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https://github.com/biopython/biopython.git
synced 2025-10-20 21:53:47 +08:00
Fix NBRF/PIR parsing so that is accepts files produced by Clustalw -- thanks to Ashleigh Smythe for the bug report.
Fix bugs in NBRF parsing where not all of the comments were passed through. Try to speed up sequence building using joins instead of sequential addition of sequence.
This commit is contained in:
chapmanb
@ -91,7 +91,7 @@ class _Scanner:
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"sequence_name", \
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"comment", \
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"sequence_line", \
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"sequence_final_line" ]
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"sequence_final_text" ]
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# make a parser that returns only the tags we are interested in
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expression = Martel.select_names( nbrf_format.nbrf_record, self.interest_tags)
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@ -115,29 +115,28 @@ class _RecordConsumer:
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"""
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def __init__(self):
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self.data = Record.Record()
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self._sequences = []
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def sequence_type(self, sequence_type ):
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self.data.sequence_type = sequence_type[ 0 ]
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self.data.sequence_type = "".join(sequence_type)
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def sequence_name(self, sequence_name ):
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self.data.sequence_name = sequence_name[ 0 ]
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self.data.sequence_name = "".join(sequence_name)
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def comment(self, comment ):
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self.data.comment = comment[ 0 ]
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self.data.comment = "".join(comment)
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def sequence_line( self, sequences ):
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for sequence in sequences:
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sequence = sequence.strip()
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sequence = sequence.replace( ' ', '' )
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self.data.sequence.data = self.data.sequence.data + sequence[:]
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new_seq = "".join(sequences)
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parts = new_seq.split()
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self._sequences.append("".join(parts))
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def sequence_final_line( self, sequences ):
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for sequence in sequences:
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sequence = sequence.strip()
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sequence = sequence.replace( ' ', '' )
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sequence = sequence[ :-1 ]
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self.data.sequence.data = self.data.sequence.data + sequence[:]
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def sequence_final_text( self, sequences ):
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new_seq = "".join(sequences)
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parts = new_seq.split()
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self._sequences.append("".join(parts))
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self.data.sequence.data = "".join(self._sequences)
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class RecordParser:
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@ -9,15 +9,6 @@ This is a huge regular regular expression for NBRF, built using
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the 'regular expressiona on steroids' capabilities of Martel.
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http://www-nbrf.georgetown.edu/pirwww/pirhome.shtml
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Notes:
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Just so I remember -- the new end of line syntax is:
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New regexp syntax - \R
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\R means "\n|\r\n?"
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[\R] means "[\n\r]"
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This helps us have endlines be consistent across platforms.
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"""
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# standard library
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#http://www-nbrf.georgetown.edu/pirwww/pirhome.shtml
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@ -27,59 +18,41 @@ import string
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import Martel
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from Martel import RecordReader
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from Martel import Str
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from Martel import AnyEol
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from Martel import AnyEol, UntilEol
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from Martel import ToEol
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from Martel import Group
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from Martel import Alt
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from Martel import Alt, Opt
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from Martel import Rep
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from Martel import Rep1
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from Martel import Any
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from Martel import AnyBut
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from Martel import UntilSep
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from Bio.NBRF.ValSeq import valid_sequence_dict
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# --- first set up some helper constants and functions
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# Copyright 2001 by Katharine Lindner. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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sequence_types = map( Str, valid_sequence_dict.keys() )
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sequence_type = Group( "sequence_type", Alt( *sequence_types ) )
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sequence_name = Group( "sequence_name", Rep1( Martel.Expression.Dot() ) )
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name_line = Martel.Group( "name_line", \
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Str( ">" ) +
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sequence_type +
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Str( ";" ) +
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sequence_name +
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UntilEol("sequence_name") +
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AnyEol() )
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comment_line = Group( "comment_line",
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Rep1(AnyBut(' ')) +
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ToEol( "comment" ) )
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excluded_chars = chr( 0x2a ) + chr( 10 ) + chr( 13 )
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comment_line = UntilEol("comment") + AnyEol()
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# 0x2a -- '*'
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# 10 -- '\n', 13 -- '\r' newline endings
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excluded_chars = chr(0x2a) + chr(10) + chr(13)
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# sequence lines with only sequence
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sequence_text = Group( "sequence_text", \
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Martel.Rep1( AnyBut( excluded_chars ) ) )
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sequence_final_text = Group( "sequence_final_text", \
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Martel.Rep1( AnyBut( excluded_chars ) ) )
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sequence_final_line = Group( "sequence_final_line",
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sequence_final_text +
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Str( chr( 0x2a ) ) +
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AnyEol() )
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sequence_line = Group( "sequence_line", sequence_text +
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AnyEol() )
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sequence_block = Group( "sequence_block", Rep( sequence_line ) )
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AnyEol())
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# the final line, has a '*' and potentially some sequence
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sequence_final_line = Group( "sequence_final_line",
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UntilSep("sequence_final_text", chr(0x2a)) + Str(chr(0x2a)) +
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Rep1(AnyEol()))
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sequence_block = Group("sequence_block", Rep( sequence_line ))
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nbrf_record = name_line + comment_line + sequence_block + sequence_final_line
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108
Tests/NBRF/clustalw.pir
Normal file
108
Tests/NBRF/clustalw.pir
Normal file
@ -0,0 +1,108 @@
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>DL;804Angiostrongylus_cantonensis
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--------------------------------------------------
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----------------------------------ATT-AAGCCATG-CA-
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T-GAG-GA--GTTC-A--GC------TT--TA-A----G-T-GA--AA-C
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-TGCGAACGGCTCATTAG-AGCAGATG-T-GATT---TATT-CG--G--A
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A-A--A-T--CC-T----ATT-GGA--TAACTGCG--GTAAT-TCTGGAG
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CTAATACATGCGTAT-A-A-AC-CCTG-AC---T--T-T--C---GAAA-
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-GGGTGCAAT-TA-TTAGAG---C---AA-A-TCAAT-CAT---------
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----T-T---TC----------G-GA------TG----TAGTT-------
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---T---GCT---G-A-C-TC-TGAATA-A---CG--CAG--CATA-TCG
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G-CGGC-T-T-GT---TCGCCGATAAT-CCGAAAA----AG---TGT-C-
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TGCCC-TATCA--AC---CT---GA-TGGTAGTCTATTAGTCTA-CCATG
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GTTATTACGGGTAACGGAGAATAAGGGTT-CGACTCCGGAGAGGGAGCCT
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TAGAAACGGCTACCACATCCAAGGAAGGCAGCAG-GCGCGAAACTTATCC
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AA-T-CTTG-----A-ATAGATGA-GATAGTGACT---------------
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--------AAAAATAAAAA--GACCA---TTCC-T-AT-G--GAACG-GT
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TATTTCAATGAGT--TGATCATAAACCTTTTTT--C-G-AGTA--TCCAG
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TGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTC--CACTA
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GTGTA-AATCGTCATTGCTGCGGTTAAAAAGC-TCGTAGTTGGAT-C-TG
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AGTTGC---AT--GCA-AT-G-ATTCG--C-CT----T--TG--G--CGT
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----TAAT------C---AT-TG-TTGTG---ACTA---T------T-T-
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--G--CTG--G-T-T--TTCT-AT--TG-A--AA-----TTTC-----G-
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A-TT-----TCTTTA-GTG-GC-TA--GCGA-GTT-TA-CTTTGA-AT-A
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AATTAAAGTGCT-CAGAACAAG---CGTT-----T--GC-TT-G--AAT-
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G-GTCGAT-CATGGAATAA-----TAAAAGAGGAC--TTCG---GT-T--
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----CTATT-T----ATTGGTTC-AG---G-AA------CTG------AA
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GT-AATGATTAAGAGGGACA--ATTC-GGGGGCATTCGTATCCCTGCGCG
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AGAGGTGAAATTCGTG-GACCG-CAGGGGGACGCCCTAAAGCGAAAG-CA
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TTTGCC-AAGAAT--GTCTTCATTAATCA-AGAACGAAAGTCAGAGGTTC
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GAAGGCGATTAGATA--CCGCCC-TAGTTCTGACCGTAAACTATGCCATC
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TAGC-GA--TCC-GAT--GG-GG--TA--T--TG--T-T----GCCTT--
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GTCGAGG-AGCTT-CCCGGAAACGA--AA-GTCTTTCGGT-TCCTGGGGT
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AGTATGGTTGC-AAAGCT-G-AAACTTAAAGA-AATTGACGGAATGGCAC
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CACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGA--AAACT
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-CACCC-GGCCCGGACACCGTAA-GGATTGAC-----AGATTGA--A---
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AGCTCTTTCTC-GATTTGGTGGTTGGTGGTGCATGGCCGTTCTTAGTTG-
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GTGGAG-CGATTTGTCTGGTTTATTCC-GAT-AACGAGCGAGACTCT-AG
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-C-C--TG-CTAAA-TA-G--TGA--CTA---------------GA----
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TT-----------AT------T----GAGTC-------TA-G----T--C
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-------TA-------------C-TT-----CTT-AG---AGGGATAAG-
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CGG---TGTT-T-----A-G-C--CGCA--CG-AGATTGAGCGATAACAG
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GTCTGTGATGCCCTTAGATGTCCGGGG-CTG-CACGCGCGCTACAATGGA
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AG-AAT-CAGC--TGGC---CTA--T----CCAT-TGC-CG-A-AAGGT-
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AT----T----GGTAAACCG-TTGAAACT--CTTCC-GTG-ACCGGGATA
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GGGAATTGT--A-ATT---------ATT---TCCC-TTGAACG-AGGAAT
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TCCTAGTAAGTGTG-AGTCATCAGCTCACGCTGATTACGTCCC-TGCCAT
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TTGTACACACCGCCCGTCGCTGTC-CGGG-ACTG--AGC-TGTC--TCGA
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GAGGACT-GCGG-A-CTA----CT--GTA----TTGA-GG---CCT----
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---T---CGGG------TCG-----CGATA----TGGCG---GG-AAA-C
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AG-TTC-AATC-G-CAATG-G--CTTGAACCGGGTAAAAGTCGT-AACAA
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GGTATCTG------------------------------------------
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---------------------------
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*
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>DL;815Parelaphostrongylus_odocoil
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--------------------------------------------------
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----------------------------------ATT-AAGCCATG-CA-
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T-GTG-GA--GTTC-A--AC------TT--CA-A---AG-T-GA--AA-C
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-TGCGAACGGCTCATTAG-AGCAGATG-T-CATT---TATT-CG--G--A
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A-A--A-T--CC-T--T-AAT-GGA--TAACTGCG--GTAAT-TCTGGAG
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CTAATACATATGCAT-A-A-AC-CCTG-AC---T--C-TG-T---GAAA-
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-GGGTGCAAT-TA-TTAGAG---C---AA-A-TCAAT-CAT---------
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----T-T---TC----------G-GA------TG----TAGTT-------
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---T---GCT---G-A-C-TC-TGAATA-A---CG--CAG--CATA-TCG
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G-CGGC-T-T-GT---TCGCCGATATT-CCGAAAA----AG---TGT-C-
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TGCCC-TATCA--AC---CT---GA-TGGTAGTCTATTAGTCTA-CCATG
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GTTATTACGGGTAACGGAGAATAAGGGTT-CGACTCCGGAGAGGGAGCCT
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TAGAAACGGCTACCACATCCAAGGAAGGCAGCAG-GCGCGAAACTTATCC
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AA-T-CTTG-----A-ATAGATGA-GATAGTGACT---------------
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--------AAAAATAAAAA--GACCA---TTCC-T-AT-G--GAACG-GT
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CATTTCAATGAGT--TGATCATAAACCTTTTTT--C-G-AGTA--TCAAG
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TGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTC--CACTA
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GTGTA-AATCGTCATTGCTGCGGTTAAAAAGC-TCGTAGTTGGAT-C-TG
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AGTCGC---AT--GCA-AT-G-ATTCG--C-CT----T--TG--G--CGT
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----TAAT------C---AT-TG-TTGTG---ACTA---T------T-T-
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--G--CTG--G-T-T--TTCT-AT--TG-A--AA-----TTTC-----G-
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A-TT-----TCTATA-GTG-GC-TA--GCGA-GTT-TA-CTTTGA-AT-A
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AATTAAAGTGCT-CAGAACAAG---CGTT-----T--GC-TT-G--AAT-
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G-GTCGAT-CATGGAATAA-----TAAAAGAGGAC--TTCG---GT-T--
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----CTATT-T----ATTGGTTC-AG---G-AA------CTG------AA
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AT-AATGGTTAAGAGGGACA--ATTC-GGGGGCATTCGTATCCCTGCGCG
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AGAGGTGAAATTCGTG-GACCG-CAGGGGGACGCCCTAAAGCGAAAG-CA
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TTTGCC-AAGAAT--GTCTTCATTAATCA-AGAACGAAAGTCAGAGGTTC
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GAAGGCGATTAGATA--CCGCCC-TAGTTCTGACCGTAAACTATGCCATC
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TAGC-GA--TCC-GAT--GG-GG--TA--T--TG--T-T----GCCTT--
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GTCGAGG-AGCTT-CCCGGAAACGA--AA-GTCTTTCGGT-TCCTGGGGT
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AGTATGGTTGC-AAAGCT-G-AAACTTAAAGA-AATTGACGGAATGGCAC
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CACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGA--AAACT
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-CACCC-GGCCCGGACACCGTAA-GGATTGAC-----AGATTGA--A---
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AGCTCTTTCTC-GATTTGGTGGTTGGTGGTGCATGGCCGTTCTTAGTTG-
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GTGGAG-CGATTTGTCTGGTTTATTCC-GAT-AACGAGCGAGACTCT-AG
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-C-C--TG-CTAAA-TA-G--TGA--CTA---------------GA----
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T------------ACG-----T----ATGTC-------TA-G----T--C
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-------TA-------------C-TT-----CTT-AG---AGGGATAAG-
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CGG---TGTT-T-----A-G-C--CGCA--CG-AGATTGAGCGATAACAG
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GTCTGTGATGCCCTTAGATGTTCGGGG-CTG-CACGCGCGCTACAATGGA
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AG-AAT-CAGC--TGGC---CTA--T----CCAT-TAC-CG-A-AAGGT-
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AT----T----GGTAAACCG-TTGAAACT--CTTCC-GTG-ACCGGGATA
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GGGAATTGT--A-ATT---------ATT---TCCC-TTGAACG-AGGAAT
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TCCTAGTAAGTGTG-AGTCATCAGCTCACGCTGATTACGTCCC-TGCCAT
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TTGTACACACCGCCCGTCGCTGTC-CGGG-ACTG--AGC-TGTC--TCGA
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GAGGACT-GCGG-A-CTA----CT--GTA----TTGA-GG---CCT----
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---T---CGGG------TCG-----CGATA----TGGCG---GG-AAA-C
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AG-TTC-AATC-G-CAATG-G--CTTGAACCGGGTAAAAGTCGT-A----
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--------------------------------------------------
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---------------------------
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*
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15309
Tests/output/test_nbrf
15309
Tests/output/test_nbrf
File diff suppressed because it is too large
Load Diff
@ -7,8 +7,8 @@ import Bio.NBRF
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from Bio.RecordFile import RecordFile
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from Bio.File import SGMLHandle
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testfiles = [ 'B_nuc.pir', 'Cw_prot.pir', 'DMA_nuc.pir', 'DMB_prot.pir'
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]
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testfiles = [ 'B_nuc.pir', 'Cw_prot.pir', 'DMA_nuc.pir', 'DMB_prot.pir',
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'clustalw.pir']
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for file in testfiles:
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fh = open(os.path.join("NBRF", file))
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