adding records later then the Python one - while blast_parser._records: - yield blast_parser._records.pop(0) - # At this point we have finished the first XML record. # If the file is from an old version of blast, it may # contain more XML records (check if text==""). diff --git a/Bio/Nexus/Trees.py b/Bio/Nexus/Trees.py index 8c976fcf5..4f76ec724 100644 --- a/Bio/Nexus/Trees.py +++ b/Bio/Nexus/Trees.py @@ -594,8 +594,7 @@ class Tree(Nodes.Chain): table = [ ("#", "taxon", "prev", "succ", "brlen", "blen (sum)", "support", "comment") ] - # Sort this to be consistent across CPython, Jython, etc - for i in sorted(self.all_ids()): + for i in self.all_ids(): n = self.node(i) if not n.data: table.append( diff --git a/Bio/Phylo/PAML/_parse_codeml.py b/Bio/Phylo/PAML/_parse_codeml.py index 34122e172..3c90a7c9a 100644 --- a/Bio/Phylo/PAML/_parse_codeml.py +++ b/Bio/Phylo/PAML/_parse_codeml.py @@ -309,8 +309,6 @@ def parse_model(lines, results): branch = branch_res.group(1) if parameters.get("branches") is None: parameters["branches"] = {} - # Hack for Jython http://bugs.jython.org/issue1762 float("-nan") - line = line.replace(" -nan", " nan") params = line.strip().split()[1:] parameters["branches"][branch] = { "t": float(params[0].strip()), diff --git a/Bio/PopGen/GenePop/Controller.py b/Bio/PopGen/GenePop/Controller.py index 07fb63abd..0ea743459 100644 --- a/Bio/PopGen/GenePop/Controller.py +++ b/Bio/PopGen/GenePop/Controller.py @@ -160,11 +160,7 @@ class _FileIterator: def __del__(self): self.stream.close() - try: - os.remove(self.fname) - except OSError: - # Jython seems to call the iterator twice - pass + os.remove(self.fname) class _GenePopCommandline(AbstractCommandline): diff --git a/Doc/Tutorial/chapter_learning.tex b/Doc/Tutorial/chapter_learning.tex index 00ed15797..e49775918 100644 --- a/Doc/Tutorial/chapter_learning.tex +++ b/Doc/Tutorial/chapter_learning.tex @@ -75,44 +75,45 @@ Gene pair & Intergene distance ($x_1$) & Gene expression score ($x_2$) & Class\\ Table \ref{table:training} lists some of the \textit{Bacillus subtilis} gene pairs for which the operon structure is known. Let's calculate the logistic regression model from these data: -%NOTE - can't use this as a doctest in case NumPy is missing (Jython). -%Also the ... are missing but that means the user can copy/paste the example. +%doctest . lib:numpy \begin{minted}{pycon} >>> from Bio import LogisticRegression >>> xs = [[-53, -200.78], - [117, -267.14], - [57, -163.47], - [16, -190.30], - [11, -220.94], - [85, -193.94], - [16, -182.71], - [15, -180.41], - [-26, -181.73], - [58, -259.87], - [126, -414.53], - [191, -249.57], - [113, -265.28], - [145, -312.99], - [154, -213.83], - [147, -380.85], - [93, -291.13]] +... [117, -267.14], +... [57, -163.47], +... [16, -190.30], +... [11, -220.94], +... [85, -193.94], +... [16, -182.71], +... [15, -180.41], +... [-26, -181.73], +... [58, -259.87], +... [126, -414.53], +... [191, -249.57], +... [113, -265.28], +... [145, -312.99], +... [154, -213.83], +... [147, -380.85], +... [93, -291.13]] +... >>> ys = [1, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 0, - 0, - 0, - 0, - 0, - 0, - 0] +... 1, +... 1, +... 1, +... 1, +... 1, +... 1, +... 1, +... 1, +... 1, +... 0, +... 0, +... 0, +... 0, +... 0, +... 0, +... 0] +... >>> model = LogisticRegression.train(xs, ys) \end{minted} @@ -410,7 +411,7 @@ This section will describe the \verb|Bio.NaiveBayes| module. \section{Maximum Entropy} -This section will describe the \verb|Bio.MaximumEntropy| module. +This section will describe the \verb|Bio.MaxEntropy| module. \section{Markov Models} diff --git a/Tests/test_NCBITextParser.py b/Tests/test_NCBITextParser.py index 08ac71a04..53688f35e 100644 --- a/Tests/test_NCBITextParser.py +++ b/Tests/test_NCBITextParser.py @@ -730,15 +730,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.database_letters, 29652561) self.assertEqual(len(record.rounds), 3) self.assertEqual(len(record.rounds[0].new_seqs), 14) - # Rest of test broken up to avoid Jython JVM limitations - self._check_text_2010L_phiblast_002_round0(record) - self._check_text_2010L_phiblast_002_round1(record) - self._check_text_2010L_phiblast_002_round2(record) - self._check_text_2010L_phiblast_002_hsps(record) - self._check_text_2010L_phiblast_002_hsps_details(record) - self._check_text_2010L_phiblast_002_footer(record) - - def _check_text_2010L_phiblast_002_round0(self, record): self.assertEqual(record.rounds[0].new_seqs[0].title, "gi|126343|sp|P17216|LIVK_SALTY LEUCINE-SPECIFIC BINDING PROTEIN...") self.assertEqual(record.rounds[0].new_seqs[0].score, 743) self.assertAlmostEqual(record.rounds[0].new_seqs[0].e, 0.0) @@ -810,8 +801,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[0].alignments[12].length, 542) self.assertEqual(record.rounds[0].alignments[13].title, ">gi|1351310|sp|P43496|TRXB_PENCH THIOREDOXIN REDUCTASE") self.assertEqual(record.rounds[0].alignments[13].length, 334) - - def _check_text_2010L_phiblast_002_round1(self, record): self.assertEqual(len(record.rounds[1].new_seqs), 18) self.assertEqual(record.rounds[1].new_seqs[0].title, "gi|113709|sp|P27017|AMIC_PSEAE ALIPHATIC AMIDASE EXPRESSION-REG...") self.assertEqual(record.rounds[1].new_seqs[0].score, 49) @@ -915,8 +904,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[1].alignments[22].title, ">gi|1175674|sp|P45116|YCIH_HAEIN HYPOTHETICAL PROTEIN HI1225") self.assertEqual(record.rounds[1].alignments[22].length, 106) self.assertEqual(record.rounds[1].alignments[23].title, ">gi|3025270|sp|P77269|YPHF_ECOLI ABC TRANSPORTER PERIPLASMIC BINDING PROTEIN YPHF PRECURSOR") - - def _check_text_2010L_phiblast_002_round2(self, record): self.assertEqual(record.rounds[1].alignments[23].length, 327) self.assertEqual(len(record.rounds[2].new_seqs), 16) self.assertEqual(record.rounds[2].new_seqs[0].title, "gi|3024134|sp|O15303|MGR6_HUMAN METABOTROPIC GLUTAMATE RECEPTOR...") @@ -1014,8 +1001,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[2].alignments[21].length, 725) self.assertEqual(record.rounds[2].alignments[22].title, ">gi|127971|sp||NCPR_SALTR_1 [Segment 1 of 3] NADPH-CYTOCHROME P450 REDUCTASE (CPR)") self.assertEqual(record.rounds[2].alignments[22].length, 426) - - def _check_text_2010L_phiblast_002_hsps(self, record): self.assertEqual(record.rounds[0].alignments[0].hsps[0].score, 1897) self.assertAlmostEqual(record.rounds[0].alignments[0].hsps[0].bits, 743) self.assertAlmostEqual(record.rounds[0].alignments[0].hsps[0].expect, 0.0) @@ -1432,8 +1417,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[2].alignments[22].hsps[0].identities, (28, 146)) self.assertEqual(record.rounds[2].alignments[22].hsps[0].positives, (53, 146)) self.assertEqual(record.rounds[2].alignments[22].hsps[0].gaps, (8, 146)) - - def _check_text_2010L_phiblast_002_hsps_details(self, record): self.assertEqual(record.rounds[0].alignments[0].hsps[0].query, "MKRKAKTIIAGIVALAVSQGAMADDIKVAIVGAMSGPVAQWGDMEFNGARQAIKDINAKGGIKGDKLVGVEYDDACDPKQAVAVANKIVNDGIQYVIGHLCSSSTQPASDIYEDEGILMISPGATNPELTQRGYQYIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARSVQDGLKQGNANIVFFDGITAGEKDFSALIARLQKENIDFVYYGGYYPEMGQIVRQARANGLKTQFMGPEGVGNASLSNIAGGAAEGMLVTMPKRYDQDPANKAIVEALKADKKDPSGPYVWITYAAVQSLATAMTRSASHRPLDLVKDLKANGADTVIGPLKWDEKGDLKGFEFGVFQWHADGSSTVAK") self.assertEqual(record.rounds[0].alignments[0].hsps[0].match, "MKRKAKTIIAGIVALAVSQGAMADDIKVAIVGAMSGPVAQWGDMEFNGARQAIKDINAKGGIKGDKLVGVEYDDACDPKQAVAVANKIVNDGIQYVIGHLCSSSTQPASDIYEDEGILMISPGATNPELTQRGYQYIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARSVQDGLKQGNANIVFFDGITAGEKDFSALIARLQKENIDFVYYGGYYPEMGQIVRQARANGLKTQFMGPEGVGNASLSNIAGGAAEGMLVTMPKRYDQDPANKAIVEALKADKKDPSGPYVWITYAAVQSLATAMTRSASHRPLDLVKDLKANGADTVIGPLKWDEKGDLKGFEFGVFQWHADGSSTVAK") self.assertEqual(record.rounds[0].alignments[0].hsps[0].sbjct, "MKRKAKTIIAGIVALAVSQGAMADDIKVAIVGAMSGPVAQWGDMEFNGARQAIKDINAKGGIKGDKLVGVEYDDACDPKQAVAVANKIVNDGIQYVIGHLCSSSTQPASDIYEDEGILMISPGATNPELTQRGYQYIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARSVQDGLKQGNANIVFFDGITAGEKDFSALIARLQKENIDFVYYGGYYPEMGQIVRQARANGLKTQFMGPEGVGNASLSNIAGGAAEGMLVTMPKRYDQDPANKAIVEALKADKKDPSGPYVWITYAAVQSLATAMTRSASHRPLDLVKDLKANGADTVIGPLKWDEKGDLKGFEFGVFQWHADGSSTVAK") @@ -1861,8 +1844,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[2].alignments[22].hsps[0].query_end, 349) self.assertEqual(record.rounds[2].alignments[22].hsps[0].sbjct_start, 15) self.assertEqual(record.rounds[2].alignments[22].hsps[0].sbjct_end, 157) - - def _check_text_2010L_phiblast_002_footer(self, record): self.assertEqual(record.database_name, ["data/swissprot"]) self.assertEqual(record.num_letters_in_database, [29652561]) self.assertEqual(record.num_sequences_in_database, [82258]) @@ -1926,14 +1907,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.database_letters, 29652561) self.assertEqual(len(record.rounds), 2) self.assertEqual(len(record.rounds[0].new_seqs), 30) - # Rest of test broken up to avoid Jython JVM limitations - self._check_text_2010L_phiblast_003_round0(record) - self._check_text_2010L_phiblast_003_round1(record) - self._check_text_2010L_phiblast_003_hsps(record) - self._check_text_2010L_phiblast_003_hsps_details(record) - self._check_text_2010L_phiblast_003_footer(record) - - def _check_text_2010L_phiblast_003_round0(self, record): self.assertEqual(record.rounds[0].new_seqs[0].title, "gi|399896|sp|Q02134|HIS7_LACLA IMIDAZOLEGLYCEROL-PHOSPHATE DEHY...") self.assertEqual(record.rounds[0].new_seqs[0].score, 409) self.assertAlmostEqual(record.rounds[0].new_seqs[0].e, 1.e-114) @@ -2085,8 +2058,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[0].alignments[28].length, 956) self.assertEqual(record.rounds[0].alignments[29].title, ">gi|1174406|sp|P36126|SP14_YEAST PHOSPHOLIPASE D1 (PLD 1) (CHOLINE PHOSPHATASE 1) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D1) (MEIOSIS-SPECIFIC SPORULATION PROTEIN SPO14)") self.assertEqual(record.rounds[0].alignments[29].length, 1380) - - def _check_text_2010L_phiblast_003_round1(self, record): self.assertEqual(len(record.rounds[1].new_seqs), 0) self.assertEqual(len(record.rounds[1].alignments), 24) self.assertEqual(record.rounds[1].alignments[0].title, ">gi|2495230|sp|Q43072|HIS7_PEA IMIDAZOLEGLYCEROL-PHOSPHATE DEHYDRATASE (IGPD)") @@ -2138,8 +2109,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[1].alignments[23].title, ">gi|3334215|sp|O33773|HIS7_SULSO PROBABLE IMIDAZOLEGLYCEROL-PHOSPHATE DEHYDRATASE (IGPD)") self.assertEqual(record.rounds[1].alignments[23].length, 193) self.assertEqual(record.rounds[0].alignments[0].hsps[0].score, 1040) - - def _check_text_2010L_phiblast_003_hsps(self, record): self.assertAlmostEqual(record.rounds[0].alignments[0].hsps[0].bits, 409) self.assertAlmostEqual(record.rounds[0].alignments[0].hsps[0].expect, 1e-114) self.assertEqual(len(record.rounds[0].alignments[0].hsps), 1) @@ -2514,8 +2483,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[1].alignments[23].hsps[0].identities, (83, 200)) self.assertEqual(record.rounds[1].alignments[23].hsps[0].positives, (124, 200)) self.assertEqual(record.rounds[1].alignments[23].hsps[0].gaps, (7, 200)) - - def _check_text_2010L_phiblast_003_hsps_details(self, record): self.assertEqual(record.rounds[0].alignments[0].hsps[0].query, "MTRISHITRNTKETQIELSINLDGTGQADISTGIGFLDHMLTLLTFHSDFDLKIIGHGDHETVGMDPHHLIEDVAIALGKCISEDLGNKLGIRRYGSFTIPMDEALVTCDLDISGRPYLVFHADLSGNQKLGGYDTEMTEEFFRALAFNAGITLHLNEHYGQNTHHIIEGMFKSTARALKQAVSIDESKVGEIPSSKGVL") self.assertEqual(record.rounds[0].alignments[0].hsps[0].match, "MTRISHITRNTKETQIELSINLDGTGQADISTGIGFLDHMLTLLTFHSDFDLKIIGHGDHETVGMDPHHLIEDVAIALGKCISEDLGNKLGIRRYGSFTIPMDEALVTCDLDISGRPYLVFHADLSGNQKLGGYDTEMTEEFFRALAFNAGITLHLNEHYGQNTHHIIEGMFKSTARALKQAVSIDESKVGEIPSSKGVL") self.assertEqual(record.rounds[0].alignments[0].hsps[0].sbjct, "MTRISHITRNTKETQIELSINLDGTGQADISTGIGFLDHMLTLLTFHSDFDLKIIGHGDHETVGMDPHHLIEDVAIALGKCISEDLGNKLGIRRYGSFTIPMDEALVTCDLDISGRPYLVFHADLSGNQKLGGYDTEMTEEFFRALAFNAGITLHLNEHYGQNTHHIIEGMFKSTARALKQAVSIDESKVGEIPSSKGVL") @@ -2894,8 +2861,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[1].alignments[23].hsps[0].query_end, 200) self.assertEqual(record.rounds[1].alignments[23].hsps[0].sbjct_start, 1) self.assertEqual(record.rounds[1].alignments[23].hsps[0].sbjct_end, 193) - - def _check_text_2010L_phiblast_003_footer(self, record): self.assertEqual(record.database_name, ["data/swissprot"]) self.assertEqual(record.num_letters_in_database, [29652561]) self.assertEqual(record.num_sequences_in_database, [82258]) @@ -5668,14 +5633,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.database_letters, 29652561) self.assertEqual(len(record.rounds), 2) self.assertEqual(len(record.rounds[0].new_seqs), 30) - # Rest of test broken up to avoid Jython JVM limitations - self._check_text_2011L_psiblast_002_round0(record) - self._check_text_2011L_psiblast_002_round1(record) - self._check_text_2011L_psiblast_002_hsps(record) - self._check_text_2011L_psiblast_002_hsps_details(record) - self._check_text_2011L_psiblast_002_footer(record) - - def _check_text_2011L_psiblast_002_round0(self, record): self.assertEqual(record.rounds[0].new_seqs[0].title, "gi|399896|sp|Q02134|HIS7_LACLA IMIDAZOLEGLYCEROL-PHOSPHATE DEHY...") self.assertEqual(record.rounds[0].new_seqs[0].score, 409) self.assertAlmostEqual(record.rounds[0].new_seqs[0].e, 1e-114) @@ -5827,8 +5784,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[0].alignments[28].length, 1380) self.assertEqual(record.rounds[0].alignments[29].title, ">gi|3287848|sp|Q16099|GLK4_HUMAN GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 4 PRECURSOR (GLUTAMATE RECEPTOR KA-1) (KA1) (EXCITATORY AMINO ACID RECEPTOR 1) (EAA1)") self.assertEqual(record.rounds[0].alignments[29].length, 956) - - def _check_text_2011L_psiblast_002_round1(self, record): self.assertEqual(len(record.rounds[1].new_seqs), 2) self.assertEqual(record.rounds[1].new_seqs[0].title, "gi|2833252|sp|Q14571|IP3S_HUMAN INOSITOL 1,4,5-TRISPHOSPHATE-BI...") self.assertEqual(record.rounds[1].new_seqs[0].score, 30) @@ -5889,8 +5844,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[1].alignments[24].length, 2701) self.assertEqual(record.rounds[1].alignments[25].title, ">gi|266389|sp|P29995|IP3S_RAT INOSITOL 1,4,5-TRISPHOSPHATE-BINDING PROTEIN TYPE 2 RECEPTOR (TYPE 2 INSP3 RECEPTOR) (TYPE 2 INOSITOL 1,4,5-TRISPHOSPHATE RECEPTOR)") self.assertEqual(record.rounds[1].alignments[25].length, 2701) - - def _check_text_2011L_psiblast_002_hsps(self, record): self.assertEqual(record.rounds[0].alignments[0].hsps[0].score, 1040) self.assertAlmostEqual(record.rounds[0].alignments[0].hsps[0].bits, 409) self.assertAlmostEqual(record.rounds[0].alignments[0].hsps[0].expect, 1e-114) @@ -6114,8 +6067,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertAlmostEqual(record.rounds[1].alignments[25].hsps[0].bits, 28.8) self.assertAlmostEqual(record.rounds[1].alignments[25].hsps[0].expect, 8.2) self.assertEqual(len(record.rounds[1].alignments[25].hsps), 1) - - def _check_text_2011L_psiblast_002_hsps_details(self, record): self.assertEqual(record.rounds[0].alignments[0].hsps[0].identities, (200, 200)) self.assertEqual(record.rounds[0].alignments[0].hsps[0].positives, (200, 200)) self.assertEqual(record.rounds[0].alignments[1].hsps[0].identities, (99, 198)) @@ -6674,8 +6625,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[1].alignments[25].hsps[0].query_end, 141) self.assertEqual(record.rounds[1].alignments[25].hsps[0].sbjct_start, 1540) self.assertEqual(record.rounds[1].alignments[25].hsps[0].sbjct_end, 1659) - - def _check_text_2011L_psiblast_002_footer(self, record): self.assertEqual(record.database_name, ["data/swissprot"]) self.assertEqual(record.num_letters_in_database, [29652561]) self.assertEqual(record.num_sequences_in_database, [82258]) @@ -9994,17 +9943,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.database_sequences, 88201) self.assertEqual(record.database_letters, 31957340) self.assertEqual(len(record.rounds), 5) - # Rest of test broken up to avoid Jython JVM limitations - self._check_text_2012L_psiblast_001_round0(record) - self._check_text_2012L_psiblast_001_round1(record) - self._check_text_2012L_psiblast_001_round2(record) - self._check_text_2012L_psiblast_001_round4(record) - self._check_text_2012L_psiblast_001_hsps(record) - self._check_text_2012L_psiblast_001_hsps_counts(record) - self._check_text_2012L_psiblast_001_hsps_details(record) - self._check_text_2012L_psiblast_001_footer(record) - - def _check_text_2012L_psiblast_001_round0(self, record): self.assertEqual(len(record.rounds[0].new_seqs), 27) self.assertEqual(record.rounds[0].new_seqs[0].title, "100K_RAT Q62671 rattus norvegicus (rat). 100 kda protein (ec...") self.assertEqual(record.rounds[0].new_seqs[0].score, 1516) @@ -10142,8 +10080,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[0].alignments[25].length, 211) self.assertEqual(record.rounds[0].alignments[26].title, ">CC24_YEAST P11433 saccharomyces cerevisiae (baker's yeast). cell division control protein 24 (calcium regulatory protein). 7/1999") self.assertEqual(record.rounds[0].alignments[26].length, 854) - - def _check_text_2012L_psiblast_001_round1(self, record): self.assertEqual(len(record.rounds[1].new_seqs), 9) self.assertEqual(record.rounds[1].new_seqs[0].title, "PABP_DROME P21187 drosophila melanogaster (fruit fly). polya...") self.assertEqual(record.rounds[1].new_seqs[0].score, 67) @@ -10225,8 +10161,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[1].alignments[24].length, 863) self.assertEqual(record.rounds[1].alignments[25].title, ">SYQ_YEAST P13188 saccharomyces cerevisiae (baker's yeast). glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). 11/1997") self.assertEqual(record.rounds[1].alignments[25].length, 809) - - def _check_text_2012L_psiblast_001_round2(self, record): self.assertEqual(len(record.rounds[2].new_seqs), 6) self.assertEqual(record.rounds[2].new_seqs[0].title, "PAB2_ARATH P42731 arabidopsis thaliana (mouse-ear cress). po...") self.assertEqual(record.rounds[2].new_seqs[0].score, 48) @@ -10295,8 +10229,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[2].alignments[22].length, 892) self.assertEqual(record.rounds[2].alignments[23].title, ">RNR_AQUAE O67834 aquifex aeolicus. ribonuclease r (ec 3.1.-.-) (rnase r) (vacb protein homolog). 5/2000") self.assertEqual(record.rounds[2].alignments[23].length, 705) - - def _check_text_2012L_psiblast_001_round3(self, record): self.assertEqual(len(record.rounds[3].new_seqs), 4) self.assertEqual(record.rounds[3].new_seqs[0].title, "PAB5_ARATH Q05196 arabidopsis thaliana (mouse-ear cress). po...") self.assertEqual(record.rounds[3].new_seqs[0].score, 51) @@ -10359,8 +10291,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[3].alignments[22].length, 705) self.assertEqual(record.rounds[3].alignments[23].title, ">NIRA_EMENI P28348 emericella nidulans (aspergillus nidulans). nitrogen assimilation transcription factor nira. 4/1993") self.assertEqual(record.rounds[3].alignments[23].length, 892) - - def _check_text_2012L_psiblast_001_round4(self, record): self.assertEqual(len(record.rounds[4].new_seqs), 2) self.assertEqual(record.rounds[4].new_seqs[0].title, "RNR_AQUAE O67834 aquifex aeolicus. ribonuclease r (ec 3.1.-....") self.assertEqual(record.rounds[4].new_seqs[0].score, 33) @@ -10417,8 +10347,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[4].alignments[22].length, 705) self.assertEqual(record.rounds[4].alignments[23].title, ">NIRA_EMENI P28348 emericella nidulans (aspergillus nidulans). nitrogen assimilation transcription factor nira. 4/1993") self.assertEqual(record.rounds[4].alignments[23].length, 892) - - def _check_text_2012L_psiblast_001_hsps(self, record): self.assertEqual(record.rounds[0].alignments[0].hsps[0].score, 3882) self.assertAlmostEqual(record.rounds[0].alignments[0].hsps[0].bits, 1516) self.assertAlmostEqual(record.rounds[0].alignments[0].hsps[0].expect, 0.0) @@ -10930,8 +10858,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertAlmostEqual(record.rounds[4].alignments[23].hsps[0].bits, 32.9) self.assertAlmostEqual(record.rounds[4].alignments[23].hsps[0].expect, 2.9) self.assertEqual(len(record.rounds[4].alignments[23].hsps), 1) - - def _check_text_2012L_psiblast_001_hsps_counts(self, record): self.assertEqual(record.rounds[0].alignments[0].hsps[0].identities, (765, 889)) self.assertEqual(record.rounds[0].alignments[0].hsps[0].positives, (765, 889)) self.assertEqual(record.rounds[0].alignments[1].hsps[0].identities, (281, 634)) @@ -11281,8 +11207,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[4].alignments[22].hsps[0].gaps, (13, 92)) self.assertEqual(record.rounds[4].alignments[23].hsps[0].identities, (22, 95)) self.assertEqual(record.rounds[4].alignments[23].hsps[0].positives, (35, 95)) - - def _check_text_2012L_psiblast_001_hsps_details(self, record): self.assertEqual(record.rounds[0].alignments[0].hsps[0].query, "MMSARGDFLNYALSLMRSHNDEHSDVLPVLDVCSLKHVAYVFQALIYWIKAMNQQTTLDTPQXXXXXXXXXXXXGIXXXXXXXXXXXXTSQSATLNDKDDESLPAETGQNHPFFRRSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNARKEDLFGRPSQGLYSSSAGSGKCLVEVTMDRNCLEVLPTKMSYAANLKNVMNMQNRQKKAGEDQSMLAEEADSSKPGPSAHDVAAQLKSSLLAEIGLTESEGPPLTSFRPQCSFMGMVISHDMLLGRWRLSLELFGRVFMEDVGAEPGSILTELGGFEVKESKFRREMEKLRNQQSRDLSLEVDRDRDLLIQQTMRQLNNHFGRRCATTPMAVHRVKVTFKDEPGEGSGVARSFYTAIAQAFLSNEKLPNLDCIQNANKGTHTSLMQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXQLSIDTRPFRPASEGNPSDDPDPLPAHRQALGERLYPRVQAMQPAFASKITGMXXXXXXXXXXXXXXXXXXXRARVEEAMELIVAHGRENGAXXXXXXXXXXXXEKVQENRKRHGSSRSVVXXXXXXXXXXXXNAPLFYQPGKRGFYTPRPGKNTEARLNCFRNIGRILGLCLLQNELCPITLNRHVIKVLLGRKVNWHDFAFFDPVMYESLRQLILASQSSDADAVFSAMDLAFAVDLCKEEGGGQVELIPNGVNIPVTPQNVYEYVRKYAEHRMLVVAEQPLHAMRKGLLDVLPKNSLEDLTAEDFRLLVNGCGEVNVQMLISFTSFNDESGENAEKLLQFKRWFWSIVERMSMTERQDLVYFWTSSPSLPASEEGFQPMPSITIRPPDDQHLPTANTCISRLYVPXXXXXXXXXXXXXXXXXXXNFGFV") self.assertEqual(record.rounds[0].alignments[0].hsps[0].match, "MMSARGDFLNYALSLMRSHNDEHSDVLPVLDVCSLKHVAYVFQALIYWIKAMNQQTTLDTPQ GI TSQSATLNDKDDESLPAETGQNHPFFRRSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNARKEDLFGRPSQGLYSSSAGSGKCLVEVTMDRNCLEVLPTKMSYAANLKNVMNMQNRQKKAGEDQSMLAEEADSSKPGPSAHDVAAQLKSSLLAEIGLTESEGPPLTSFRPQCSFMGMVISHDMLLGRWRLSLELFGRVFMEDVGAEPGSILTELGGFEVKESKFRREMEKLRNQQSRDLSLEVDRDRDLLIQQTMRQLNNHFGRRCATTPMAVHRVKVTFKDEPGEGSGVARSFYTAIAQAFLSNEKLPNLDCIQNANKGTHTSLMQ QLSIDTRPFRPASEGNPSDDPDPLPAHRQALGERLYPRVQAMQPAFASKITGM RARVEEAMELIVAHGRENGA EKVQENRKRHGSSRSVV NAPLFYQPGKRGFYTPRPGKNTEARLNCFRNIGRILGLCLLQNELCPITLNRHVIKVLLGRKVNWHDFAFFDPVMYESLRQLILASQSSDADAVFSAMDLAFAVDLCKEEGGGQVELIPNGVNIPVTPQNVYEYVRKYAEHRMLVVAEQPLHAMRKGLLDVLPKNSLEDLTAEDFRLLVNGCGEVNVQMLISFTSFNDESGENAEKLLQFKRWFWSIVERMSMTERQDLVYFWTSSPSLPASEEGFQPMPSITIRPPDDQHLPTANTCISRLYVP NFGFV") self.assertEqual(record.rounds[0].alignments[0].hsps[0].sbjct, "MMSARGDFLNYALSLMRSHNDEHSDVLPVLDVCSLKHVAYVFQALIYWIKAMNQQTTLDTPQLERKRTRELLELGIDNEDSEHENDDDTSQSATLNDKDDESLPAETGQNHPFFRRSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNARKEDLFGRPSQGLYSSSAGSGKCLVEVTMDRNCLEVLPTKMSYAANLKNVMNMQNRQKKAGEDQSMLAEEADSSKPGPSAHDVAAQLKSSLLAEIGLTESEGPPLTSFRPQCSFMGMVISHDMLLGRWRLSLELFGRVFMEDVGAEPGSILTELGGFEVKESKFRREMEKLRNQQSRDLSLEVDRDRDLLIQQTMRQLNNHFGRRCATTPMAVHRVKVTFKDEPGEGSGVARSFYTAIAQAFLSNEKLPNLDCIQNANKGTHTSLMQRLRNRGERDREREREREMRRSSGLRAGSRRDRDRDFRRQLSIDTRPFRPASEGNPSDDPDPLPAHRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVEEAMELIVAHGRENGADSILDLGLLDSSEKVQENRKRHGSSRSVVDMDLDDTDDGDDNAPLFYQPGKRGFYTPRPGKNTEARLNCFRNIGRILGLCLLQNELCPITLNRHVIKVLLGRKVNWHDFAFFDPVMYESLRQLILASQSSDADAVFSAMDLAFAVDLCKEEGGGQVELIPNGVNIPVTPQNVYEYVRKYAEHRMLVVAEQPLHAMRKGLLDVLPKNSLEDLTAEDFRLLVNGCGEVNVQMLISFTSFNDESGENAEKLLQFKRWFWSIVERMSMTERQDLVYFWTSSPSLPASEEGFQPMPSITIRPPDDQHLPTANTCISRLYVPLYSSKQILKQKLLLAIKTKNFGFV") @@ -12193,8 +12117,6 @@ class TestNCBITextParser(unittest.TestCase): self.assertEqual(record.rounds[4].alignments[23].hsps[0].query_end, 313) self.assertEqual(record.rounds[4].alignments[23].hsps[0].sbjct_start, 702) self.assertEqual(record.rounds[4].alignments[23].hsps[0].sbjct_end, 796) - - def _check_text_2012L_psiblast_001_footer(self, record): self.assertEqual(record.database_name, ["/dbase/swissprot/main/release/sp", "/dbase/swissprot/main/update/spu"]) self.assertEqual(record.posted_date, [("Jun 21, 2000 12:39 PM",), ("Nov 3, 1999 8:09 PM",)]) self.assertEqual(record.num_letters_in_database, [31411157, 546183]) diff --git a/Tests/test_SeqIO.py b/Tests/test_SeqIO.py index ca660b637..703573dbf 100644 --- a/Tests/test_SeqIO.py +++ b/Tests/test_SeqIO.py @@ -252,16 +252,7 @@ class TestSeqIO(SeqIOTestBaseClass): self.assertEqual(record_one.name, record_two.name, msg=msg) self.assertEqual(record_one.description, record_two.description, msg=msg) self.assertEqual(len(record_one), len(record_two), msg=msg) - if isinstance(record_one.seq, UnknownSeq) and isinstance( - record_two.seq, UnknownSeq - ): - # Jython didn't like us comparing the string of very long UnknownSeq - # object (out of heap memory error) - self.assertEqual( - record_one.seq._character, record_two.seq._character, msg=msg - ) - else: - self.assertEqual(str(record_one.seq), str(record_two.seq), msg=msg) + self.assertEqual(str(record_one.seq), str(record_two.seq), msg=msg) # TODO - check features and annotation (see code for BioSQL tests) for key in set(record_one.letter_annotations).intersection( record_two.letter_annotations @@ -377,14 +368,7 @@ class TestSeqIO(SeqIOTestBaseClass): # Check the sequence if fmt in ["gb", "genbank", "embl", "imgt"]: # The GenBank/EMBL parsers will convert to upper case. - if isinstance(r1.seq, UnknownSeq) and isinstance( - r2.seq, UnknownSeq - ): - # Jython didn't like us comparing the string of very long - # UnknownSeq object (out of heap memory error) - self.assertEqual(r1.seq._character.upper(), r2.seq._character) - else: - self.assertEqual(str(r1.seq).upper(), str(r2.seq)) + self.assertEqual(str(r1.seq).upper(), str(r2.seq)) elif fmt == "qual": self.assertIsInstance(r2.seq, UnknownSeq) self.assertEqual(len(r2), len(r1)) diff --git a/Tests/test_SeqIO_SeqXML.py b/Tests/test_SeqIO_SeqXML.py index ee8e938f6..0ecb19367 100644 --- a/Tests/test_SeqIO_SeqXML.py +++ b/Tests/test_SeqIO_SeqXML.py @@ -210,20 +210,11 @@ class TestReadAndWrite(unittest.TestCase): text = output.decode("UTF-8") self.assertIn("Homo sapiens (Human)", text) self.assertIn("9606", text) - if '' in text: - # Good, but don't get this (do we?) - pass - elif '' in text: - # Not as concise, but fine (seen on C Python) - pass - elif '' in text: - # Jython uses a different order - pass - elif '' in text: - # This would be fine too, but don't get this (do we?) - pass - else: - raise ValueError("Mising expected tag: %r" % text) + if ( + '' + not in text + ): + raise ValueError("Missing expected tag: %r" % text) class TestReadCorruptFiles(unittest.TestCase): diff --git a/Tests/test_SeqIO_features.py b/Tests/test_SeqIO_features.py index 4c35681ec..0b0a4e1f3 100644 --- a/Tests/test_SeqIO_features.py +++ b/Tests/test_SeqIO_features.py @@ -56,12 +56,7 @@ def compare_record(old, new, expect_minor_diffs=False): ) if len(old.seq) != len(new.seq): raise ValueError("%i vs %i" % (len(old.seq), len(new.seq))) - if isinstance(old.seq, UnknownSeq) and isinstance(new.seq, UnknownSeq): - # Jython didn't like us comparing the string of very long - # UnknownSeq object (out of heap memory error) - if old.seq._character.upper() != new.seq._character: - raise ValueError("%r vs %r" % (old.seq, new.seq)) - elif str(old.seq).upper() != str(new.seq).upper(): + if str(old.seq).upper() != str(new.seq).upper(): if len(old.seq) < 200: raise ValueError("'%s' vs '%s'" % (old.seq, new.seq)) else: diff --git a/Tests/test_SeqIO_index.py b/Tests/test_SeqIO_index.py index 91b2a542f..ee107ea1f 100644 --- a/Tests/test_SeqIO_index.py +++ b/Tests/test_SeqIO_index.py @@ -8,8 +8,7 @@ try: import sqlite3 except ImportError: - # Try to run what tests we can on Jython - # where we don't expect this to be installed. + # Try to run what tests we can in case sqlite3 was not installed sqlite3 = None import os diff --git a/Tests/test_prosite1.py b/Tests/test_prosite.py similarity index 78% rename from Tests/test_prosite1.py rename to Tests/test_prosite.py index 9829be9ee..3c0bc2f9b 100644 --- a/Tests/test_prosite1.py +++ b/Tests/test_prosite.py @@ -2,10 +2,8 @@ # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. -# -# NOTE - This file has been split in two as a workaround for Jython JVM limits. -"""Tests for prosite1 module.""" +"""Tests for Bio.ExPASy.Prosite module.""" import os import unittest @@ -2724,6 +2722,775 @@ class TestPrositeRead(unittest.TestCase): self.assertEqual(record.pdb_structs[8], "2C2B") self.assertEqual(record.pdb_structs[9], "2C2G") + def test_read4(self): + """Parsing Prosite record ps00432.txt.""" + filename = os.path.join("Prosite", "ps00432.txt") + with open(filename) as handle: + record = Prosite.read(handle) + self.assertEqual(record.name, "ACTINS_2") + self.assertEqual(record.type, "PATTERN") + self.assertEqual(record.accession, "PS00432") + self.assertEqual(record.created, "NOV-1990") + self.assertEqual(record.data_update, "DEC-2004") + self.assertEqual(record.info_update, "MAR-2006") + self.assertEqual(record.pdoc, "PDOC00340") + self.assertEqual(record.description, "Actins signature 2.") + self.assertEqual(record.pattern, "W-[IVC]-[STAK]-[RK]-x-[DE]-Y-[DNE]-[DE].") + self.assertEqual(record.matrix, []) + self.assertEqual(record.rules, []) + self.assertEqual(record.nr_sp_release, "49.3") + self.assertEqual(record.nr_sp_seqs, 212425) + self.assertEqual(record.cc_taxo_range, "??E??") + self.assertEqual(record.cc_max_repeat, "1") + self.assertEqual(len(record.cc_site), 0) + self.read4_positive(record) + self.read4_false_etc(record) + + def read4_positive(self, record): + self.assertEqual(len(record.dr_positive), 295) + self.assertEqual(record.dr_positive[0], ("O96019", "ACL6A_HUMAN")) + self.assertEqual(record.dr_positive[1], ("Q9Z2N8", "ACL6A_MOUSE")) + self.assertEqual(record.dr_positive[2], ("O94805", "ACL6B_HUMAN")) + self.assertEqual(record.dr_positive[3], ("Q99MR0", "ACL6B_MOUSE")) + self.assertEqual(record.dr_positive[4], ("P53496", "ACT11_ARATH")) + self.assertEqual(record.dr_positive[5], ("P30171", "ACT11_SOLTU")) + self.assertEqual(record.dr_positive[6], ("P53497", "ACT12_ARATH")) + self.assertEqual(record.dr_positive[7], ("P30172", "ACT12_SOLTU")) + self.assertEqual(record.dr_positive[8], ("P30173", "ACT13_SOLTU")) + self.assertEqual(record.dr_positive[9], ("P84185", "ACT1D_ANOGA")) + self.assertEqual(record.dr_positive[10], ("P02578", "ACT1_ACACA")) + self.assertEqual(record.dr_positive[11], ("P49128", "ACT1_AEDAE")) + self.assertEqual(record.dr_positive[12], ("P10671", "ACT1_ARATH")) + self.assertEqual(record.dr_positive[13], ("P18600", "ACT1_ARTSX")) + self.assertEqual(record.dr_positive[14], ("P83969", "ACT1_BACDO")) + self.assertEqual(record.dr_positive[15], ("P07836", "ACT1_BOMMO")) + self.assertEqual(record.dr_positive[16], ("P10983", "ACT1_CAEEL")) + self.assertEqual(record.dr_positive[17], ("P23343", "ACT1_DAUCA")) + self.assertEqual(record.dr_positive[18], ("P02577", "ACT1_DICDI")) + self.assertEqual(record.dr_positive[19], ("P68556", "ACT1_DIPDE")) + self.assertEqual(record.dr_positive[20], ("P10987", "ACT1_DROME")) + self.assertEqual(record.dr_positive[21], ("P35432", "ACT1_ECHGR")) + self.assertEqual(record.dr_positive[22], ("P68142", "ACT1_FUGRU")) + self.assertEqual(record.dr_positive[23], ("P53460", "ACT1_HALRO")) + self.assertEqual(record.dr_positive[24], ("P69002", "ACT1_HELER")) + self.assertEqual(record.dr_positive[25], ("P69003", "ACT1_HELTB")) + self.assertEqual(record.dr_positive[26], ("P92182", "ACT1_LUMTE")) + self.assertEqual(record.dr_positive[27], ("P53465", "ACT1_LYTPI")) + self.assertEqual(record.dr_positive[28], ("P02582", "ACT1_MAIZE")) + self.assertEqual(record.dr_positive[29], ("P27131", "ACT1_NAEFO")) + self.assertEqual(record.dr_positive[30], ("P30162", "ACT1_ONCVO")) + self.assertEqual(record.dr_positive[31], ("Q98972", "ACT1_ORYLA")) + self.assertEqual(record.dr_positive[32], ("P13362", "ACT1_ORYSA")) + self.assertEqual(record.dr_positive[33], ("P53503", "ACT1_OXYFA")) + self.assertEqual(record.dr_positive[34], ("P12715", "ACT1_OXYNO")) + self.assertEqual(record.dr_positive[35], ("P53468", "ACT1_OXYTR")) + self.assertEqual(record.dr_positive[36], ("P30164", "ACT1_PEA")) + self.assertEqual(record.dr_positive[37], ("P22131", "ACT1_PHYIN")) + self.assertEqual(record.dr_positive[38], ("P10988", "ACT1_PLAFA")) + self.assertEqual(record.dr_positive[39], ("P43239", "ACT1_PNECA")) + self.assertEqual(record.dr_positive[40], ("P41112", "ACT1_PODCA")) + self.assertEqual(record.dr_positive[41], ("O18499", "ACT1_SACKO")) + self.assertEqual(record.dr_positive[42], ("Q9Y702", "ACT1_SCHCO")) + self.assertEqual(record.dr_positive[43], ("P53470", "ACT1_SCHMA")) + self.assertEqual(record.dr_positive[44], ("P53504", "ACT1_SORBI")) + self.assertEqual(record.dr_positive[45], ("P02581", "ACT1_SOYBN")) + self.assertEqual(record.dr_positive[46], ("P10990", "ACT1_STRFN")) + self.assertEqual(record.dr_positive[47], ("Q9Y701", "ACT1_SUIBO")) + self.assertEqual(record.dr_positive[48], ("P10992", "ACT1_TETTH")) + self.assertEqual(record.dr_positive[49], ("Q05214", "ACT1_TOBAC")) + self.assertEqual(record.dr_positive[50], ("P12432", "ACT1_TRYBB")) + self.assertEqual(record.dr_positive[51], ("P04751", "ACT1_XENLA")) + self.assertEqual(record.dr_positive[52], ("P26197", "ACT2_ABSGL")) + self.assertEqual(record.dr_positive[53], ("Q96292", "ACT2_ARATH")) + self.assertEqual(record.dr_positive[54], ("P18601", "ACT2_ARTSX")) + self.assertEqual(record.dr_positive[55], ("P45885", "ACT2_BACDO")) + self.assertEqual(record.dr_positive[56], ("P07837", "ACT2_BOMMO")) + self.assertEqual(record.dr_positive[57], ("P10984", "ACT2_CAEEL")) + self.assertEqual(record.dr_positive[58], ("P23344", "ACT2_DAUCA")) + self.assertEqual(record.dr_positive[59], ("P07827", "ACT2_DICDI")) + self.assertEqual(record.dr_positive[60], ("P53456", "ACT2_DIPDE")) + self.assertEqual(record.dr_positive[61], ("P02572", "ACT2_DROME")) + self.assertEqual(record.dr_positive[62], ("Q03341", "ACT2_ECHGR")) + self.assertEqual(record.dr_positive[63], ("P53485", "ACT2_FUGRU")) + self.assertEqual(record.dr_positive[64], ("P27130", "ACT2_HALRO")) + self.assertEqual(record.dr_positive[65], ("P92176", "ACT2_LUMTE")) + self.assertEqual(record.dr_positive[66], ("P53466", "ACT2_LYTPI")) + self.assertEqual(record.dr_positive[67], ("Q25472", "ACT2_MOLOC")) + self.assertEqual(record.dr_positive[68], ("P27132", "ACT2_NAEFO")) + self.assertEqual(record.dr_positive[69], ("P30163", "ACT2_ONCVO")) + self.assertEqual(record.dr_positive[70], ("P17298", "ACT2_ORYSA")) + self.assertEqual(record.dr_positive[71], ("P02583", "ACT2_OXYFA")) + self.assertEqual(record.dr_positive[72], ("P55805", "ACT2_OXYNO")) + self.assertEqual(record.dr_positive[73], ("P53469", "ACT2_OXYTR")) + self.assertEqual(record.dr_positive[74], ("P30165", "ACT2_PEA")) + self.assertEqual(record.dr_positive[75], ("P22132", "ACT2_PHYIN")) + self.assertEqual(record.dr_positive[76], ("P14883", "ACT2_PLAFA")) + self.assertEqual(record.dr_positive[77], ("O18500", "ACT2_SACKO")) + self.assertEqual(record.dr_positive[78], ("Q9Y896", "ACT2_SCHCO")) + self.assertEqual(record.dr_positive[79], ("P53471", "ACT2_SCHMA")) + self.assertEqual(record.dr_positive[80], ("P69004", "ACT2_STRFN")) + self.assertEqual(record.dr_positive[81], ("Q9Y707", "ACT2_SUIBO")) + self.assertEqual(record.dr_positive[82], ("P10993", "ACT2_TETPY")) + self.assertEqual(record.dr_positive[83], ("P12433", "ACT2_TRYBB")) + self.assertEqual(record.dr_positive[84], ("P10995", "ACT2_XENLA")) + self.assertEqual(record.dr_positive[85], ("P20399", "ACT2_XENTR")) + self.assertEqual(record.dr_positive[86], ("Q25010", "ACT3A_HELAM")) + self.assertEqual(record.dr_positive[87], ("P84184", "ACT3B_HELAM")) + self.assertEqual(record.dr_positive[88], ("P18602", "ACT3_ARTSX")) + self.assertEqual(record.dr_positive[89], ("P45886", "ACT3_BACDO")) + self.assertEqual(record.dr_positive[90], ("P04829", "ACT3_BOMMO")) + self.assertEqual(record.dr_positive[91], ("P07829", "ACT3_DICDI")) + self.assertEqual(record.dr_positive[92], ("P53457", "ACT3_DIPDE")) + self.assertEqual(record.dr_positive[93], ("P53501", "ACT3_DROME")) + self.assertEqual(record.dr_positive[94], ("Q03342", "ACT3_ECHGR")) + self.assertEqual(record.dr_positive[95], ("P53486", "ACT3_FUGRU")) + self.assertEqual(record.dr_positive[96], ("P41340", "ACT3_LIMPO")) + self.assertEqual(record.dr_positive[97], ("Q25379", "ACT3_LYTPI")) + self.assertEqual(record.dr_positive[98], ("P17299", "ACT3_ORYSA")) + self.assertEqual(record.dr_positive[99], ("P46258", "ACT3_PEA")) + self.assertEqual(record.dr_positive[100], ("P41113", "ACT3_PODCA")) + self.assertEqual(record.dr_positive[101], ("P30167", "ACT3_SOLTU")) + self.assertEqual(record.dr_positive[102], ("P02580", "ACT3_SOYBN")) + self.assertEqual(record.dr_positive[103], ("P04752", "ACT3_XENLA")) + self.assertEqual(record.dr_positive[104], ("P53494", "ACT4_ARATH")) + self.assertEqual(record.dr_positive[105], ("P18603", "ACT4_ARTSX")) + self.assertEqual(record.dr_positive[106], ("P84183", "ACT4_BOMMO")) + self.assertEqual(record.dr_positive[107], ("P10986", "ACT4_CAEEL")) + self.assertEqual(record.dr_positive[108], ("P07828", "ACT4_DICDI")) + self.assertEqual(record.dr_positive[109], ("P02574", "ACT4_DROME")) + self.assertEqual(record.dr_positive[110], ("Q25380", "ACT4_LYTPI")) + self.assertEqual(record.dr_positive[111], ("Q8RYC2", "ACT5_ARATH")) + self.assertEqual(record.dr_positive[112], ("P45887", "ACT5_BACDO")) + self.assertEqual(record.dr_positive[113], ("P53478", "ACT5_CHICK")) + self.assertEqual(record.dr_positive[114], ("P53458", "ACT5_DIPDE")) + self.assertEqual(record.dr_positive[115], ("P10981", "ACT5_DROME")) + self.assertEqual(record.dr_positive[116], ("P53505", "ACT5_XENLA")) + self.assertEqual(record.dr_positive[117], ("P53459", "ACT6_DIPDE")) + self.assertEqual(record.dr_positive[118], ("P83967", "ACT6_DROME")) + self.assertEqual(record.dr_positive[119], ("P83968", "ACT6_DROSI")) + self.assertEqual(record.dr_positive[120], ("P30168", "ACT6_SOLTU")) + self.assertEqual(record.dr_positive[121], ("P53492", "ACT7_ARATH")) + self.assertEqual(record.dr_positive[122], ("P17300", "ACT7_ORYSA")) + self.assertEqual(record.dr_positive[123], ("Q96293", "ACT8_ARATH")) + self.assertEqual(record.dr_positive[124], ("P07830", "ACT8_DICDI")) + self.assertEqual(record.dr_positive[125], ("P53506", "ACT8_XENLA")) + self.assertEqual(record.dr_positive[126], ("P93738", "ACT9_ARATH")) + self.assertEqual(record.dr_positive[127], ("P62739", "ACTA_BOVIN")) + self.assertEqual(record.dr_positive[128], ("P08023", "ACTA_CHICK")) + self.assertEqual(record.dr_positive[129], ("P62736", "ACTA_HUMAN")) + self.assertEqual(record.dr_positive[130], ("P41339", "ACTA_LIMPO")) + self.assertEqual(record.dr_positive[131], ("P62737", "ACTA_MOUSE")) + self.assertEqual(record.dr_positive[132], ("P02576", "ACTA_PHYPO")) + self.assertEqual(record.dr_positive[133], ("P62740", "ACTA_RABIT")) + self.assertEqual(record.dr_positive[134], ("P62738", "ACTA_RAT")) + self.assertEqual(record.dr_positive[135], ("P53472", "ACTA_STRPU")) + self.assertEqual(record.dr_positive[136], ("Q7ZVI7", "ACTB1_BRARE")) + self.assertEqual(record.dr_positive[137], ("Q7ZVF9", "ACTB2_BRARE")) + self.assertEqual(record.dr_positive[138], ("P60712", "ACTB_BOVIN")) + self.assertEqual(record.dr_positive[139], ("P84336", "ACTB_CAMDR")) + self.assertEqual(record.dr_positive[140], ("O18840", "ACTB_CANFA")) + self.assertEqual(record.dr_positive[141], ("Q71FK5", "ACTB_CAVPO")) + self.assertEqual(record.dr_positive[142], ("Q76N69", "ACTB_CERAE")) + self.assertEqual(record.dr_positive[143], ("P60706", "ACTB_CHICK")) + self.assertEqual(record.dr_positive[144], ("P48975", "ACTB_CRIGR")) + self.assertEqual(record.dr_positive[145], ("P83751", "ACTB_CTEID")) + self.assertEqual(record.dr_positive[146], ("P83750", "ACTB_CYPCA")) + self.assertEqual(record.dr_positive[147], ("P60708", "ACTB_HORSE")) + self.assertEqual(record.dr_positive[148], ("P60709", "ACTB_HUMAN")) + self.assertEqual(record.dr_positive[149], ("Q711N9", "ACTB_MESAU")) + self.assertEqual(len(record.dr_positive), 295) + self.assertEqual(record.dr_positive[150], ("P60710", "ACTB_MOUSE")) + self.assertEqual(record.dr_positive[151], ("P68143", "ACTB_OREMO")) + self.assertEqual(record.dr_positive[152], ("P79818", "ACTB_ORYLA")) + self.assertEqual(record.dr_positive[153], ("Q5R1X3", "ACTB_PANTR")) + self.assertEqual(record.dr_positive[154], ("P29751", "ACTB_RABIT")) + self.assertEqual(record.dr_positive[155], ("P60711", "ACTB_RAT")) + self.assertEqual(record.dr_positive[156], ("O42161", "ACTB_SALSA")) + self.assertEqual(record.dr_positive[157], ("P60713", "ACTB_SHEEP")) + self.assertEqual(record.dr_positive[158], ("Q91ZK5", "ACTB_SIGHI")) + self.assertEqual(record.dr_positive[159], ("P53473", "ACTB_STRPU")) + self.assertEqual(record.dr_positive[160], ("P60707", "ACTB_TRIVU")) + self.assertEqual(record.dr_positive[161], ("P15475", "ACTB_XENBO")) + self.assertEqual(record.dr_positive[162], ("O93400", "ACTB_XENLA")) + self.assertEqual(record.dr_positive[163], ("Q964E3", "ACTC_BIOAL")) + self.assertEqual(record.dr_positive[164], ("P92179", "ACTC_BIOGL")) + self.assertEqual(record.dr_positive[165], ("Q964E1", "ACTC_BIOOB")) + self.assertEqual(record.dr_positive[166], ("Q964E2", "ACTC_BIOPF")) + self.assertEqual(record.dr_positive[167], ("Q964E0", "ACTC_BIOTE")) + self.assertEqual(record.dr_positive[168], ("Q93129", "ACTC_BRABE")) + self.assertEqual(record.dr_positive[169], ("Q93131", "ACTC_BRAFL")) + self.assertEqual(record.dr_positive[170], ("O17503", "ACTC_BRALA")) + self.assertEqual(record.dr_positive[171], ("P68034", "ACTC_CHICK")) + self.assertEqual(record.dr_positive[172], ("P53480", "ACTC_FUGRU")) + self.assertEqual(record.dr_positive[173], ("P53461", "ACTC_HALRO")) + self.assertEqual(record.dr_positive[174], ("Q964D9", "ACTC_HELTI")) + self.assertEqual(record.dr_positive[175], ("P68032", "ACTC_HUMAN")) + self.assertEqual(record.dr_positive[176], ("P68033", "ACTC_MOUSE")) + self.assertEqual(record.dr_positive[177], ("P12716", "ACTC_PISOC")) + self.assertEqual(record.dr_positive[178], ("P68035", "ACTC_RAT")) + self.assertEqual(record.dr_positive[179], ("Q07903", "ACTC_STRPU")) + self.assertEqual(record.dr_positive[180], ("Q00215", "ACTC_STYPL")) + self.assertEqual(record.dr_positive[181], ("P69005", "ACTD_STRPU")) + self.assertEqual(record.dr_positive[182], ("P53474", "ACTE_STRPU")) + self.assertEqual(record.dr_positive[183], ("P18499", "ACTF_STRPU")) + self.assertEqual(record.dr_positive[184], ("P63256", "ACTG_ANSAN")) + self.assertEqual(record.dr_positive[185], ("P63258", "ACTG_BOVIN")) + self.assertEqual(record.dr_positive[186], ("Q9UVW9", "ACTG_CEPAC")) + self.assertEqual(record.dr_positive[187], ("P20359", "ACTG_EMENI")) + self.assertEqual(record.dr_positive[188], ("P63261", "ACTG_HUMAN")) + self.assertEqual(record.dr_positive[189], ("P63260", "ACTG_MOUSE")) + self.assertEqual(record.dr_positive[190], ("Q9URS0", "ACTG_PENCH")) + self.assertEqual(record.dr_positive[191], ("P63259", "ACTG_RAT")) + self.assertEqual(record.dr_positive[192], ("P63257", "ACTG_TRIVU")) + self.assertEqual(record.dr_positive[193], ("P63270", "ACTH_CHICK")) + self.assertEqual(record.dr_positive[194], ("P63267", "ACTH_HUMAN")) + self.assertEqual(record.dr_positive[195], ("P63268", "ACTH_MOUSE")) + self.assertEqual(record.dr_positive[196], ("P63269", "ACTH_RAT")) + self.assertEqual(record.dr_positive[197], ("P17304", "ACTM_APLCA")) + self.assertEqual(record.dr_positive[198], ("Q93130", "ACTM_BRABE")) + self.assertEqual(record.dr_positive[199], ("Q93132", "ACTM_BRAFL")) + self.assertEqual(record.dr_positive[200], ("O17502", "ACTM_BRALA")) + self.assertEqual(record.dr_positive[201], ("O15998", "ACTM_CIOSA")) + self.assertEqual(record.dr_positive[202], ("P53463", "ACTM_HELER")) + self.assertEqual(record.dr_positive[203], ("P53464", "ACTM_HELTB")) + self.assertEqual(record.dr_positive[204], ("Q25381", "ACTM_LYTPI")) + self.assertEqual(record.dr_positive[205], ("P53467", "ACTM_MOLOC")) + self.assertEqual(record.dr_positive[206], ("P12717", "ACTM_PISOC")) + self.assertEqual(record.dr_positive[207], ("P26198", "ACTM_STYCL")) + self.assertEqual(record.dr_positive[208], ("Q00214", "ACTM_STYPL")) + self.assertEqual(record.dr_positive[209], ("P53475", "ACTN_STYCL")) + self.assertEqual(record.dr_positive[210], ("Q90X97", "ACTS_ATRMM")) + self.assertEqual(record.dr_positive[211], ("P68138", "ACTS_BOVIN")) + self.assertEqual(record.dr_positive[212], ("P49055", "ACTS_CARAU")) + self.assertEqual(record.dr_positive[213], ("P68139", "ACTS_CHICK")) + self.assertEqual(record.dr_positive[214], ("P53479", "ACTS_CYPCA")) + self.assertEqual(record.dr_positive[215], ("P68140", "ACTS_FUGRU")) + self.assertEqual(record.dr_positive[216], ("P68133", "ACTS_HUMAN")) + self.assertEqual(record.dr_positive[217], ("P68134", "ACTS_MOUSE")) + self.assertEqual(record.dr_positive[218], ("P68264", "ACTS_OREMO")) + self.assertEqual(record.dr_positive[219], ("P68137", "ACTS_PIG")) + self.assertEqual(record.dr_positive[220], ("P10994", "ACTS_PLEWA")) + self.assertEqual(record.dr_positive[221], ("P68135", "ACTS_RABIT")) + self.assertEqual(record.dr_positive[222], ("P68136", "ACTS_RAT")) + self.assertEqual(record.dr_positive[223], ("P53482", "ACTT_FUGRU")) + self.assertEqual(record.dr_positive[224], ("P53483", "ACTX_FUGRU")) + self.assertEqual(record.dr_positive[225], ("P42025", "ACTY_HUMAN")) + self.assertEqual(record.dr_positive[226], ("P41341", "ACTY_LIMPO")) + self.assertEqual(record.dr_positive[227], ("Q8R5C5", "ACTY_MOUSE")) + self.assertEqual(record.dr_positive[228], ("P61162", "ACTZ_CANFA")) + self.assertEqual(record.dr_positive[229], ("P45889", "ACTZ_DROME")) + self.assertEqual(record.dr_positive[230], ("P61163", "ACTZ_HUMAN")) + self.assertEqual(record.dr_positive[231], ("P61164", "ACTZ_MOUSE")) + self.assertEqual(record.dr_positive[232], ("P53491", "ACT_ACECL")) + self.assertEqual(record.dr_positive[233], ("P26182", "ACT_ACHBI")) + self.assertEqual(record.dr_positive[234], ("P53455", "ACT_AJECA")) + self.assertEqual(record.dr_positive[235], ("Q75D00", "ACT_ASHGO")) + self.assertEqual(record.dr_positive[236], ("O13419", "ACT_BOTCI")) + self.assertEqual(record.dr_positive[237], ("P90689", "ACT_BRUMA")) + self.assertEqual(record.dr_positive[238], ("P14235", "ACT_CANAL")) + self.assertEqual(record.dr_positive[239], ("Q9UVZ8", "ACT_CANDU")) + self.assertEqual(record.dr_positive[240], ("P60009", "ACT_CANGA")) + self.assertEqual(record.dr_positive[241], ("P53498", "ACT_CHLRE")) + self.assertEqual(record.dr_positive[242], ("P53499", "ACT_CHOCR")) + self.assertEqual(record.dr_positive[243], ("O65315", "ACT_COLSC")) + self.assertEqual(record.dr_positive[244], ("Q9UVX4", "ACT_COPCI")) + self.assertEqual(record.dr_positive[245], ("P30161", "ACT_COSCS")) + self.assertEqual(record.dr_positive[246], ("O17320", "ACT_CRAGI")) + self.assertEqual(record.dr_positive[247], ("P48465", "ACT_CRYNV")) + self.assertEqual(record.dr_positive[248], ("P26183", "ACT_CRYPV")) + self.assertEqual(record.dr_positive[249], ("P53500", "ACT_CYAME")) + self.assertEqual(record.dr_positive[250], ("Q24733", "ACT_DICVI")) + self.assertEqual(record.dr_positive[251], ("P11426", "ACT_ENTHI")) + self.assertEqual(record.dr_positive[252], ("Q8X119", "ACT_EXODE")) + self.assertEqual(record.dr_positive[253], ("P53502", "ACT_FUCDI")) + self.assertEqual(record.dr_positive[254], ("Q39758", "ACT_FUCVE")) + self.assertEqual(record.dr_positive[255], ("Q6TCF2", "ACT_GAEGA")) + self.assertEqual(record.dr_positive[256], ("O81221", "ACT_GOSHI")) + self.assertEqual(record.dr_positive[257], ("O00937", "ACT_HISCA")) + self.assertEqual(record.dr_positive[258], ("P17126", "ACT_HYDAT")) + self.assertEqual(record.dr_positive[259], ("P17128", "ACT_KLULA")) + self.assertEqual(record.dr_positive[260], ("P45520", "ACT_LEIMA")) + self.assertEqual(record.dr_positive[261], ("P91754", "ACT_LUMRU")) + self.assertEqual(record.dr_positive[262], ("P49871", "ACT_MANSE")) + self.assertEqual(record.dr_positive[263], ("O16808", "ACT_MAYDE")) + self.assertEqual(record.dr_positive[264], ("O65316", "ACT_MESVI")) + self.assertEqual(record.dr_positive[265], ("P78711", "ACT_NEUCR")) + self.assertEqual(record.dr_positive[266], ("P53689", "ACT_PHARH")) + self.assertEqual(record.dr_positive[267], ("P13363", "ACT_PHYME")) + self.assertEqual(record.dr_positive[268], ("O74258", "ACT_PICAN")) + self.assertEqual(record.dr_positive[269], ("Q9P4D1", "ACT_PICPA")) + self.assertEqual(record.dr_positive[270], ("P24902", "ACT_PINCO")) + self.assertEqual(record.dr_positive[271], ("Q26065", "ACT_PLAMG")) + self.assertEqual(record.dr_positive[272], ("P45521", "ACT_PROCL")) + self.assertEqual(record.dr_positive[273], ("P50138", "ACT_PUCGR")) + self.assertEqual(record.dr_positive[274], ("P60011", "ACT_SACBA")) + self.assertEqual(record.dr_positive[275], ("O65314", "ACT_SCHDU")) + self.assertEqual(record.dr_positive[276], ("P10989", "ACT_SCHPO")) + self.assertEqual(record.dr_positive[277], ("P68555", "ACT_TAESO")) + self.assertEqual(record.dr_positive[278], ("P10365", "ACT_THELA")) + self.assertEqual(record.dr_positive[279], ("P53476", "ACT_TOXGO")) + self.assertEqual(record.dr_positive[280], ("Q99023", "ACT_TRIRE")) + self.assertEqual(record.dr_positive[281], ("P53477", "ACT_TRYCR")) + self.assertEqual(record.dr_positive[282], ("P20904", "ACT_VOLCA")) + self.assertEqual(record.dr_positive[283], ("Q9UVF3", "ACT_YARLI")) + self.assertEqual(record.dr_positive[284], ("P60010", "ACT_YEAST")) + self.assertEqual(record.dr_positive[285], ("Q61JZ2", "ARP2_CAEBR")) + self.assertEqual(record.dr_positive[286], ("P53489", "ARP2_CAEEL")) + self.assertEqual(record.dr_positive[287], ("Q4WHA3", "ARP4_ASPFU")) + self.assertEqual(record.dr_positive[288], ("Q5AC48", "ARP4_CANAL")) + self.assertEqual(record.dr_positive[289], ("Q6BXN0", "ARP4_DEBHA")) + self.assertEqual(record.dr_positive[290], ("Q4IPI4", "ARP4_GIBZE")) + self.assertEqual(record.dr_positive[291], ("Q7SHR0", "ARP4_NEUCR")) + self.assertEqual(record.dr_positive[292], ("Q9P7X7", "ARP4_SCHPO")) + self.assertEqual(record.dr_positive[293], ("Q4P2E8", "ARP4_USTMA")) + self.assertEqual(record.dr_positive[294], ("Q09849", "YAE9_SCHPO")) + + def read4_false_etc(self, record): + self.assertEqual(len(record.dr_false_neg), 22) + self.assertEqual(record.dr_false_neg[0], ("P30169", "ACT7_SOLTU")) + self.assertEqual(record.dr_false_neg[1], ("P24263", "ACTD_PHYPO")) + self.assertEqual(record.dr_false_neg[2], ("P12431", "ACTM_STRPU")) + self.assertEqual(record.dr_false_neg[3], ("P20360", "ACT_EUPCR")) + self.assertEqual(record.dr_false_neg[4], ("P51775", "ACT_GIALA")) + self.assertEqual(record.dr_false_neg[5], ("Q754G5", "ARP4_ASHGO")) + self.assertEqual(record.dr_false_neg[6], ("Q6FJV8", "ARP4_CANGA")) + self.assertEqual(record.dr_false_neg[7], ("Q5AW89", "ARP4_EMENI")) + self.assertEqual(record.dr_false_neg[8], ("Q6CSB9", "ARP4_KLULA")) + self.assertEqual(record.dr_false_neg[9], ("Q6C061", "ARP4_YARLI")) + self.assertEqual(record.dr_false_neg[10], ("P80428", "ARP4_YEAST")) + self.assertEqual(record.dr_false_neg[11], ("Q74ZV8", "ARP6_ASHGO")) + self.assertEqual(record.dr_false_neg[12], ("Q4W9M3", "ARP6_ASPFU")) + self.assertEqual(record.dr_false_neg[13], ("Q5AP59", "ARP6_CANAL")) + self.assertEqual(record.dr_false_neg[14], ("Q6FKE7", "ARP6_CANGA")) + self.assertEqual(record.dr_false_neg[15], ("Q5KAQ4", "ARP6_CRYNE")) + self.assertEqual(record.dr_false_neg[16], ("Q6BML9", "ARP6_DEBHA")) + self.assertEqual(record.dr_false_neg[17], ("Q5AXH1", "ARP6_EMENI")) + self.assertEqual(record.dr_false_neg[18], ("Q6CJF4", "ARP6_KLULA")) + self.assertEqual(record.dr_false_neg[19], ("Q7S6X6", "ARP6_NEUCR")) + self.assertEqual(record.dr_false_neg[20], ("O94241", "ARP6_SCHPO")) + self.assertEqual(record.dr_false_neg[21], ("Q6C982", "ARP6_YARLI")) + self.assertEqual(len(record.dr_false_pos), 0) + self.assertEqual(len(record.dr_potential), 26) + self.assertEqual(record.dr_potential[0], ("P30170", "ACT10_SOLTU")) + self.assertEqual(record.dr_potential[1], ("P10982", "ACT1_ABSGL")) + self.assertEqual(record.dr_potential[2], ("Q96482", "ACT1_LYCES")) + self.assertEqual(record.dr_potential[3], ("P93587", "ACT1_SOLTU")) + self.assertEqual(record.dr_potential[4], ("Q96483", "ACT2_LYCES")) + self.assertEqual(record.dr_potential[5], ("P93586", "ACT2_SOLTU")) + self.assertEqual(record.dr_potential[6], ("P93374", "ACT2_TOBAC")) + self.assertEqual(record.dr_potential[7], ("Q96484", "ACT3_LYCES")) + self.assertEqual(record.dr_potential[8], ("P93373", "ACT3_TOBAC")) + self.assertEqual(record.dr_potential[9], ("Q96481", "ACT4_LYCES")) + self.assertEqual(record.dr_potential[10], ("P93585", "ACT4_SOLTU")) + self.assertEqual(record.dr_potential[11], ("P93372", "ACT4_TOBAC")) + self.assertEqual(record.dr_potential[12], ("P81228", "ACT5_SOLTU")) + self.assertEqual(record.dr_potential[13], ("P93371", "ACT5_TOBAC")) + self.assertEqual(record.dr_potential[14], ("P15986", "ACT6_SOYBN")) + self.assertEqual(record.dr_potential[15], ("P93376", "ACT6_TOBAC")) + self.assertEqual(record.dr_potential[16], ("P15987", "ACT7_SOYBN")) + self.assertEqual(record.dr_potential[17], ("P93375", "ACT7_TOBAC")) + self.assertEqual(record.dr_potential[18], ("P81229", "ACT8_SOLTU")) + self.assertEqual(record.dr_potential[19], ("P93584", "ACT9_SOLTU")) + self.assertEqual(record.dr_potential[20], ("Q92192", "ACT_CALFI")) + self.assertEqual(record.dr_potential[21], ("P80709", "ACT_CARMA")) + self.assertEqual(record.dr_potential[22], ("Q39596", "ACT_CHERU")) + self.assertEqual(record.dr_potential[23], ("Q92193", "ACT_CRAVI")) + self.assertEqual(record.dr_potential[24], ("P81085", "ACT_PINPS")) + self.assertEqual(record.dr_potential[25], ("Q11212", "ACT_SPOLI")) + self.assertEqual(len(record.dr_unknown), 0) + self.assertEqual(len(record.pdb_structs), 60) + self.assertEqual(record.pdb_structs[0], "1ALM") + self.assertEqual(record.pdb_structs[1], "1ATN") + self.assertEqual(record.pdb_structs[2], "1C0F") + self.assertEqual(record.pdb_structs[3], "1C0G") + self.assertEqual(record.pdb_structs[4], "1D4X") + self.assertEqual(record.pdb_structs[5], "1DEJ") + self.assertEqual(record.pdb_structs[6], "1EQY") + self.assertEqual(record.pdb_structs[7], "1ESV") + self.assertEqual(record.pdb_structs[8], "1H1V") + self.assertEqual(record.pdb_structs[9], "1HLU") + self.assertEqual(record.pdb_structs[10], "1IJJ") + self.assertEqual(record.pdb_structs[11], "1J6Z") + self.assertEqual(record.pdb_structs[12], "1KXP") + self.assertEqual(record.pdb_structs[13], "1LCU") + self.assertEqual(record.pdb_structs[14], "1LOT") + self.assertEqual(record.pdb_structs[15], "1LVT") + self.assertEqual(record.pdb_structs[16], "1M8Q") + self.assertEqual(record.pdb_structs[17], "1M8Q0") + self.assertEqual(record.pdb_structs[18], "1MA9") + self.assertEqual(record.pdb_structs[19], "1MDU") + self.assertEqual(record.pdb_structs[20], "1MVW") + self.assertEqual(record.pdb_structs[21], "1N58") + self.assertEqual(record.pdb_structs[22], "1NLV") + self.assertEqual(record.pdb_structs[23], "1NM1") + self.assertEqual(record.pdb_structs[24], "1NMD") + self.assertEqual(record.pdb_structs[25], "1NWK") + self.assertEqual(record.pdb_structs[26], "1O18") + self.assertEqual(record.pdb_structs[27], "1O19") + self.assertEqual(record.pdb_structs[28], "1O1A") + self.assertEqual(record.pdb_structs[29], "1O1B") + self.assertEqual(record.pdb_structs[30], "1O1B0") + self.assertEqual(record.pdb_structs[31], "1O1C") + self.assertEqual(record.pdb_structs[32], "1O1C0") + self.assertEqual(record.pdb_structs[33], "1O1D") + self.assertEqual(record.pdb_structs[34], "1O1D0") + self.assertEqual(record.pdb_structs[35], "1O1E") + self.assertEqual(record.pdb_structs[36], "1O1F") + self.assertEqual(record.pdb_structs[37], "1O1F0") + self.assertEqual(record.pdb_structs[38], "1O1G") + self.assertEqual(record.pdb_structs[39], "1P8Z") + self.assertEqual(record.pdb_structs[40], "1QZ5") + self.assertEqual(record.pdb_structs[41], "1QZ6") + self.assertEqual(record.pdb_structs[42], "1RDW") + self.assertEqual(record.pdb_structs[43], "1RFQ") + self.assertEqual(record.pdb_structs[44], "1RGI") + self.assertEqual(record.pdb_structs[45], "1S22") + self.assertEqual(record.pdb_structs[46], "1SQK") + self.assertEqual(record.pdb_structs[47], "1T44") + self.assertEqual(record.pdb_structs[48], "1Y64") + self.assertEqual(record.pdb_structs[49], "1YAG") + self.assertEqual(record.pdb_structs[50], "1YVN") + self.assertEqual(record.pdb_structs[51], "2A3Z") + self.assertEqual(record.pdb_structs[52], "2A40") + self.assertEqual(record.pdb_structs[53], "2A41") + self.assertEqual(record.pdb_structs[54], "2A42") + self.assertEqual(record.pdb_structs[55], "2A5X") + self.assertEqual(record.pdb_structs[56], "2ASM") + self.assertEqual(record.pdb_structs[57], "2ASO") + self.assertEqual(record.pdb_structs[58], "2ASP") + self.assertEqual(record.pdb_structs[59], "2BTF") + + def test_read5(self): + """Parsing Prosite record ps00488.txt.""" + filename = os.path.join("Prosite", "ps00488.txt") + with open(filename) as handle: + record = Prosite.read(handle) + self.assertEqual(record.name, "PAL_HISTIDASE") + self.assertEqual(record.type, "PATTERN") + self.assertEqual(record.accession, "PS00488") + self.assertEqual(record.created, "MAY-1991") + self.assertEqual(record.data_update, "DEC-2004") + self.assertEqual(record.info_update, "MAR-2006") + self.assertEqual(record.pdoc, "PDOC00424") + self.assertEqual( + record.description, "Phenylalanine and histidine ammonia-lyases signature." + ) + self.assertEqual( + record.pattern, + "[GS]-[STG]-[LIVM]-[STG]-[SAC]-S-G-[DH]-L-x-P-L-[SA]-x(2,3)-[SAGVT].", + ) + self.assertEqual(record.matrix, []) + self.assertEqual(record.rules, []) + self.assertEqual(record.nr_sp_release, "49.3") + self.assertEqual(record.nr_sp_seqs, 212425) + self.assertEqual(record.cc_taxo_range, "A?EP?") + self.assertEqual(record.cc_max_repeat, "1") + self.assertEqual(len(record.cc_site), 1) + self.assertEqual(record.cc_site[0], (6, "active_site")) + self.assertEqual(len(record.dr_positive), 127) + self.assertEqual(record.dr_positive[0], ("Q8RFC2", "HUTH1_FUSNN")) + self.assertEqual(record.dr_positive[1], ("Q8RDU4", "HUTH2_FUSNN")) + self.assertEqual(record.dr_positive[2], ("Q9KWE4", "HUTH_AGRRH")) + self.assertEqual(record.dr_positive[3], ("Q8U8Z7", "HUTH_AGRT5")) + self.assertEqual(record.dr_positive[4], ("Q5NZX8", "HUTH_AZOSE")) + self.assertEqual(record.dr_positive[5], ("Q81Y45", "HUTH_BACAN")) + self.assertEqual(record.dr_positive[6], ("Q733H8", "HUTH_BACC1")) + self.assertEqual(record.dr_positive[7], ("Q81AC6", "HUTH_BACCR")) + self.assertEqual(record.dr_positive[8], ("Q9KBE6", "HUTH_BACHD")) + self.assertEqual(record.dr_positive[9], ("Q6HFE9", "HUTH_BACHK")) + self.assertEqual(record.dr_positive[10], ("Q5WAZ6", "HUTH_BACSK")) + self.assertEqual(record.dr_positive[11], ("P10944", "HUTH_BACSU")) + self.assertEqual(record.dr_positive[12], ("Q6G3U8", "HUTH_BARHE")) + self.assertEqual(record.dr_positive[13], ("Q6FZP9", "HUTH_BARQU")) + self.assertEqual(record.dr_positive[14], ("Q89GV3", "HUTH_BRAJA")) + self.assertEqual(record.dr_positive[15], ("Q579E8", "HUTH_BRUAB")) + self.assertEqual(record.dr_positive[16], ("Q8FVB4", "HUTH_BRUSU")) + self.assertEqual(record.dr_positive[17], ("Q62LJ6", "HUTH_BURMA")) + self.assertEqual(record.dr_positive[18], ("Q63SH6", "HUTH_BURPS")) + self.assertEqual(record.dr_positive[19], ("Q20502", "HUTH_CAEEL")) + self.assertEqual(record.dr_positive[20], ("P58082", "HUTH_CAUCR")) + self.assertEqual(record.dr_positive[21], ("Q7P188", "HUTH_CHRVO")) + self.assertEqual(record.dr_positive[22], ("Q891Q1", "HUTH_CLOTE")) + self.assertEqual(record.dr_positive[23], ("Q9RZ06", "HUTH_DEIRA")) + self.assertEqual(record.dr_positive[24], ("Q6AKP3", "HUTH_DESPS")) + self.assertEqual(record.dr_positive[25], ("Q5L310", "HUTH_GEOKA")) + self.assertEqual(record.dr_positive[26], ("Q7NCB3", "HUTH_GLOVI")) + self.assertEqual(record.dr_positive[27], ("Q5FRR8", "HUTH_GLUOX")) + self.assertEqual(record.dr_positive[28], ("Q9HQD5", "HUTH_HALSA")) + self.assertEqual(record.dr_positive[29], ("P42357", "HUTH_HUMAN")) + self.assertEqual(record.dr_positive[30], ("Q5QV30", "HUTH_IDILO")) + self.assertEqual(record.dr_positive[31], ("Q5X5I5", "HUTH_LEGPA")) + self.assertEqual(record.dr_positive[32], ("Q5ZVR0", "HUTH_LEGPH")) + self.assertEqual(record.dr_positive[33], ("Q5WWW8", "HUTH_LEGPL")) + self.assertEqual(record.dr_positive[34], ("P35492", "HUTH_MOUSE")) + self.assertEqual(record.dr_positive[35], ("Q7N296", "HUTH_PHOLL")) + self.assertEqual(record.dr_positive[36], ("Q6LQ56", "HUTH_PHOPR")) + self.assertEqual(record.dr_positive[37], ("Q9HU85", "HUTH_PSEAE")) + self.assertEqual(record.dr_positive[38], ("Q8VMR3", "HUTH_PSEFL")) + self.assertEqual(record.dr_positive[39], ("Q88CZ7", "HUTH_PSEPK")) + self.assertEqual(record.dr_positive[40], ("P21310", "HUTH_PSEPU")) + self.assertEqual(record.dr_positive[41], ("Q87UM1", "HUTH_PSESM")) + self.assertEqual(record.dr_positive[42], ("Q8XW29", "HUTH_RALSO")) + self.assertEqual(record.dr_positive[43], ("P21213", "HUTH_RAT")) + self.assertEqual(record.dr_positive[44], ("Q983I0", "HUTH_RHILO")) + self.assertEqual(record.dr_positive[45], ("O31197", "HUTH_RHIME")) + self.assertEqual(record.dr_positive[46], ("Q57RG6", "HUTH_SALCH")) + self.assertEqual(record.dr_positive[47], ("Q5PG61", "HUTH_SALPA")) + self.assertEqual(record.dr_positive[48], ("Q8Z896", "HUTH_SALTI")) + self.assertEqual(record.dr_positive[49], ("Q8ZQQ9", "HUTH_SALTY")) + self.assertEqual(record.dr_positive[50], ("Q5LRD8", "HUTH_SILPO")) + self.assertEqual(record.dr_positive[51], ("Q5HJY8", "HUTH_STAAC")) + self.assertEqual(record.dr_positive[52], ("P64415", "HUTH_STAAM")) + self.assertEqual(record.dr_positive[53], ("P64416", "HUTH_STAAN")) + self.assertEqual(record.dr_positive[54], ("Q6GKT7", "HUTH_STAAR")) + self.assertEqual(record.dr_positive[55], ("Q6GD82", "HUTH_STAAS")) + self.assertEqual(record.dr_positive[56], ("Q8NYY3", "HUTH_STAAW")) + self.assertEqual(record.dr_positive[57], ("Q93TX3", "HUTH_STIAU")) + self.assertEqual(record.dr_positive[58], ("Q82I33", "HUTH_STRAW")) + self.assertEqual(record.dr_positive[59], ("Q9EWW1", "HUTH_STRCO")) + self.assertEqual(record.dr_positive[60], ("P24221", "HUTH_STRGR")) + self.assertEqual(record.dr_positive[61], ("P58083", "HUTH_STRP1")) + self.assertEqual(record.dr_positive[62], ("Q8K5L5", "HUTH_STRP3")) + self.assertEqual(record.dr_positive[63], ("Q5X9K4", "HUTH_STRP6")) + self.assertEqual(record.dr_positive[64], ("Q8NZ46", "HUTH_STRP8")) + self.assertEqual(record.dr_positive[65], ("Q67JH4", "HUTH_SYMTH")) + self.assertEqual(record.dr_positive[66], ("Q9HLI6", "HUTH_THEAC")) + self.assertEqual(record.dr_positive[67], ("Q8RBH4", "HUTH_THETN")) + self.assertEqual(record.dr_positive[68], ("Q978N8", "HUTH_THEVO")) + self.assertEqual(record.dr_positive[69], ("Q9KSQ4", "HUTH_VIBCH")) + self.assertEqual(record.dr_positive[70], ("Q5E0C6", "HUTH_VIBF1")) + self.assertEqual(record.dr_positive[71], ("Q87Q77", "HUTH_VIBPA")) + self.assertEqual(record.dr_positive[72], ("Q8DA21", "HUTH_VIBVU")) + self.assertEqual(record.dr_positive[73], ("Q7MK58", "HUTH_VIBVY")) + self.assertEqual(record.dr_positive[74], ("Q8PLZ8", "HUTH_XANAC")) + self.assertEqual(record.dr_positive[75], ("Q8PAA7", "HUTH_XANCP")) + self.assertEqual(record.dr_positive[76], ("Q8ZA10", "HUTH_YERPE")) + self.assertEqual(record.dr_positive[77], ("Q664B8", "HUTH_YERPS")) + self.assertEqual(record.dr_positive[78], ("Q8YD09", "HUTIH_BRUME")) + self.assertEqual(record.dr_positive[79], ("P35510", "PAL1_ARATH")) + self.assertEqual(record.dr_positive[80], ("O23865", "PAL1_DAUCA")) + self.assertEqual(record.dr_positive[81], ("P14166", "PAL1_IPOBA")) + self.assertEqual(record.dr_positive[82], ("O49835", "PAL1_LITER")) + self.assertEqual(record.dr_positive[83], ("P35511", "PAL1_LYCES")) + self.assertEqual(record.dr_positive[84], ("P14717", "PAL1_ORYSA")) + self.assertEqual(record.dr_positive[85], ("Q01861", "PAL1_PEA")) + self.assertEqual(record.dr_positive[86], ("P24481", "PAL1_PETCR")) + self.assertEqual(record.dr_positive[87], ("P45731", "PAL1_POPKI")) + self.assertEqual(record.dr_positive[88], ("O64963", "PAL1_PRUAV")) + self.assertEqual(record.dr_positive[89], ("Q9M568", "PAL1_RUBID")) + self.assertEqual(record.dr_positive[90], ("P31425", "PAL1_SOLTU")) + self.assertEqual(record.dr_positive[91], ("P27991", "PAL1_SOYBN")) + self.assertEqual(record.dr_positive[92], ("P25872", "PAL1_TOBAC")) + self.assertEqual(record.dr_positive[93], ("P45724", "PAL2_ARATH")) + self.assertEqual(record.dr_positive[94], ("Q9SMK9", "PAL2_CICAR")) + self.assertEqual(record.dr_positive[95], ("Q42858", "PAL2_IPOBA")) + self.assertEqual(record.dr_positive[96], ("O49836", "PAL2_LITER")) + self.assertEqual(record.dr_positive[97], ("P53443", "PAL2_ORYSA")) + self.assertEqual(record.dr_positive[98], ("Q04593", "PAL2_PEA")) + self.assertEqual(record.dr_positive[99], ("P45728", "PAL2_PETCR")) + self.assertEqual(record.dr_positive[100], ("P19142", "PAL2_PHAVU")) + self.assertEqual(record.dr_positive[101], ("Q43052", "PAL2_POPKI")) + self.assertEqual(record.dr_positive[102], ("P31426", "PAL2_SOLTU")) + self.assertEqual(record.dr_positive[103], ("P35513", "PAL2_TOBAC")) + self.assertEqual(record.dr_positive[104], ("P45725", "PAL3_ARATH")) + self.assertEqual(record.dr_positive[105], ("P45729", "PAL3_PETCR")) + self.assertEqual(record.dr_positive[106], ("P19143", "PAL3_PHAVU")) + self.assertEqual(record.dr_positive[107], ("P45733", "PAL3_TOBAC")) + self.assertEqual(record.dr_positive[108], ("Q9SS45", "PAL4_ARATH")) + self.assertEqual(record.dr_positive[109], ("Q40910", "PAL4_POPKI")) + self.assertEqual(record.dr_positive[110], ("P26600", "PAL5_LYCES")) + self.assertEqual(record.dr_positive[111], ("O93967", "PALY_AMAMU")) + self.assertEqual(record.dr_positive[112], ("Q42609", "PALY_BROFI")) + self.assertEqual(record.dr_positive[113], ("P45726", "PALY_CAMSI")) + self.assertEqual(record.dr_positive[114], ("Q42667", "PALY_CITLI")) + self.assertEqual(record.dr_positive[115], ("O23924", "PALY_DIGLA")) + self.assertEqual(record.dr_positive[116], ("O04058", "PALY_HELAN")) + self.assertEqual(record.dr_positive[117], ("P27990", "PALY_MEDSA")) + self.assertEqual(record.dr_positive[118], ("P45727", "PALY_PERAE")) + self.assertEqual(record.dr_positive[119], ("P52777", "PALY_PINTA")) + self.assertEqual(record.dr_positive[120], ("P45730", "PALY_POPTR")) + self.assertEqual(record.dr_positive[121], ("P10248", "PALY_RHORB")) + self.assertEqual(record.dr_positive[122], ("P11544", "PALY_RHOTO")) + self.assertEqual(record.dr_positive[123], ("P45732", "PALY_STYHU")) + self.assertEqual(record.dr_positive[124], ("P45734", "PALY_TRISU")) + self.assertEqual(record.dr_positive[125], ("Q96V77", "PALY_USTMA")) + self.assertEqual(record.dr_positive[126], ("Q43210", "PALY_WHEAT")) + self.assertEqual(len(record.dr_false_neg), 2) + self.assertEqual(record.dr_false_neg[0], ("Q8EKJ4", "HUTH_SHEON")) + self.assertEqual(record.dr_false_neg[1], ("Q73Q56", "HUTH_TREDE")) + self.assertEqual(len(record.dr_false_pos), 0) + self.assertEqual(len(record.dr_potential), 4) + self.assertEqual(record.dr_potential[0], ("P07218", "PAL1_PHAVU")) + self.assertEqual(record.dr_potential[1], ("Q92195", "PALY_AGABI")) + self.assertEqual(record.dr_potential[2], ("P35512", "PALY_MALDO")) + self.assertEqual(record.dr_potential[3], ("P45735", "PALY_VITVI")) + self.assertEqual(len(record.dr_unknown), 0) + self.assertEqual(record.pdb_structs[0], "1B8F") + self.assertEqual(record.pdb_structs[1], "1EB4") + self.assertEqual(record.pdb_structs[2], "1GK2") + self.assertEqual(record.pdb_structs[3], "1GKJ") + self.assertEqual(record.pdb_structs[4], "1GKM") + self.assertEqual(record.pdb_structs[5], "1Y2M") + + def test_read6(self): + """Parsing Prosite record ps00546.txt.""" + filename = os.path.join("Prosite", "ps00546.txt") + with open(filename) as handle: + record = Prosite.read(handle) + self.assertEqual(record.name, "CYSTEINE_SWITCH") + self.assertEqual(record.type, "PATTERN") + self.assertEqual(record.accession, "PS00546") + self.assertEqual(record.created, "DEC-1991") + self.assertEqual(record.data_update, "NOV-1997") + self.assertEqual(record.info_update, "MAR-2006") + self.assertEqual(record.pdoc, "PDOC00472") + self.assertEqual(record.description, "Matrixins cysteine switch.") + self.assertEqual(record.pattern, "P-R-C-[GN]-x-P-[DR]-[LIVSAPKQ].") + self.assertEqual(record.matrix, []) + self.assertEqual(record.rules, []) + self.assertEqual(record.nr_sp_release, "49.3") + self.assertEqual(record.nr_sp_seqs, 212425) + self.assertEqual(record.cc_taxo_range, "??E??") + self.assertEqual(record.cc_max_repeat, "1") + self.assertEqual(len(record.cc_site), 1) + self.assertEqual(record.cc_site[0], (3, "chelates_zinc")) + self.assertEqual(len(record.dr_positive), 62) + self.assertEqual(record.dr_positive[0], ("P31178", "GLE_CHLRE")) + self.assertEqual(record.dr_positive[1], ("P91953", "HE_HEMPU")) + self.assertEqual(record.dr_positive[2], ("P22757", "HE_PARLI")) + self.assertEqual(record.dr_positive[3], ("P29136", "MEP1_SOYBN")) + self.assertEqual(record.dr_positive[4], ("P09238", "MMP10_HUMAN")) + self.assertEqual(record.dr_positive[5], ("O55123", "MMP10_MOUSE")) + self.assertEqual(record.dr_positive[6], ("P07152", "MMP10_RAT")) + self.assertEqual(record.dr_positive[7], ("P24347", "MMP11_HUMAN")) + self.assertEqual(record.dr_positive[8], ("Q11005", "MMP11_XENLA")) + self.assertEqual(record.dr_positive[9], ("P39900", "MMP12_HUMAN")) + self.assertEqual(record.dr_positive[10], ("P34960", "MMP12_MOUSE")) + self.assertEqual(record.dr_positive[11], ("P79227", "MMP12_RABIT")) + self.assertEqual(record.dr_positive[12], ("O77656", "MMP13_BOVIN")) + self.assertEqual(record.dr_positive[13], ("O18927", "MMP13_HORSE")) + self.assertEqual(record.dr_positive[14], ("P45452", "MMP13_HUMAN")) + self.assertEqual(record.dr_positive[15], ("P33435", "MMP13_MOUSE")) + self.assertEqual(record.dr_positive[16], ("O62806", "MMP13_RABIT")) + self.assertEqual(record.dr_positive[17], ("P23097", "MMP13_RAT")) + self.assertEqual(record.dr_positive[18], ("Q10835", "MMP13_XENLA")) + self.assertEqual(record.dr_positive[19], ("P50281", "MMP14_HUMAN")) + self.assertEqual(record.dr_positive[20], ("P53690", "MMP14_MOUSE")) + self.assertEqual(record.dr_positive[21], ("Q9XT90", "MMP14_PIG")) + self.assertEqual(record.dr_positive[22], ("Q95220", "MMP14_RABIT")) + self.assertEqual(record.dr_positive[23], ("Q10739", "MMP14_RAT")) + self.assertEqual(record.dr_positive[24], ("P51511", "MMP15_HUMAN")) + self.assertEqual(record.dr_positive[25], ("O54732", "MMP15_MOUSE")) + self.assertEqual(record.dr_positive[26], ("P51512", "MMP16_HUMAN")) + self.assertEqual(record.dr_positive[27], ("Q9WTR0", "MMP16_MOUSE")) + self.assertEqual(record.dr_positive[28], ("O35548", "MMP16_RAT")) + self.assertEqual(record.dr_positive[29], ("Q9EPL5", "MMP1A_MOUSE")) + self.assertEqual(record.dr_positive[30], ("Q9EPL6", "MMP1B_MOUSE")) + self.assertEqual(record.dr_positive[31], ("P28053", "MMP1_BOVIN")) + self.assertEqual(record.dr_positive[32], ("Q9XSZ5", "MMP1_HORSE")) + self.assertEqual(record.dr_positive[33], ("P03956", "MMP1_HUMAN")) + self.assertEqual(record.dr_positive[34], ("P21692", "MMP1_PIG")) + self.assertEqual(record.dr_positive[35], ("P13943", "MMP1_RABIT")) + self.assertEqual(record.dr_positive[36], ("O18767", "MMP20_BOVIN")) + self.assertEqual(record.dr_positive[37], ("O60882", "MMP20_HUMAN")) + self.assertEqual(record.dr_positive[38], ("P57748", "MMP20_MOUSE")) + self.assertEqual(record.dr_positive[39], ("P79287", "MMP20_PIG")) + self.assertEqual(record.dr_positive[40], ("Q90611", "MMP2_CHICK")) + self.assertEqual(record.dr_positive[41], ("P08253", "MMP2_HUMAN")) + self.assertEqual(record.dr_positive[42], ("P33434", "MMP2_MOUSE")) + self.assertEqual(record.dr_positive[43], ("P50757", "MMP2_RABIT")) + self.assertEqual(record.dr_positive[44], ("P33436", "MMP2_RAT")) + self.assertEqual(record.dr_positive[45], ("Q6Y4Q5", "MMP3_CANFA")) + self.assertEqual(record.dr_positive[46], ("P08254", "MMP3_HUMAN")) + self.assertEqual(record.dr_positive[47], ("P28862", "MMP3_MOUSE")) + self.assertEqual(record.dr_positive[48], ("P28863", "MMP3_RABIT")) + self.assertEqual(record.dr_positive[49], ("P03957", "MMP3_RAT")) + self.assertEqual(record.dr_positive[50], ("P09237", "MMP7_HUMAN")) + self.assertEqual(record.dr_positive[51], ("Q10738", "MMP7_MOUSE")) + self.assertEqual(record.dr_positive[52], ("P50280", "MMP7_RAT")) + self.assertEqual(record.dr_positive[53], ("P22894", "MMP8_HUMAN")) + self.assertEqual(record.dr_positive[54], ("O70138", "MMP8_MOUSE")) + self.assertEqual(record.dr_positive[55], ("O88766", "MMP8_RAT")) + self.assertEqual(record.dr_positive[56], ("P52176", "MMP9_BOVIN")) + self.assertEqual(record.dr_positive[57], ("O18733", "MMP9_CANFA")) + self.assertEqual(record.dr_positive[58], ("P14780", "MMP9_HUMAN")) + self.assertEqual(record.dr_positive[59], ("P41245", "MMP9_MOUSE")) + self.assertEqual(record.dr_positive[60], ("P41246", "MMP9_RABIT")) + self.assertEqual(record.dr_positive[61], ("P50282", "MMP9_RAT")) + self.assertEqual(len(record.dr_false_neg), 59) + self.assertEqual(record.dr_false_neg[0], ("Q9R158", "AD26A_MOUSE")) + self.assertEqual(record.dr_false_neg[1], ("Q10741", "ADA10_BOVIN")) + self.assertEqual(record.dr_false_neg[2], ("O14672", "ADA10_HUMAN")) + self.assertEqual(record.dr_false_neg[3], ("O35598", "ADA10_MOUSE")) + self.assertEqual(record.dr_false_neg[4], ("Q10743", "ADA10_RAT")) + self.assertEqual(record.dr_false_neg[5], ("Q8JIY1", "ADA10_XENLA")) + self.assertEqual(record.dr_false_neg[6], ("Q61824", "ADA12_MOUSE")) + self.assertEqual(record.dr_false_neg[7], ("Q13444", "ADA15_HUMAN")) + self.assertEqual(record.dr_false_neg[8], ("O88839", "ADA15_MOUSE")) + self.assertEqual(record.dr_false_neg[9], ("Q9QYV0", "ADA15_RAT")) + self.assertEqual(record.dr_false_neg[10], ("P78536", "ADA17_HUMAN")) + self.assertEqual(record.dr_false_neg[11], ("Q9Z0F8", "ADA17_MOUSE")) + self.assertEqual(record.dr_false_neg[12], ("Q9Z1K9", "ADA17_RAT")) + self.assertEqual(record.dr_false_neg[13], ("Q9H013", "ADA19_HUMAN")) + self.assertEqual(record.dr_false_neg[14], ("O35674", "ADA19_MOUSE")) + self.assertEqual(record.dr_false_neg[15], ("O43506", "ADA20_HUMAN")) + self.assertEqual(record.dr_false_neg[16], ("Q9UKJ8", "ADA21_HUMAN")) + self.assertEqual(record.dr_false_neg[17], ("Q9JI76", "ADA21_MOUSE")) + self.assertEqual(record.dr_false_neg[18], ("Q9R160", "ADA24_MOUSE")) + self.assertEqual(record.dr_false_neg[19], ("Q9R159", "ADA25_MOUSE")) + self.assertEqual(record.dr_false_neg[20], ("Q9UKQ2", "ADA28_HUMAN")) + self.assertEqual(record.dr_false_neg[21], ("Q9XSL6", "ADA28_MACFA")) + self.assertEqual(record.dr_false_neg[22], ("Q9JLN6", "ADA28_MOUSE")) + self.assertEqual(record.dr_false_neg[23], ("Q9UKF2", "ADA30_HUMAN")) + self.assertEqual(record.dr_false_neg[24], ("Q9BZ11", "ADA33_HUMAN")) + self.assertEqual(record.dr_false_neg[25], ("Q923W9", "ADA33_MOUSE")) + self.assertEqual(record.dr_false_neg[26], ("O15204", "ADEC1_HUMAN")) + self.assertEqual(record.dr_false_neg[27], ("P58397", "ATS12_HUMAN")) + self.assertEqual(record.dr_false_neg[28], ("Q811B3", "ATS12_MOUSE")) + self.assertEqual(record.dr_false_neg[29], ("Q8WXS8", "ATS14_HUMAN")) + self.assertEqual(record.dr_false_neg[30], ("Q8TE58", "ATS15_HUMAN")) + self.assertEqual(record.dr_false_neg[31], ("P59384", "ATS15_MOUSE")) + self.assertEqual(record.dr_false_neg[32], ("Q8TE57", "ATS16_HUMAN")) + self.assertEqual(record.dr_false_neg[33], ("Q69Z28", "ATS16_MOUSE")) + self.assertEqual(record.dr_false_neg[34], ("Q8TE56", "ATS17_HUMAN")) + self.assertEqual(record.dr_false_neg[35], ("Q8TE60", "ATS18_HUMAN")) + self.assertEqual(record.dr_false_neg[36], ("Q4VC17", "ATS18_MOUSE")) + self.assertEqual(record.dr_false_neg[37], ("Q8TE59", "ATS19_HUMAN")) + self.assertEqual(record.dr_false_neg[38], ("P59509", "ATS19_MOUSE")) + self.assertEqual(record.dr_false_neg[39], ("Q9UKP4", "ATS7_HUMAN")) + self.assertEqual(record.dr_false_neg[40], ("Q9P2N4", "ATS9_HUMAN")) + self.assertEqual(record.dr_false_neg[41], ("Q02853", "MMP11_MOUSE")) + self.assertEqual(record.dr_false_neg[42], ("Q63341", "MMP12_RAT")) + self.assertEqual(record.dr_false_neg[43], ("Q9ULZ9", "MMP17_HUMAN")) + self.assertEqual(record.dr_false_neg[44], ("Q9R0S3", "MMP17_MOUSE")) + self.assertEqual(record.dr_false_neg[45], ("O13065", "MMP18_XENLA")) + self.assertEqual(record.dr_false_neg[46], ("Q99542", "MMP19_HUMAN")) + self.assertEqual(record.dr_false_neg[47], ("Q9JHI0", "MMP19_MOUSE")) + self.assertEqual(record.dr_false_neg[48], ("Q11133", "MMP1_RANCA")) + self.assertEqual(record.dr_false_neg[49], ("Q90YC2", "MMP21_CYNPY")) + self.assertEqual(record.dr_false_neg[50], ("Q8N119", "MMP21_HUMAN")) + self.assertEqual(record.dr_false_neg[51], ("Q8K3F2", "MMP21_MOUSE")) + self.assertEqual(record.dr_false_neg[52], ("O93470", "MMP21_XENLA")) + self.assertEqual(record.dr_false_neg[53], ("Q9Y5R2", "MMP24_HUMAN")) + self.assertEqual(record.dr_false_neg[54], ("Q9R0S2", "MMP24_MOUSE")) + self.assertEqual(record.dr_false_neg[55], ("Q9NRE1", "MMP26_HUMAN")) + self.assertEqual(record.dr_false_neg[56], ("Q9H239", "MMP28_HUMAN")) + self.assertEqual(record.dr_false_neg[57], ("Q28397", "MMP3_HORSE")) + self.assertEqual(record.dr_false_neg[58], ("P55032", "MMP7_FELCA")) + self.assertEqual(len(record.dr_false_pos), 1) + self.assertEqual(record.dr_false_pos[0], ("Q9YC75", "RGYR2_AERPE")) + self.assertEqual(len(record.dr_potential), 0) + self.assertEqual(len(record.dr_unknown), 0) + self.assertEqual(len(record.pdb_structs), 8) + self.assertEqual(record.pdb_structs[0], "1CK7") + self.assertEqual(record.pdb_structs[1], "1EAK") + self.assertEqual(record.pdb_structs[2], "1GXD") + self.assertEqual(record.pdb_structs[3], "1L6J") + self.assertEqual(record.pdb_structs[4], "1LKG") + self.assertEqual(record.pdb_structs[5], "1SLM") + self.assertEqual(record.pdb_structs[6], "1SU3") + self.assertEqual(record.pdb_structs[7], "1UC1") + if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) diff --git a/Tests/test_prosite2.py b/Tests/test_prosite2.py deleted file mode 100644 index 422b3e3de..000000000 --- a/Tests/test_prosite2.py +++ /dev/null @@ -1,789 +0,0 @@ -# Copyright 1999 by Cayte Lindner. All rights reserved. -# This code is part of the Biopython distribution and governed by its -# license. Please see the LICENSE file that should have been included -# as part of this package. -# -# NOTE - This file has been split in two as a workaround for Jython JVM limits. - -"""Tests for prosite2 module.""" - -import os -import unittest - -from Bio.ExPASy import Prosite - - -class TestPrositeRead(unittest.TestCase): - def test_read4(self): - """Parsing Prosite record ps00432.txt.""" - filename = os.path.join("Prosite", "ps00432.txt") - with open(filename) as handle: - record = Prosite.read(handle) - self.assertEqual(record.name, "ACTINS_2") - self.assertEqual(record.type, "PATTERN") - self.assertEqual(record.accession, "PS00432") - self.assertEqual(record.created, "NOV-1990") - self.assertEqual(record.data_update, "DEC-2004") - self.assertEqual(record.info_update, "MAR-2006") - self.assertEqual(record.pdoc, "PDOC00340") - self.assertEqual(record.description, "Actins signature 2.") - self.assertEqual(record.pattern, "W-[IVC]-[STAK]-[RK]-x-[DE]-Y-[DNE]-[DE].") - self.assertEqual(record.matrix, []) - self.assertEqual(record.rules, []) - self.assertEqual(record.nr_sp_release, "49.3") - self.assertEqual(record.nr_sp_seqs, 212425) - self.assertEqual(record.cc_taxo_range, "??E??") - self.assertEqual(record.cc_max_repeat, "1") - self.assertEqual(len(record.cc_site), 0) - self.read4_positive(record) - self.read4_false_etc(record) - - def read4_positive(self, record): - self.assertEqual(len(record.dr_positive), 295) - self.assertEqual(record.dr_positive[0], ("O96019", "ACL6A_HUMAN")) - self.assertEqual(record.dr_positive[1], ("Q9Z2N8", "ACL6A_MOUSE")) - self.assertEqual(record.dr_positive[2], ("O94805", "ACL6B_HUMAN")) - self.assertEqual(record.dr_positive[3], ("Q99MR0", "ACL6B_MOUSE")) - self.assertEqual(record.dr_positive[4], ("P53496", "ACT11_ARATH")) - self.assertEqual(record.dr_positive[5], ("P30171", "ACT11_SOLTU")) - self.assertEqual(record.dr_positive[6], ("P53497", "ACT12_ARATH")) - self.assertEqual(record.dr_positive[7], ("P30172", "ACT12_SOLTU")) - self.assertEqual(record.dr_positive[8], ("P30173", "ACT13_SOLTU")) - self.assertEqual(record.dr_positive[9], ("P84185", "ACT1D_ANOGA")) - self.assertEqual(record.dr_positive[10], ("P02578", "ACT1_ACACA")) - self.assertEqual(record.dr_positive[11], ("P49128", "ACT1_AEDAE")) - self.assertEqual(record.dr_positive[12], ("P10671", "ACT1_ARATH")) - self.assertEqual(record.dr_positive[13], ("P18600", "ACT1_ARTSX")) - self.assertEqual(record.dr_positive[14], ("P83969", "ACT1_BACDO")) - self.assertEqual(record.dr_positive[15], ("P07836", "ACT1_BOMMO")) - self.assertEqual(record.dr_positive[16], ("P10983", "ACT1_CAEEL")) - self.assertEqual(record.dr_positive[17], ("P23343", "ACT1_DAUCA")) - self.assertEqual(record.dr_positive[18], ("P02577", "ACT1_DICDI")) - self.assertEqual(record.dr_positive[19], ("P68556", "ACT1_DIPDE")) - self.assertEqual(record.dr_positive[20], ("P10987", "ACT1_DROME")) - self.assertEqual(record.dr_positive[21], ("P35432", "ACT1_ECHGR")) - self.assertEqual(record.dr_positive[22], ("P68142", "ACT1_FUGRU")) - self.assertEqual(record.dr_positive[23], ("P53460", "ACT1_HALRO")) - self.assertEqual(record.dr_positive[24], ("P69002", "ACT1_HELER")) - self.assertEqual(record.dr_positive[25], ("P69003", "ACT1_HELTB")) - self.assertEqual(record.dr_positive[26], ("P92182", "ACT1_LUMTE")) - self.assertEqual(record.dr_positive[27], ("P53465", "ACT1_LYTPI")) - self.assertEqual(record.dr_positive[28], ("P02582", "ACT1_MAIZE")) - self.assertEqual(record.dr_positive[29], ("P27131", "ACT1_NAEFO")) - self.assertEqual(record.dr_positive[30], ("P30162", "ACT1_ONCVO")) - self.assertEqual(record.dr_positive[31], ("Q98972", "ACT1_ORYLA")) - self.assertEqual(record.dr_positive[32], ("P13362", "ACT1_ORYSA")) - self.assertEqual(record.dr_positive[33], ("P53503", "ACT1_OXYFA")) - self.assertEqual(record.dr_positive[34], ("P12715", "ACT1_OXYNO")) - self.assertEqual(record.dr_positive[35], ("P53468", "ACT1_OXYTR")) - self.assertEqual(record.dr_positive[36], ("P30164", "ACT1_PEA")) - self.assertEqual(record.dr_positive[37], ("P22131", "ACT1_PHYIN")) - self.assertEqual(record.dr_positive[38], ("P10988", "ACT1_PLAFA")) - self.assertEqual(record.dr_positive[39], ("P43239", "ACT1_PNECA")) - self.assertEqual(record.dr_positive[40], ("P41112", "ACT1_PODCA")) - self.assertEqual(record.dr_positive[41], ("O18499", "ACT1_SACKO")) - self.assertEqual(record.dr_positive[42], ("Q9Y702", "ACT1_SCHCO")) - self.assertEqual(record.dr_positive[43], ("P53470", "ACT1_SCHMA")) - self.assertEqual(record.dr_positive[44], ("P53504", "ACT1_SORBI")) - self.assertEqual(record.dr_positive[45], ("P02581", "ACT1_SOYBN")) - self.assertEqual(record.dr_positive[46], ("P10990", "ACT1_STRFN")) - self.assertEqual(record.dr_positive[47], ("Q9Y701", "ACT1_SUIBO")) - self.assertEqual(record.dr_positive[48], ("P10992", "ACT1_TETTH")) - self.assertEqual(record.dr_positive[49], ("Q05214", "ACT1_TOBAC")) - self.assertEqual(record.dr_positive[50], ("P12432", "ACT1_TRYBB")) - self.assertEqual(record.dr_positive[51], ("P04751", "ACT1_XENLA")) - self.assertEqual(record.dr_positive[52], ("P26197", "ACT2_ABSGL")) - self.assertEqual(record.dr_positive[53], ("Q96292", "ACT2_ARATH")) - self.assertEqual(record.dr_positive[54], ("P18601", "ACT2_ARTSX")) - self.assertEqual(record.dr_positive[55], ("P45885", "ACT2_BACDO")) - self.assertEqual(record.dr_positive[56], ("P07837", "ACT2_BOMMO")) - self.assertEqual(record.dr_positive[57], ("P10984", "ACT2_CAEEL")) - self.assertEqual(record.dr_positive[58], ("P23344", "ACT2_DAUCA")) - self.assertEqual(record.dr_positive[59], ("P07827", "ACT2_DICDI")) - self.assertEqual(record.dr_positive[60], ("P53456", "ACT2_DIPDE")) - self.assertEqual(record.dr_positive[61], ("P02572", "ACT2_DROME")) - self.assertEqual(record.dr_positive[62], ("Q03341", "ACT2_ECHGR")) - self.assertEqual(record.dr_positive[63], ("P53485", "ACT2_FUGRU")) - self.assertEqual(record.dr_positive[64], ("P27130", "ACT2_HALRO")) - self.assertEqual(record.dr_positive[65], ("P92176", "ACT2_LUMTE")) - self.assertEqual(record.dr_positive[66], ("P53466", "ACT2_LYTPI")) - self.assertEqual(record.dr_positive[67], ("Q25472", "ACT2_MOLOC")) - self.assertEqual(record.dr_positive[68], ("P27132", "ACT2_NAEFO")) - self.assertEqual(record.dr_positive[69], ("P30163", "ACT2_ONCVO")) - self.assertEqual(record.dr_positive[70], ("P17298", "ACT2_ORYSA")) - self.assertEqual(record.dr_positive[71], ("P02583", "ACT2_OXYFA")) - self.assertEqual(record.dr_positive[72], ("P55805", "ACT2_OXYNO")) - self.assertEqual(record.dr_positive[73], ("P53469", "ACT2_OXYTR")) - self.assertEqual(record.dr_positive[74], ("P30165", "ACT2_PEA")) - self.assertEqual(record.dr_positive[75], ("P22132", "ACT2_PHYIN")) - self.assertEqual(record.dr_positive[76], ("P14883", "ACT2_PLAFA")) - self.assertEqual(record.dr_positive[77], ("O18500", "ACT2_SACKO")) - self.assertEqual(record.dr_positive[78], ("Q9Y896", "ACT2_SCHCO")) - self.assertEqual(record.dr_positive[79], ("P53471", "ACT2_SCHMA")) - self.assertEqual(record.dr_positive[80], ("P69004", "ACT2_STRFN")) - self.assertEqual(record.dr_positive[81], ("Q9Y707", "ACT2_SUIBO")) - self.assertEqual(record.dr_positive[82], ("P10993", "ACT2_TETPY")) - self.assertEqual(record.dr_positive[83], ("P12433", "ACT2_TRYBB")) - self.assertEqual(record.dr_positive[84], ("P10995", "ACT2_XENLA")) - self.assertEqual(record.dr_positive[85], ("P20399", "ACT2_XENTR")) - self.assertEqual(record.dr_positive[86], ("Q25010", "ACT3A_HELAM")) - self.assertEqual(record.dr_positive[87], ("P84184", "ACT3B_HELAM")) - self.assertEqual(record.dr_positive[88], ("P18602", "ACT3_ARTSX")) - self.assertEqual(record.dr_positive[89], ("P45886", "ACT3_BACDO")) - self.assertEqual(record.dr_positive[90], ("P04829", "ACT3_BOMMO")) - self.assertEqual(record.dr_positive[91], ("P07829", "ACT3_DICDI")) - self.assertEqual(record.dr_positive[92], ("P53457", "ACT3_DIPDE")) - self.assertEqual(record.dr_positive[93], ("P53501", "ACT3_DROME")) - self.assertEqual(record.dr_positive[94], ("Q03342", "ACT3_ECHGR")) - self.assertEqual(record.dr_positive[95], ("P53486", "ACT3_FUGRU")) - self.assertEqual(record.dr_positive[96], ("P41340", "ACT3_LIMPO")) - self.assertEqual(record.dr_positive[97], ("Q25379", "ACT3_LYTPI")) - self.assertEqual(record.dr_positive[98], ("P17299", "ACT3_ORYSA")) - self.assertEqual(record.dr_positive[99], ("P46258", "ACT3_PEA")) - self.assertEqual(record.dr_positive[100], ("P41113", "ACT3_PODCA")) - self.assertEqual(record.dr_positive[101], ("P30167", "ACT3_SOLTU")) - self.assertEqual(record.dr_positive[102], ("P02580", "ACT3_SOYBN")) - self.assertEqual(record.dr_positive[103], ("P04752", "ACT3_XENLA")) - self.assertEqual(record.dr_positive[104], ("P53494", "ACT4_ARATH")) - self.assertEqual(record.dr_positive[105], ("P18603", "ACT4_ARTSX")) - self.assertEqual(record.dr_positive[106], ("P84183", "ACT4_BOMMO")) - self.assertEqual(record.dr_positive[107], ("P10986", "ACT4_CAEEL")) - self.assertEqual(record.dr_positive[108], ("P07828", "ACT4_DICDI")) - self.assertEqual(record.dr_positive[109], ("P02574", "ACT4_DROME")) - self.assertEqual(record.dr_positive[110], ("Q25380", "ACT4_LYTPI")) - self.assertEqual(record.dr_positive[111], ("Q8RYC2", "ACT5_ARATH")) - self.assertEqual(record.dr_positive[112], ("P45887", "ACT5_BACDO")) - self.assertEqual(record.dr_positive[113], ("P53478", "ACT5_CHICK")) - self.assertEqual(record.dr_positive[114], ("P53458", "ACT5_DIPDE")) - self.assertEqual(record.dr_positive[115], ("P10981", "ACT5_DROME")) - self.assertEqual(record.dr_positive[116], ("P53505", "ACT5_XENLA")) - self.assertEqual(record.dr_positive[117], ("P53459", "ACT6_DIPDE")) - self.assertEqual(record.dr_positive[118], ("P83967", "ACT6_DROME")) - self.assertEqual(record.dr_positive[119], ("P83968", "ACT6_DROSI")) - self.assertEqual(record.dr_positive[120], ("P30168", "ACT6_SOLTU")) - self.assertEqual(record.dr_positive[121], ("P53492", "ACT7_ARATH")) - self.assertEqual(record.dr_positive[122], ("P17300", "ACT7_ORYSA")) - self.assertEqual(record.dr_positive[123], ("Q96293", "ACT8_ARATH")) - self.assertEqual(record.dr_positive[124], ("P07830", "ACT8_DICDI")) - self.assertEqual(record.dr_positive[125], ("P53506", "ACT8_XENLA")) - self.assertEqual(record.dr_positive[126], ("P93738", "ACT9_ARATH")) - self.assertEqual(record.dr_positive[127], ("P62739", "ACTA_BOVIN")) - self.assertEqual(record.dr_positive[128], ("P08023", "ACTA_CHICK")) - self.assertEqual(record.dr_positive[129], ("P62736", "ACTA_HUMAN")) - self.assertEqual(record.dr_positive[130], ("P41339", "ACTA_LIMPO")) - self.assertEqual(record.dr_positive[131], ("P62737", "ACTA_MOUSE")) - self.assertEqual(record.dr_positive[132], ("P02576", "ACTA_PHYPO")) - self.assertEqual(record.dr_positive[133], ("P62740", "ACTA_RABIT")) - self.assertEqual(record.dr_positive[134], ("P62738", "ACTA_RAT")) - self.assertEqual(record.dr_positive[135], ("P53472", "ACTA_STRPU")) - self.assertEqual(record.dr_positive[136], ("Q7ZVI7", "ACTB1_BRARE")) - self.assertEqual(record.dr_positive[137], ("Q7ZVF9", "ACTB2_BRARE")) - self.assertEqual(record.dr_positive[138], ("P60712", "ACTB_BOVIN")) - self.assertEqual(record.dr_positive[139], ("P84336", "ACTB_CAMDR")) - self.assertEqual(record.dr_positive[140], ("O18840", "ACTB_CANFA")) - self.assertEqual(record.dr_positive[141], ("Q71FK5", "ACTB_CAVPO")) - self.assertEqual(record.dr_positive[142], ("Q76N69", "ACTB_CERAE")) - self.assertEqual(record.dr_positive[143], ("P60706", "ACTB_CHICK")) - self.assertEqual(record.dr_positive[144], ("P48975", "ACTB_CRIGR")) - self.assertEqual(record.dr_positive[145], ("P83751", "ACTB_CTEID")) - self.assertEqual(record.dr_positive[146], ("P83750", "ACTB_CYPCA")) - self.assertEqual(record.dr_positive[147], ("P60708", "ACTB_HORSE")) - self.assertEqual(record.dr_positive[148], ("P60709", "ACTB_HUMAN")) - self.assertEqual(record.dr_positive[149], ("Q711N9", "ACTB_MESAU")) - self.assertEqual(len(record.dr_positive), 295) - self.assertEqual(record.dr_positive[150], ("P60710", "ACTB_MOUSE")) - self.assertEqual(record.dr_positive[151], ("P68143", "ACTB_OREMO")) - self.assertEqual(record.dr_positive[152], ("P79818", "ACTB_ORYLA")) - self.assertEqual(record.dr_positive[153], ("Q5R1X3", "ACTB_PANTR")) - self.assertEqual(record.dr_positive[154], ("P29751", "ACTB_RABIT")) - self.assertEqual(record.dr_positive[155], ("P60711", "ACTB_RAT")) - self.assertEqual(record.dr_positive[156], ("O42161", "ACTB_SALSA")) - self.assertEqual(record.dr_positive[157], ("P60713", "ACTB_SHEEP")) - self.assertEqual(record.dr_positive[158], ("Q91ZK5", "ACTB_SIGHI")) - self.assertEqual(record.dr_positive[159], ("P53473", "ACTB_STRPU")) - self.assertEqual(record.dr_positive[160], ("P60707", "ACTB_TRIVU")) - self.assertEqual(record.dr_positive[161], ("P15475", "ACTB_XENBO")) - self.assertEqual(record.dr_positive[162], ("O93400", "ACTB_XENLA")) - self.assertEqual(record.dr_positive[163], ("Q964E3", "ACTC_BIOAL")) - self.assertEqual(record.dr_positive[164], ("P92179", "ACTC_BIOGL")) - self.assertEqual(record.dr_positive[165], ("Q964E1", "ACTC_BIOOB")) - self.assertEqual(record.dr_positive[166], ("Q964E2", "ACTC_BIOPF")) - self.assertEqual(record.dr_positive[167], ("Q964E0", "ACTC_BIOTE")) - self.assertEqual(record.dr_positive[168], ("Q93129", "ACTC_BRABE")) - self.assertEqual(record.dr_positive[169], ("Q93131", "ACTC_BRAFL")) - self.assertEqual(record.dr_positive[170], ("O17503", "ACTC_BRALA")) - self.assertEqual(record.dr_positive[171], ("P68034", "ACTC_CHICK")) - self.assertEqual(record.dr_positive[172], ("P53480", "ACTC_FUGRU")) - self.assertEqual(record.dr_positive[173], ("P53461", "ACTC_HALRO")) - self.assertEqual(record.dr_positive[174], ("Q964D9", "ACTC_HELTI")) - self.assertEqual(record.dr_positive[175], ("P68032", "ACTC_HUMAN")) - self.assertEqual(record.dr_positive[176], ("P68033", "ACTC_MOUSE")) - self.assertEqual(record.dr_positive[177], ("P12716", "ACTC_PISOC")) - self.assertEqual(record.dr_positive[178], ("P68035", "ACTC_RAT")) - self.assertEqual(record.dr_positive[179], ("Q07903", "ACTC_STRPU")) - self.assertEqual(record.dr_positive[180], ("Q00215", "ACTC_STYPL")) - self.assertEqual(record.dr_positive[181], ("P69005", "ACTD_STRPU")) - self.assertEqual(record.dr_positive[182], ("P53474", "ACTE_STRPU")) - self.assertEqual(record.dr_positive[183], ("P18499", "ACTF_STRPU")) - self.assertEqual(record.dr_positive[184], ("P63256", "ACTG_ANSAN")) - self.assertEqual(record.dr_positive[185], ("P63258", "ACTG_BOVIN")) - self.assertEqual(record.dr_positive[186], ("Q9UVW9", "ACTG_CEPAC")) - self.assertEqual(record.dr_positive[187], ("P20359", "ACTG_EMENI")) - self.assertEqual(record.dr_positive[188], ("P63261", "ACTG_HUMAN")) - self.assertEqual(record.dr_positive[189], ("P63260", "ACTG_MOUSE")) - self.assertEqual(record.dr_positive[190], ("Q9URS0", "ACTG_PENCH")) - self.assertEqual(record.dr_positive[191], ("P63259", "ACTG_RAT")) - self.assertEqual(record.dr_positive[192], ("P63257", "ACTG_TRIVU")) - self.assertEqual(record.dr_positive[193], ("P63270", "ACTH_CHICK")) - self.assertEqual(record.dr_positive[194], ("P63267", "ACTH_HUMAN")) - self.assertEqual(record.dr_positive[195], ("P63268", "ACTH_MOUSE")) - self.assertEqual(record.dr_positive[196], ("P63269", "ACTH_RAT")) - self.assertEqual(record.dr_positive[197], ("P17304", "ACTM_APLCA")) - self.assertEqual(record.dr_positive[198], ("Q93130", "ACTM_BRABE")) - self.assertEqual(record.dr_positive[199], ("Q93132", "ACTM_BRAFL")) - self.assertEqual(record.dr_positive[200], ("O17502", "ACTM_BRALA")) - self.assertEqual(record.dr_positive[201], ("O15998", "ACTM_CIOSA")) - self.assertEqual(record.dr_positive[202], ("P53463", "ACTM_HELER")) - self.assertEqual(record.dr_positive[203], ("P53464", "ACTM_HELTB")) - self.assertEqual(record.dr_positive[204], ("Q25381", "ACTM_LYTPI")) - self.assertEqual(record.dr_positive[205], ("P53467", "ACTM_MOLOC")) - self.assertEqual(record.dr_positive[206], ("P12717", "ACTM_PISOC")) - self.assertEqual(record.dr_positive[207], ("P26198", "ACTM_STYCL")) - self.assertEqual(record.dr_positive[208], ("Q00214", "ACTM_STYPL")) - self.assertEqual(record.dr_positive[209], ("P53475", "ACTN_STYCL")) - self.assertEqual(record.dr_positive[210], ("Q90X97", "ACTS_ATRMM")) - self.assertEqual(record.dr_positive[211], ("P68138", "ACTS_BOVIN")) - self.assertEqual(record.dr_positive[212], ("P49055", "ACTS_CARAU")) - self.assertEqual(record.dr_positive[213], ("P68139", "ACTS_CHICK")) - self.assertEqual(record.dr_positive[214], ("P53479", "ACTS_CYPCA")) - self.assertEqual(record.dr_positive[215], ("P68140", "ACTS_FUGRU")) - self.assertEqual(record.dr_positive[216], ("P68133", "ACTS_HUMAN")) - self.assertEqual(record.dr_positive[217], ("P68134", "ACTS_MOUSE")) - self.assertEqual(record.dr_positive[218], ("P68264", "ACTS_OREMO")) - self.assertEqual(record.dr_positive[219], ("P68137", "ACTS_PIG")) - self.assertEqual(record.dr_positive[220], ("P10994", "ACTS_PLEWA")) - self.assertEqual(record.dr_positive[221], ("P68135", "ACTS_RABIT")) - self.assertEqual(record.dr_positive[222], ("P68136", "ACTS_RAT")) - self.assertEqual(record.dr_positive[223], ("P53482", "ACTT_FUGRU")) - self.assertEqual(record.dr_positive[224], ("P53483", "ACTX_FUGRU")) - self.assertEqual(record.dr_positive[225], ("P42025", "ACTY_HUMAN")) - self.assertEqual(record.dr_positive[226], ("P41341", "ACTY_LIMPO")) - self.assertEqual(record.dr_positive[227], ("Q8R5C5", "ACTY_MOUSE")) - self.assertEqual(record.dr_positive[228], ("P61162", "ACTZ_CANFA")) - self.assertEqual(record.dr_positive[229], ("P45889", "ACTZ_DROME")) - self.assertEqual(record.dr_positive[230], ("P61163", "ACTZ_HUMAN")) - self.assertEqual(record.dr_positive[231], ("P61164", "ACTZ_MOUSE")) - self.assertEqual(record.dr_positive[232], ("P53491", "ACT_ACECL")) - self.assertEqual(record.dr_positive[233], ("P26182", "ACT_ACHBI")) - self.assertEqual(record.dr_positive[234], ("P53455", "ACT_AJECA")) - self.assertEqual(record.dr_positive[235], ("Q75D00", "ACT_ASHGO")) - self.assertEqual(record.dr_positive[236], ("O13419", "ACT_BOTCI")) - self.assertEqual(record.dr_positive[237], ("P90689", "ACT_BRUMA")) - self.assertEqual(record.dr_positive[238], ("P14235", "ACT_CANAL")) - self.assertEqual(record.dr_positive[239], ("Q9UVZ8", "ACT_CANDU")) - self.assertEqual(record.dr_positive[240], ("P60009", "ACT_CANGA")) - self.assertEqual(record.dr_positive[241], ("P53498", "ACT_CHLRE")) - self.assertEqual(record.dr_positive[242], ("P53499", "ACT_CHOCR")) - self.assertEqual(record.dr_positive[243], ("O65315", "ACT_COLSC")) - self.assertEqual(record.dr_positive[244], ("Q9UVX4", "ACT_COPCI")) - self.assertEqual(record.dr_positive[245], ("P30161", "ACT_COSCS")) - self.assertEqual(record.dr_positive[246], ("O17320", "ACT_CRAGI")) - self.assertEqual(record.dr_positive[247], ("P48465", "ACT_CRYNV")) - self.assertEqual(record.dr_positive[248], ("P26183", "ACT_CRYPV")) - self.assertEqual(record.dr_positive[249], ("P53500", "ACT_CYAME")) - self.assertEqual(record.dr_positive[250], ("Q24733", "ACT_DICVI")) - self.assertEqual(record.dr_positive[251], ("P11426", "ACT_ENTHI")) - self.assertEqual(record.dr_positive[252], ("Q8X119", "ACT_EXODE")) - self.assertEqual(record.dr_positive[253], ("P53502", "ACT_FUCDI")) - self.assertEqual(record.dr_positive[254], ("Q39758", "ACT_FUCVE")) - self.assertEqual(record.dr_positive[255], ("Q6TCF2", "ACT_GAEGA")) - self.assertEqual(record.dr_positive[256], ("O81221", "ACT_GOSHI")) - self.assertEqual(record.dr_positive[257], ("O00937", "ACT_HISCA")) - self.assertEqual(record.dr_positive[258], ("P17126", "ACT_HYDAT")) - self.assertEqual(record.dr_positive[259], ("P17128", "ACT_KLULA")) - self.assertEqual(record.dr_positive[260], ("P45520", "ACT_LEIMA")) - self.assertEqual(record.dr_positive[261], ("P91754", "ACT_LUMRU")) - self.assertEqual(record.dr_positive[262], ("P49871", "ACT_MANSE")) - self.assertEqual(record.dr_positive[263], ("O16808", "ACT_MAYDE")) - self.assertEqual(record.dr_positive[264], ("O65316", "ACT_MESVI")) - self.assertEqual(record.dr_positive[265], ("P78711", "ACT_NEUCR")) - self.assertEqual(record.dr_positive[266], ("P53689", "ACT_PHARH")) - self.assertEqual(record.dr_positive[267], ("P13363", "ACT_PHYME")) - self.assertEqual(record.dr_positive[268], ("O74258", "ACT_PICAN")) - self.assertEqual(record.dr_positive[269], ("Q9P4D1", "ACT_PICPA")) - self.assertEqual(record.dr_positive[270], ("P24902", "ACT_PINCO")) - self.assertEqual(record.dr_positive[271], ("Q26065", "ACT_PLAMG")) - self.assertEqual(record.dr_positive[272], ("P45521", "ACT_PROCL")) - self.assertEqual(record.dr_positive[273], ("P50138", "ACT_PUCGR")) - self.assertEqual(record.dr_positive[274], ("P60011", "ACT_SACBA")) - self.assertEqual(record.dr_positive[275], ("O65314", "ACT_SCHDU")) - self.assertEqual(record.dr_positive[276], ("P10989", "ACT_SCHPO")) - self.assertEqual(record.dr_positive[277], ("P68555", "ACT_TAESO")) - self.assertEqual(record.dr_positive[278], ("P10365", "ACT_THELA")) - self.assertEqual(record.dr_positive[279], ("P53476", "ACT_TOXGO")) - self.assertEqual(record.dr_positive[280], ("Q99023", "ACT_TRIRE")) - self.assertEqual(record.dr_positive[281], ("P53477", "ACT_TRYCR")) - self.assertEqual(record.dr_positive[282], ("P20904", "ACT_VOLCA")) - self.assertEqual(record.dr_positive[283], ("Q9UVF3", "ACT_YARLI")) - self.assertEqual(record.dr_positive[284], ("P60010", "ACT_YEAST")) - self.assertEqual(record.dr_positive[285], ("Q61JZ2", "ARP2_CAEBR")) - self.assertEqual(record.dr_positive[286], ("P53489", "ARP2_CAEEL")) - self.assertEqual(record.dr_positive[287], ("Q4WHA3", "ARP4_ASPFU")) - self.assertEqual(record.dr_positive[288], ("Q5AC48", "ARP4_CANAL")) - self.assertEqual(record.dr_positive[289], ("Q6BXN0", "ARP4_DEBHA")) - self.assertEqual(record.dr_positive[290], ("Q4IPI4", "ARP4_GIBZE")) - self.assertEqual(record.dr_positive[291], ("Q7SHR0", "ARP4_NEUCR")) - self.assertEqual(record.dr_positive[292], ("Q9P7X7", "ARP4_SCHPO")) - self.assertEqual(record.dr_positive[293], ("Q4P2E8", "ARP4_USTMA")) - self.assertEqual(record.dr_positive[294], ("Q09849", "YAE9_SCHPO")) - - def read4_false_etc(self, record): - self.assertEqual(len(record.dr_false_neg), 22) - self.assertEqual(record.dr_false_neg[0], ("P30169", "ACT7_SOLTU")) - self.assertEqual(record.dr_false_neg[1], ("P24263", "ACTD_PHYPO")) - self.assertEqual(record.dr_false_neg[2], ("P12431", "ACTM_STRPU")) - self.assertEqual(record.dr_false_neg[3], ("P20360", "ACT_EUPCR")) - self.assertEqual(record.dr_false_neg[4], ("P51775", "ACT_GIALA")) - self.assertEqual(record.dr_false_neg[5], ("Q754G5", "ARP4_ASHGO")) - self.assertEqual(record.dr_false_neg[6], ("Q6FJV8", "ARP4_CANGA")) - self.assertEqual(record.dr_false_neg[7], ("Q5AW89", "ARP4_EMENI")) - self.assertEqual(record.dr_false_neg[8], ("Q6CSB9", "ARP4_KLULA")) - self.assertEqual(record.dr_false_neg[9], ("Q6C061", "ARP4_YARLI")) - self.assertEqual(record.dr_false_neg[10], ("P80428", "ARP4_YEAST")) - self.assertEqual(record.dr_false_neg[11], ("Q74ZV8", "ARP6_ASHGO")) - self.assertEqual(record.dr_false_neg[12], ("Q4W9M3", "ARP6_ASPFU")) - self.assertEqual(record.dr_false_neg[13], ("Q5AP59", "ARP6_CANAL")) - self.assertEqual(record.dr_false_neg[14], ("Q6FKE7", "ARP6_CANGA")) - self.assertEqual(record.dr_false_neg[15], ("Q5KAQ4", "ARP6_CRYNE")) - self.assertEqual(record.dr_false_neg[16], ("Q6BML9", "ARP6_DEBHA")) - self.assertEqual(record.dr_false_neg[17], ("Q5AXH1", "ARP6_EMENI")) - self.assertEqual(record.dr_false_neg[18], ("Q6CJF4", "ARP6_KLULA")) - self.assertEqual(record.dr_false_neg[19], ("Q7S6X6", "ARP6_NEUCR")) - self.assertEqual(record.dr_false_neg[20], ("O94241", "ARP6_SCHPO")) - self.assertEqual(record.dr_false_neg[21], ("Q6C982", "ARP6_YARLI")) - self.assertEqual(len(record.dr_false_pos), 0) - self.assertEqual(len(record.dr_potential), 26) - self.assertEqual(record.dr_potential[0], ("P30170", "ACT10_SOLTU")) - self.assertEqual(record.dr_potential[1], ("P10982", "ACT1_ABSGL")) - self.assertEqual(record.dr_potential[2], ("Q96482", "ACT1_LYCES")) - self.assertEqual(record.dr_potential[3], ("P93587", "ACT1_SOLTU")) - self.assertEqual(record.dr_potential[4], ("Q96483", "ACT2_LYCES")) - self.assertEqual(record.dr_potential[5], ("P93586", "ACT2_SOLTU")) - self.assertEqual(record.dr_potential[6], ("P93374", "ACT2_TOBAC")) - self.assertEqual(record.dr_potential[7], ("Q96484", "ACT3_LYCES")) - self.assertEqual(record.dr_potential[8], ("P93373", "ACT3_TOBAC")) - self.assertEqual(record.dr_potential[9], ("Q96481", "ACT4_LYCES")) - self.assertEqual(record.dr_potential[10], ("P93585", "ACT4_SOLTU")) - self.assertEqual(record.dr_potential[11], ("P93372", "ACT4_TOBAC")) - self.assertEqual(record.dr_potential[12], ("P81228", "ACT5_SOLTU")) - self.assertEqual(record.dr_potential[13], ("P93371", "ACT5_TOBAC")) - self.assertEqual(record.dr_potential[14], ("P15986", "ACT6_SOYBN")) - self.assertEqual(record.dr_potential[15], ("P93376", "ACT6_TOBAC")) - self.assertEqual(record.dr_potential[16], ("P15987", "ACT7_SOYBN")) - self.assertEqual(record.dr_potential[17], ("P93375", "ACT7_TOBAC")) - self.assertEqual(record.dr_potential[18], ("P81229", "ACT8_SOLTU")) - self.assertEqual(record.dr_potential[19], ("P93584", "ACT9_SOLTU")) - self.assertEqual(record.dr_potential[20], ("Q92192", "ACT_CALFI")) - self.assertEqual(record.dr_potential[21], ("P80709", "ACT_CARMA")) - self.assertEqual(record.dr_potential[22], ("Q39596", "ACT_CHERU")) - self.assertEqual(record.dr_potential[23], ("Q92193", "ACT_CRAVI")) - self.assertEqual(record.dr_potential[24], ("P81085", "ACT_PINPS")) - self.assertEqual(record.dr_potential[25], ("Q11212", "ACT_SPOLI")) - self.assertEqual(len(record.dr_unknown), 0) - self.assertEqual(len(record.pdb_structs), 60) - self.assertEqual(record.pdb_structs[0], "1ALM") - self.assertEqual(record.pdb_structs[1], "1ATN") - self.assertEqual(record.pdb_structs[2], "1C0F") - self.assertEqual(record.pdb_structs[3], "1C0G") - self.assertEqual(record.pdb_structs[4], "1D4X") - self.assertEqual(record.pdb_structs[5], "1DEJ") - self.assertEqual(record.pdb_structs[6], "1EQY") - self.assertEqual(record.pdb_structs[7], "1ESV") - self.assertEqual(record.pdb_structs[8], "1H1V") - self.assertEqual(record.pdb_structs[9], "1HLU") - self.assertEqual(record.pdb_structs[10], "1IJJ") - self.assertEqual(record.pdb_structs[11], "1J6Z") - self.assertEqual(record.pdb_structs[12], "1KXP") - self.assertEqual(record.pdb_structs[13], "1LCU") - self.assertEqual(record.pdb_structs[14], "1LOT") - self.assertEqual(record.pdb_structs[15], "1LVT") - self.assertEqual(record.pdb_structs[16], "1M8Q") - self.assertEqual(record.pdb_structs[17], "1M8Q0") - self.assertEqual(record.pdb_structs[18], "1MA9") - self.assertEqual(record.pdb_structs[19], "1MDU") - self.assertEqual(record.pdb_structs[20], "1MVW") - self.assertEqual(record.pdb_structs[21], "1N58") - self.assertEqual(record.pdb_structs[22], "1NLV") - self.assertEqual(record.pdb_structs[23], "1NM1") - self.assertEqual(record.pdb_structs[24], "1NMD") - self.assertEqual(record.pdb_structs[25], "1NWK") - self.assertEqual(record.pdb_structs[26], "1O18") - self.assertEqual(record.pdb_structs[27], "1O19") - self.assertEqual(record.pdb_structs[28], "1O1A") - self.assertEqual(record.pdb_structs[29], "1O1B") - self.assertEqual(record.pdb_structs[30], "1O1B0") - self.assertEqual(record.pdb_structs[31], "1O1C") - self.assertEqual(record.pdb_structs[32], "1O1C0") - self.assertEqual(record.pdb_structs[33], "1O1D") - self.assertEqual(record.pdb_structs[34], "1O1D0") - self.assertEqual(record.pdb_structs[35], "1O1E") - self.assertEqual(record.pdb_structs[36], "1O1F") - self.assertEqual(record.pdb_structs[37], "1O1F0") - self.assertEqual(record.pdb_structs[38], "1O1G") - self.assertEqual(record.pdb_structs[39], "1P8Z") - self.assertEqual(record.pdb_structs[40], "1QZ5") - self.assertEqual(record.pdb_structs[41], "1QZ6") - self.assertEqual(record.pdb_structs[42], "1RDW") - self.assertEqual(record.pdb_structs[43], "1RFQ") - self.assertEqual(record.pdb_structs[44], "1RGI") - self.assertEqual(record.pdb_structs[45], "1S22") - self.assertEqual(record.pdb_structs[46], "1SQK") - self.assertEqual(record.pdb_structs[47], "1T44") - self.assertEqual(record.pdb_structs[48], "1Y64") - self.assertEqual(record.pdb_structs[49], "1YAG") - self.assertEqual(record.pdb_structs[50], "1YVN") - self.assertEqual(record.pdb_structs[51], "2A3Z") - self.assertEqual(record.pdb_structs[52], "2A40") - self.assertEqual(record.pdb_structs[53], "2A41") - self.assertEqual(record.pdb_structs[54], "2A42") - self.assertEqual(record.pdb_structs[55], "2A5X") - self.assertEqual(record.pdb_structs[56], "2ASM") - self.assertEqual(record.pdb_structs[57], "2ASO") - self.assertEqual(record.pdb_structs[58], "2ASP") - self.assertEqual(record.pdb_structs[59], "2BTF") - - def test_read5(self): - """Parsing Prosite record ps00488.txt.""" - filename = os.path.join("Prosite", "ps00488.txt") - with open(filename) as handle: - record = Prosite.read(handle) - self.assertEqual(record.name, "PAL_HISTIDASE") - self.assertEqual(record.type, "PATTERN") - self.assertEqual(record.accession, "PS00488") - self.assertEqual(record.created, "MAY-1991") - self.assertEqual(record.data_update, "DEC-2004") - self.assertEqual(record.info_update, "MAR-2006") - self.assertEqual(record.pdoc, "PDOC00424") - self.assertEqual( - record.description, "Phenylalanine and histidine ammonia-lyases signature." - ) - self.assertEqual( - record.pattern, - "[GS]-[STG]-[LIVM]-[STG]-[SAC]-S-G-[DH]-L-x-P-L-[SA]-x(2,3)-[SAGVT].", - ) - self.assertEqual(record.matrix, []) - self.assertEqual(record.rules, []) - self.assertEqual(record.nr_sp_release, "49.3") - self.assertEqual(record.nr_sp_seqs, 212425) - self.assertEqual(record.cc_taxo_range, "A?EP?") - self.assertEqual(record.cc_max_repeat, "1") - self.assertEqual(len(record.cc_site), 1) - self.assertEqual(record.cc_site[0], (6, "active_site")) - self.assertEqual(len(record.dr_positive), 127) - self.assertEqual(record.dr_positive[0], ("Q8RFC2", "HUTH1_FUSNN")) - self.assertEqual(record.dr_positive[1], ("Q8RDU4", "HUTH2_FUSNN")) - self.assertEqual(record.dr_positive[2], ("Q9KWE4", "HUTH_AGRRH")) - self.assertEqual(record.dr_positive[3], ("Q8U8Z7", "HUTH_AGRT5")) - self.assertEqual(record.dr_positive[4], ("Q5NZX8", "HUTH_AZOSE")) - self.assertEqual(record.dr_positive[5], ("Q81Y45", "HUTH_BACAN")) - self.assertEqual(record.dr_positive[6], ("Q733H8", "HUTH_BACC1")) - self.assertEqual(record.dr_positive[7], ("Q81AC6", "HUTH_BACCR")) - self.assertEqual(record.dr_positive[8], ("Q9KBE6", "HUTH_BACHD")) - self.assertEqual(record.dr_positive[9], ("Q6HFE9", "HUTH_BACHK")) - self.assertEqual(record.dr_positive[10], ("Q5WAZ6", "HUTH_BACSK")) - self.assertEqual(record.dr_positive[11], ("P10944", "HUTH_BACSU")) - self.assertEqual(record.dr_positive[12], ("Q6G3U8", "HUTH_BARHE")) - self.assertEqual(record.dr_positive[13], ("Q6FZP9", "HUTH_BARQU")) - self.assertEqual(record.dr_positive[14], ("Q89GV3", "HUTH_BRAJA")) - self.assertEqual(record.dr_positive[15], ("Q579E8", "HUTH_BRUAB")) - self.assertEqual(record.dr_positive[16], ("Q8FVB4", "HUTH_BRUSU")) - self.assertEqual(record.dr_positive[17], ("Q62LJ6", "HUTH_BURMA")) - self.assertEqual(record.dr_positive[18], ("Q63SH6", "HUTH_BURPS")) - self.assertEqual(record.dr_positive[19], ("Q20502", "HUTH_CAEEL")) - self.assertEqual(record.dr_positive[20], ("P58082", "HUTH_CAUCR")) - self.assertEqual(record.dr_positive[21], ("Q7P188", "HUTH_CHRVO")) - self.assertEqual(record.dr_positive[22], ("Q891Q1", "HUTH_CLOTE")) - self.assertEqual(record.dr_positive[23], ("Q9RZ06", "HUTH_DEIRA")) - self.assertEqual(record.dr_positive[24], ("Q6AKP3", "HUTH_DESPS")) - self.assertEqual(record.dr_positive[25], ("Q5L310", "HUTH_GEOKA")) - self.assertEqual(record.dr_positive[26], ("Q7NCB3", "HUTH_GLOVI")) - self.assertEqual(record.dr_positive[27], ("Q5FRR8", "HUTH_GLUOX")) - self.assertEqual(record.dr_positive[28], ("Q9HQD5", "HUTH_HALSA")) - self.assertEqual(record.dr_positive[29], ("P42357", "HUTH_HUMAN")) - self.assertEqual(record.dr_positive[30], ("Q5QV30", "HUTH_IDILO")) - self.assertEqual(record.dr_positive[31], ("Q5X5I5", "HUTH_LEGPA")) - self.assertEqual(record.dr_positive[32], ("Q5ZVR0", "HUTH_LEGPH")) - self.assertEqual(record.dr_positive[33], ("Q5WWW8", "HUTH_LEGPL")) - self.assertEqual(record.dr_positive[34], ("P35492", "HUTH_MOUSE")) - self.assertEqual(record.dr_positive[35], ("Q7N296", "HUTH_PHOLL")) - self.assertEqual(record.dr_positive[36], ("Q6LQ56", "HUTH_PHOPR")) - self.assertEqual(record.dr_positive[37], ("Q9HU85", "HUTH_PSEAE")) - self.assertEqual(record.dr_positive[38], ("Q8VMR3", "HUTH_PSEFL")) - self.assertEqual(record.dr_positive[39], ("Q88CZ7", "HUTH_PSEPK")) - self.assertEqual(record.dr_positive[40], ("P21310", "HUTH_PSEPU")) - self.assertEqual(record.dr_positive[41], ("Q87UM1", "HUTH_PSESM")) - self.assertEqual(record.dr_positive[42], ("Q8XW29", "HUTH_RALSO")) - self.assertEqual(record.dr_positive[43], ("P21213", "HUTH_RAT")) - self.assertEqual(record.dr_positive[44], ("Q983I0", "HUTH_RHILO")) - self.assertEqual(record.dr_positive[45], ("O31197", "HUTH_RHIME")) - self.assertEqual(record.dr_positive[46], ("Q57RG6", "HUTH_SALCH")) - self.assertEqual(record.dr_positive[47], ("Q5PG61", "HUTH_SALPA")) - self.assertEqual(record.dr_positive[48], ("Q8Z896", "HUTH_SALTI")) - self.assertEqual(record.dr_positive[49], ("Q8ZQQ9", "HUTH_SALTY")) - self.assertEqual(record.dr_positive[50], ("Q5LRD8", "HUTH_SILPO")) - self.assertEqual(record.dr_positive[51], ("Q5HJY8", "HUTH_STAAC")) - self.assertEqual(record.dr_positive[52], ("P64415", "HUTH_STAAM")) - self.assertEqual(record.dr_positive[53], ("P64416", "HUTH_STAAN")) - self.assertEqual(record.dr_positive[54], ("Q6GKT7", "HUTH_STAAR")) - self.assertEqual(record.dr_positive[55], ("Q6GD82", "HUTH_STAAS")) - self.assertEqual(record.dr_positive[56], ("Q8NYY3", "HUTH_STAAW")) - self.assertEqual(record.dr_positive[57], ("Q93TX3", "HUTH_STIAU")) - self.assertEqual(record.dr_positive[58], ("Q82I33", "HUTH_STRAW")) - self.assertEqual(record.dr_positive[59], ("Q9EWW1", "HUTH_STRCO")) - self.assertEqual(record.dr_positive[60], ("P24221", "HUTH_STRGR")) - self.assertEqual(record.dr_positive[61], ("P58083", "HUTH_STRP1")) - self.assertEqual(record.dr_positive[62], ("Q8K5L5", "HUTH_STRP3")) - self.assertEqual(record.dr_positive[63], ("Q5X9K4", "HUTH_STRP6")) - self.assertEqual(record.dr_positive[64], ("Q8NZ46", "HUTH_STRP8")) - self.assertEqual(record.dr_positive[65], ("Q67JH4", "HUTH_SYMTH")) - self.assertEqual(record.dr_positive[66], ("Q9HLI6", "HUTH_THEAC")) - self.assertEqual(record.dr_positive[67], ("Q8RBH4", "HUTH_THETN")) - self.assertEqual(record.dr_positive[68], ("Q978N8", "HUTH_THEVO")) - self.assertEqual(record.dr_positive[69], ("Q9KSQ4", "HUTH_VIBCH")) - self.assertEqual(record.dr_positive[70], ("Q5E0C6", "HUTH_VIBF1")) - self.assertEqual(record.dr_positive[71], ("Q87Q77", "HUTH_VIBPA")) - self.assertEqual(record.dr_positive[72], ("Q8DA21", "HUTH_VIBVU")) - self.assertEqual(record.dr_positive[73], ("Q7MK58", "HUTH_VIBVY")) - self.assertEqual(record.dr_positive[74], ("Q8PLZ8", "HUTH_XANAC")) - self.assertEqual(record.dr_positive[75], ("Q8PAA7", "HUTH_XANCP")) - self.assertEqual(record.dr_positive[76], ("Q8ZA10", "HUTH_YERPE")) - self.assertEqual(record.dr_positive[77], ("Q664B8", "HUTH_YERPS")) - self.assertEqual(record.dr_positive[78], ("Q8YD09", "HUTIH_BRUME")) - self.assertEqual(record.dr_positive[79], ("P35510", "PAL1_ARATH")) - self.assertEqual(record.dr_positive[80], ("O23865", "PAL1_DAUCA")) - self.assertEqual(record.dr_positive[81], ("P14166", "PAL1_IPOBA")) - self.assertEqual(record.dr_positive[82], ("O49835", "PAL1_LITER")) - self.assertEqual(record.dr_positive[83], ("P35511", "PAL1_LYCES")) - self.assertEqual(record.dr_positive[84], ("P14717", "PAL1_ORYSA")) - self.assertEqual(record.dr_positive[85], ("Q01861", "PAL1_PEA")) - self.assertEqual(record.dr_positive[86], ("P24481", "PAL1_PETCR")) - self.assertEqual(record.dr_positive[87], ("P45731", "PAL1_POPKI")) - self.assertEqual(record.dr_positive[88], ("O64963", "PAL1_PRUAV")) - self.assertEqual(record.dr_positive[89], ("Q9M568", "PAL1_RUBID")) - self.assertEqual(record.dr_positive[90], ("P31425", "PAL1_SOLTU")) - self.assertEqual(record.dr_positive[91], ("P27991", "PAL1_SOYBN")) - self.assertEqual(record.dr_positive[92], ("P25872", "PAL1_TOBAC")) - self.assertEqual(record.dr_positive[93], ("P45724", "PAL2_ARATH")) - self.assertEqual(record.dr_positive[94], ("Q9SMK9", "PAL2_CICAR")) - self.assertEqual(record.dr_positive[95], ("Q42858", "PAL2_IPOBA")) - self.assertEqual(record.dr_positive[96], ("O49836", "PAL2_LITER")) - self.assertEqual(record.dr_positive[97], ("P53443", "PAL2_ORYSA")) - self.assertEqual(record.dr_positive[98], ("Q04593", "PAL2_PEA")) - self.assertEqual(record.dr_positive[99], ("P45728", "PAL2_PETCR")) - self.assertEqual(record.dr_positive[100], ("P19142", "PAL2_PHAVU")) - self.assertEqual(record.dr_positive[101], ("Q43052", "PAL2_POPKI")) - self.assertEqual(record.dr_positive[102], ("P31426", "PAL2_SOLTU")) - self.assertEqual(record.dr_positive[103], ("P35513", "PAL2_TOBAC")) - self.assertEqual(record.dr_positive[104], ("P45725", "PAL3_ARATH")) - self.assertEqual(record.dr_positive[105], ("P45729", "PAL3_PETCR")) - self.assertEqual(record.dr_positive[106], ("P19143", "PAL3_PHAVU")) - self.assertEqual(record.dr_positive[107], ("P45733", "PAL3_TOBAC")) - self.assertEqual(record.dr_positive[108], ("Q9SS45", "PAL4_ARATH")) - self.assertEqual(record.dr_positive[109], ("Q40910", "PAL4_POPKI")) - self.assertEqual(record.dr_positive[110], ("P26600", "PAL5_LYCES")) - self.assertEqual(record.dr_positive[111], ("O93967", "PALY_AMAMU")) - self.assertEqual(record.dr_positive[112], ("Q42609", "PALY_BROFI")) - self.assertEqual(record.dr_positive[113], ("P45726", "PALY_CAMSI")) - self.assertEqual(record.dr_positive[114], ("Q42667", "PALY_CITLI")) - self.assertEqual(record.dr_positive[115], ("O23924", "PALY_DIGLA")) - self.assertEqual(record.dr_positive[116], ("O04058", "PALY_HELAN")) - self.assertEqual(record.dr_positive[117], ("P27990", "PALY_MEDSA")) - self.assertEqual(record.dr_positive[118], ("P45727", "PALY_PERAE")) - self.assertEqual(record.dr_positive[119], ("P52777", "PALY_PINTA")) - self.assertEqual(record.dr_positive[120], ("P45730", "PALY_POPTR")) - self.assertEqual(record.dr_positive[121], ("P10248", "PALY_RHORB")) - self.assertEqual(record.dr_positive[122], ("P11544", "PALY_RHOTO")) - self.assertEqual(record.dr_positive[123], ("P45732", "PALY_STYHU")) - self.assertEqual(record.dr_positive[124], ("P45734", "PALY_TRISU")) - self.assertEqual(record.dr_positive[125], ("Q96V77", "PALY_USTMA")) - self.assertEqual(record.dr_positive[126], ("Q43210", "PALY_WHEAT")) - self.assertEqual(len(record.dr_false_neg), 2) - self.assertEqual(record.dr_false_neg[0], ("Q8EKJ4", "HUTH_SHEON")) - self.assertEqual(record.dr_false_neg[1], ("Q73Q56", "HUTH_TREDE")) - self.assertEqual(len(record.dr_false_pos), 0) - self.assertEqual(len(record.dr_potential), 4) - self.assertEqual(record.dr_potential[0], ("P07218", "PAL1_PHAVU")) - self.assertEqual(record.dr_potential[1], ("Q92195", "PALY_AGABI")) - self.assertEqual(record.dr_potential[2], ("P35512", "PALY_MALDO")) - self.assertEqual(record.dr_potential[3], ("P45735", "PALY_VITVI")) - self.assertEqual(len(record.dr_unknown), 0) - self.assertEqual(record.pdb_structs[0], "1B8F") - self.assertEqual(record.pdb_structs[1], "1EB4") - self.assertEqual(record.pdb_structs[2], "1GK2") - self.assertEqual(record.pdb_structs[3], "1GKJ") - self.assertEqual(record.pdb_structs[4], "1GKM") - self.assertEqual(record.pdb_structs[5], "1Y2M") - - def test_read6(self): - """Parsing Prosite record ps00546.txt.""" - filename = os.path.join("Prosite", "ps00546.txt") - with open(filename) as handle: - record = Prosite.read(handle) - self.assertEqual(record.name, "CYSTEINE_SWITCH") - self.assertEqual(record.type, "PATTERN") - self.assertEqual(record.accession, "PS00546") - self.assertEqual(record.created, "DEC-1991") - self.assertEqual(record.data_update, "NOV-1997") - self.assertEqual(record.info_update, "MAR-2006") - self.assertEqual(record.pdoc, "PDOC00472") - self.assertEqual(record.description, "Matrixins cysteine switch.") - self.assertEqual(record.pattern, "P-R-C-[GN]-x-P-[DR]-[LIVSAPKQ].") - self.assertEqual(record.matrix, []) - self.assertEqual(record.rules, []) - self.assertEqual(record.nr_sp_release, "49.3") - self.assertEqual(record.nr_sp_seqs, 212425) - self.assertEqual(record.cc_taxo_range, "??E??") - self.assertEqual(record.cc_max_repeat, "1") - self.assertEqual(len(record.cc_site), 1) - self.assertEqual(record.cc_site[0], (3, "chelates_zinc")) - self.assertEqual(len(record.dr_positive), 62) - self.assertEqual(record.dr_positive[0], ("P31178", "GLE_CHLRE")) - self.assertEqual(record.dr_positive[1], ("P91953", "HE_HEMPU")) - self.assertEqual(record.dr_positive[2], ("P22757", "HE_PARLI")) - self.assertEqual(record.dr_positive[3], ("P29136", "MEP1_SOYBN")) - self.assertEqual(record.dr_positive[4], ("P09238", "MMP10_HUMAN")) - self.assertEqual(record.dr_positive[5], ("O55123", "MMP10_MOUSE")) - self.assertEqual(record.dr_positive[6], ("P07152", "MMP10_RAT")) - self.assertEqual(record.dr_positive[7], ("P24347", "MMP11_HUMAN")) - self.assertEqual(record.dr_positive[8], ("Q11005", "MMP11_XENLA")) - self.assertEqual(record.dr_positive[9], ("P39900", "MMP12_HUMAN")) - self.assertEqual(record.dr_positive[10], ("P34960", "MMP12_MOUSE")) - self.assertEqual(record.dr_positive[11], ("P79227", "MMP12_RABIT")) - self.assertEqual(record.dr_positive[12], ("O77656", "MMP13_BOVIN")) - self.assertEqual(record.dr_positive[13], ("O18927", "MMP13_HORSE")) - self.assertEqual(record.dr_positive[14], ("P45452", "MMP13_HUMAN")) - self.assertEqual(record.dr_positive[15], ("P33435", "MMP13_MOUSE")) - self.assertEqual(record.dr_positive[16], ("O62806", "MMP13_RABIT")) - self.assertEqual(record.dr_positive[17], ("P23097", "MMP13_RAT")) - self.assertEqual(record.dr_positive[18], ("Q10835", "MMP13_XENLA")) - self.assertEqual(record.dr_positive[19], ("P50281", "MMP14_HUMAN")) - self.assertEqual(record.dr_positive[20], ("P53690", "MMP14_MOUSE")) - self.assertEqual(record.dr_positive[21], ("Q9XT90", "MMP14_PIG")) - self.assertEqual(record.dr_positive[22], ("Q95220", "MMP14_RABIT")) - self.assertEqual(record.dr_positive[23], ("Q10739", "MMP14_RAT")) - self.assertEqual(record.dr_positive[24], ("P51511", "MMP15_HUMAN")) - self.assertEqual(record.dr_positive[25], ("O54732", "MMP15_MOUSE")) - self.assertEqual(record.dr_positive[26], ("P51512", "MMP16_HUMAN")) - self.assertEqual(record.dr_positive[27], ("Q9WTR0", "MMP16_MOUSE")) - self.assertEqual(record.dr_positive[28], ("O35548", "MMP16_RAT")) - self.assertEqual(record.dr_positive[29], ("Q9EPL5", "MMP1A_MOUSE")) - self.assertEqual(record.dr_positive[30], ("Q9EPL6", "MMP1B_MOUSE")) - self.assertEqual(record.dr_positive[31], ("P28053", "MMP1_BOVIN")) - self.assertEqual(record.dr_positive[32], ("Q9XSZ5", "MMP1_HORSE")) - self.assertEqual(record.dr_positive[33], ("P03956", "MMP1_HUMAN")) - self.assertEqual(record.dr_positive[34], ("P21692", "MMP1_PIG")) - self.assertEqual(record.dr_positive[35], ("P13943", "MMP1_RABIT")) - self.assertEqual(record.dr_positive[36], ("O18767", "MMP20_BOVIN")) - self.assertEqual(record.dr_positive[37], ("O60882", "MMP20_HUMAN")) - self.assertEqual(record.dr_positive[38], ("P57748", "MMP20_MOUSE")) - self.assertEqual(record.dr_positive[39], ("P79287", "MMP20_PIG")) - self.assertEqual(record.dr_positive[40], ("Q90611", "MMP2_CHICK")) - self.assertEqual(record.dr_positive[41], ("P08253", "MMP2_HUMAN")) - self.assertEqual(record.dr_positive[42], ("P33434", "MMP2_MOUSE")) - self.assertEqual(record.dr_positive[43], ("P50757", "MMP2_RABIT")) - self.assertEqual(record.dr_positive[44], ("P33436", "MMP2_RAT")) - self.assertEqual(record.dr_positive[45], ("Q6Y4Q5", "MMP3_CANFA")) - self.assertEqual(record.dr_positive[46], ("P08254", "MMP3_HUMAN")) - self.assertEqual(record.dr_positive[47], ("P28862", "MMP3_MOUSE")) - self.assertEqual(record.dr_positive[48], ("P28863", "MMP3_RABIT")) - self.assertEqual(record.dr_positive[49], ("P03957", "MMP3_RAT")) - self.assertEqual(record.dr_positive[50], ("P09237", "MMP7_HUMAN")) - self.assertEqual(record.dr_positive[51], ("Q10738", "MMP7_MOUSE")) - self.assertEqual(record.dr_positive[52], ("P50280", "MMP7_RAT")) - self.assertEqual(record.dr_positive[53], ("P22894", "MMP8_HUMAN")) - self.assertEqual(record.dr_positive[54], ("O70138", "MMP8_MOUSE")) - self.assertEqual(record.dr_positive[55], ("O88766", "MMP8_RAT")) - self.assertEqual(record.dr_positive[56], ("P52176", "MMP9_BOVIN")) - self.assertEqual(record.dr_positive[57], ("O18733", "MMP9_CANFA")) - self.assertEqual(record.dr_positive[58], ("P14780", "MMP9_HUMAN")) - self.assertEqual(record.dr_positive[59], ("P41245", "MMP9_MOUSE")) - self.assertEqual(record.dr_positive[60], ("P41246", "MMP9_RABIT")) - self.assertEqual(record.dr_positive[61], ("P50282", "MMP9_RAT")) - self.assertEqual(len(record.dr_false_neg), 59) - self.assertEqual(record.dr_false_neg[0], ("Q9R158", "AD26A_MOUSE")) - self.assertEqual(record.dr_false_neg[1], ("Q10741", "ADA10_BOVIN")) - self.assertEqual(record.dr_false_neg[2], ("O14672", "ADA10_HUMAN")) - self.assertEqual(record.dr_false_neg[3], ("O35598", "ADA10_MOUSE")) - self.assertEqual(record.dr_false_neg[4], ("Q10743", "ADA10_RAT")) - self.assertEqual(record.dr_false_neg[5], ("Q8JIY1", "ADA10_XENLA")) - self.assertEqual(record.dr_false_neg[6], ("Q61824", "ADA12_MOUSE")) - self.assertEqual(record.dr_false_neg[7], ("Q13444", "ADA15_HUMAN")) - self.assertEqual(record.dr_false_neg[8], ("O88839", "ADA15_MOUSE")) - self.assertEqual(record.dr_false_neg[9], ("Q9QYV0", "ADA15_RAT")) - self.assertEqual(record.dr_false_neg[10], ("P78536", "ADA17_HUMAN")) - self.assertEqual(record.dr_false_neg[11], ("Q9Z0F8", "ADA17_MOUSE")) - self.assertEqual(record.dr_false_neg[12], ("Q9Z1K9", "ADA17_RAT")) - self.assertEqual(record.dr_false_neg[13], ("Q9H013", "ADA19_HUMAN")) - self.assertEqual(record.dr_false_neg[14], ("O35674", "ADA19_MOUSE")) - self.assertEqual(record.dr_false_neg[15], ("O43506", "ADA20_HUMAN")) - self.assertEqual(record.dr_false_neg[16], ("Q9UKJ8", "ADA21_HUMAN")) - self.assertEqual(record.dr_false_neg[17], ("Q9JI76", "ADA21_MOUSE")) - self.assertEqual(record.dr_false_neg[18], ("Q9R160", "ADA24_MOUSE")) - self.assertEqual(record.dr_false_neg[19], ("Q9R159", "ADA25_MOUSE")) - self.assertEqual(record.dr_false_neg[20], ("Q9UKQ2", "ADA28_HUMAN")) - self.assertEqual(record.dr_false_neg[21], ("Q9XSL6", "ADA28_MACFA")) - self.assertEqual(record.dr_false_neg[22], ("Q9JLN6", "ADA28_MOUSE")) - self.assertEqual(record.dr_false_neg[23], ("Q9UKF2", "ADA30_HUMAN")) - self.assertEqual(record.dr_false_neg[24], ("Q9BZ11", "ADA33_HUMAN")) - self.assertEqual(record.dr_false_neg[25], ("Q923W9", "ADA33_MOUSE")) - self.assertEqual(record.dr_false_neg[26], ("O15204", "ADEC1_HUMAN")) - self.assertEqual(record.dr_false_neg[27], ("P58397", "ATS12_HUMAN")) - self.assertEqual(record.dr_false_neg[28], ("Q811B3", "ATS12_MOUSE")) - self.assertEqual(record.dr_false_neg[29], ("Q8WXS8", "ATS14_HUMAN")) - self.assertEqual(record.dr_false_neg[30], ("Q8TE58", "ATS15_HUMAN")) - self.assertEqual(record.dr_false_neg[31], ("P59384", "ATS15_MOUSE")) - self.assertEqual(record.dr_false_neg[32], ("Q8TE57", "ATS16_HUMAN")) - self.assertEqual(record.dr_false_neg[33], ("Q69Z28", "ATS16_MOUSE")) - self.assertEqual(record.dr_false_neg[34], ("Q8TE56", "ATS17_HUMAN")) - self.assertEqual(record.dr_false_neg[35], ("Q8TE60", "ATS18_HUMAN")) - self.assertEqual(record.dr_false_neg[36], ("Q4VC17", "ATS18_MOUSE")) - self.assertEqual(record.dr_false_neg[37], ("Q8TE59", "ATS19_HUMAN")) - self.assertEqual(record.dr_false_neg[38], ("P59509", "ATS19_MOUSE")) - self.assertEqual(record.dr_false_neg[39], ("Q9UKP4", "ATS7_HUMAN")) - self.assertEqual(record.dr_false_neg[40], ("Q9P2N4", "ATS9_HUMAN")) - self.assertEqual(record.dr_false_neg[41], ("Q02853", "MMP11_MOUSE")) - self.assertEqual(record.dr_false_neg[42], ("Q63341", "MMP12_RAT")) - self.assertEqual(record.dr_false_neg[43], ("Q9ULZ9", "MMP17_HUMAN")) - self.assertEqual(record.dr_false_neg[44], ("Q9R0S3", "MMP17_MOUSE")) - self.assertEqual(record.dr_false_neg[45], ("O13065", "MMP18_XENLA")) - self.assertEqual(record.dr_false_neg[46], ("Q99542", "MMP19_HUMAN")) - self.assertEqual(record.dr_false_neg[47], ("Q9JHI0", "MMP19_MOUSE")) - self.assertEqual(record.dr_false_neg[48], ("Q11133", "MMP1_RANCA")) - self.assertEqual(record.dr_false_neg[49], ("Q90YC2", "MMP21_CYNPY")) - self.assertEqual(record.dr_false_neg[50], ("Q8N119", "MMP21_HUMAN")) - self.assertEqual(record.dr_false_neg[51], ("Q8K3F2", "MMP21_MOUSE")) - self.assertEqual(record.dr_false_neg[52], ("O93470", "MMP21_XENLA")) - self.assertEqual(record.dr_false_neg[53], ("Q9Y5R2", "MMP24_HUMAN")) - self.assertEqual(record.dr_false_neg[54], ("Q9R0S2", "MMP24_MOUSE")) - self.assertEqual(record.dr_false_neg[55], ("Q9NRE1", "MMP26_HUMAN")) - self.assertEqual(record.dr_false_neg[56], ("Q9H239", "MMP28_HUMAN")) - self.assertEqual(record.dr_false_neg[57], ("Q28397", "MMP3_HORSE")) - self.assertEqual(record.dr_false_neg[58], ("P55032", "MMP7_FELCA")) - self.assertEqual(len(record.dr_false_pos), 1) - self.assertEqual(record.dr_false_pos[0], ("Q9YC75", "RGYR2_AERPE")) - self.assertEqual(len(record.dr_potential), 0) - self.assertEqual(len(record.dr_unknown), 0) - self.assertEqual(len(record.pdb_structs), 8) - self.assertEqual(record.pdb_structs[0], "1CK7") - self.assertEqual(record.pdb_structs[1], "1EAK") - self.assertEqual(record.pdb_structs[2], "1GXD") - self.assertEqual(record.pdb_structs[3], "1L6J") - self.assertEqual(record.pdb_structs[4], "1LKG") - self.assertEqual(record.pdb_structs[5], "1SLM") - self.assertEqual(record.pdb_structs[6], "1SU3") - self.assertEqual(record.pdb_structs[7], "1UC1") - - -if __name__ == "__main__": - runner = unittest.TextTestRunner(verbosity=2) - unittest.main(testRunner=runner)