4775: raise warnings instead of errors if dashes are not in the expected places for dates

Bio/GenBank/Scanner.py

@@ -1306,17 +1306,17 @@ class GenBankScanner(InsdcScanner):
                 )
             # if line[55:62] != '       ':
             #      raise ValueError('LOCUS line does not contain spaces from position 56 to 62:\n' + line)
+            parse_date = False
             if line[62:73].strip():
+                parse_date = True
                 if line[64:65] != "-":
-                    raise ValueError(
+                    parse_date = False
-                        "LOCUS line does not contain - at "
+                    warnings.warn("LOCUS line does not contain - at position 65 in date:\n" + line,
-                        "position 65 in date:\n" + line
+                                  BiopythonParserWarning)    
-                    )
                 if line[68:69] != "-":
-                    raise ValueError(
+                    parse_date = False
-                        "LOCUS line does not contain - at "
+                    warnings.warn("LOCUS line does not contain - at position 69 in date:\n" + line,
-                        "position 69 in date:\n" + line
+                                  BiopythonParserWarning)
-                    )
 
             name_and_length_str = line[self.GENBANK_INDENT : 29]
             while "  " in name_and_length_str:
@@ -1353,7 +1353,7 @@ class GenBankScanner(InsdcScanner):
             consumer.molecule_type(line[33:41].strip())
             consumer.topology(line[42:51].strip())
             consumer.data_file_division(line[52:55])
-            if line[62:73].strip():
+            if parse_date:
                 consumer.date(line[62:73])
         elif line[40:44] in [" bp ", " aa ", " rc "] and line[54:64].strip() in [
             "",
@@ -1429,17 +1429,17 @@ class GenBankScanner(InsdcScanner):
                 raise ValueError(
                     "LOCUS line does not contain space at position 68:\n" + line
                 )
+            parse_date = False
             if line[68:79].strip():
+                parse_date = True
                 if line[70:71] != "-":
-                    raise ValueError(
+                    parse_date = False
-                        "LOCUS line does not contain - at "
+                    warnings.warn("LOCUS line does not contain - at position 71 in date:\n" + line,
-                        "position 71 in date:\n" + line
+                                  BiopythonParserWarning)    
-                    )
                 if line[74:75] != "-":
-                    raise ValueError(
+                    parse_date = False
-                        "LOCUS line does not contain - at "
+                    warnings.warn("LOCUS line does not contain - at position 75 in date:\n" + line,
-                        "position 75 in date:\n" + line
+                                  BiopythonParserWarning)
-                    )
 
             name_and_length_str = line[self.GENBANK_INDENT : 40]
             while "  " in name_and_length_str:
@@ -1467,7 +1467,7 @@ class GenBankScanner(InsdcScanner):
             consumer.topology(line[55:63].strip())
             if line[64:76].strip():
                 consumer.data_file_division(line[64:67])
-            if line[68:79].strip():
+            if parse_date:
                 consumer.date(line[68:79])
         elif line[self.GENBANK_INDENT :].strip().count(" ") == 0:
             # Truncated LOCUS line, as produced by some EMBOSS tools - see bug 1762

Tests/GenBank/noref_date_warning.gb

@@ -0,0 +1,72 @@
+LOCUS       NM_006141    1622 bp    mRNA            PRI       yyyy/mon/dd
+DEFINITION  Homo sapiens dynein, cytoplasmic, light intermediate polypeptide 2
+            (DNCLI2), mRNA.
+ACCESSION   NM_006141
+VERSION     NM_006141.1  GI:5453633
+KEYWORDS    .
+SOURCE      human.
+  ORGANISM  Homo sapiens
+            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
+            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
+COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
+            NCBI review. The reference sequence was derived from AF035812.1.
+FEATURES             Location/Qualifiers
+     source          1..1622
+                     /organism="Homo sapiens"
+                     /db_xref="taxon:9606"
+                     /map="16"
+     gene            1..1622
+                     /gene="DNCLI2"
+                     /note="LIC2"
+                     /db_xref="LocusID:1783"
+     CDS             7..1485
+                     /gene="DNCLI2"
+                     /note="similar to R. norvegicus and G. gallus dynein light
+                     intermediate chain 2, Swiss-Prot Accession Numbers Q62698
+                     and Q90828, respectively"
+                     /codon_start=1
+                     /db_xref="LocusID:1783"
+                     /product="dynein, cytoplasmic, light intermediate
+                     polypeptide 2"
+                     /protein_id="NP_006132.1"
+                     /db_xref="GI:5453634"
+                     /translation="MAPVGVEKKLLLGPNGPAVAAAGDLTSEEEEGQSLWSSILSEVS
+                     TRARSKLPSGKNILVFGEDGSGKTTLMTKLQGAEHGKKGRGLEYLYLSVHDEDRDDHT
+                     RCNVWILDGDLYHKGLLKFAVSAESLPETLVIFVADMSRPWTVMESLQKWASVLREHI
+                     DKMKIPPEKMRELERKFVKDFQDYMEPEEGCQGSPQRRGPLTSGSDEENVALPLGDNV
+                     LTHNLGIPVLVVCTKCDAVSVLEKEHDYRDEHLDFIQSHLRRFCLQYGAALIYTSVKE
+                     EKNLDLLYKYIVHKTYGFHFTTPALVVEKDAVFIPAGWDNEKKIAILHENFTTVKPED
+                     AYEDFIVKPPVRKLVHDKELAAEDEQVFLMKQQSLLAKQPATPTRASESPARGPSGSP
+                     RTQGRGGPASVPSSSPGTSVKKPDPNIKNNAASEGVLASFFNSLLSKKTGSPGSPGAG
+                     GVQSTAKKSGQKTVLSNVQEELDRMTRKPDSMVTNSSTENEA"
+BASE COUNT      474 a    356 c    428 g    364 t
+ORIGIN      
+        1 ggcaagatgg cgccggtggg ggtggagaag aagctgctgc taggtcccaa cgggcccgcg
+       61 gtggcggccg ccggcgacct gaccagtgag gaggaggaag gccagagcct atggtcctcc
+      121 attctgagcg aagtgtccac ccgcgccagg tccaagctgc cgtccggcaa gaacatcctg
+      181 gtcttcggtg aagatggttc tggtaaaaca accctcatga ctaaactaca aggagctgag
+      241 catggcaaaa aaggaagagg cctagaatat ctctacctca gtgtccatga tgaggaccga
+      301 gatgatcaca cgcgctgcaa cgtgtggatt ctggatggag acttgtacca caaaggcctg
+      361 ctgaaatttg cagtttctgc tgaatccttg ccagagaccc tcgtcatttt tgttgcagac
+      421 atgtctagac cttggactgt gatggaatct ctgcagaaat gggctagtgt tttacgtgag
+      481 cacattgata aaatgaaaat tccaccagaa aaaatgaggg agctggaacg gaagtttgtg
+      541 aaagattttc aagactatat ggaacctgaa gaaggttgtc aaggttcccc acagagaaga
+      601 ggccctctga cctcaggctc cgatgaagaa aatgttgccc tgcctctggg tgacaatgtg
+      661 ctgactcata acctggggat cccggtgttg gtggtgtgca caaagtgtga tgcggtgagt
+      721 gtcctggaga aggagcacga ttacagggat gagcatttgg actttatcca gtcacacctg
+      781 cggaggttct gccttcagta tggagctgcc ttgatttaca catcagtgaa agaagagaaa
+      841 aacctcgact tgttgtataa gtatattgtt cataaaacat acggtttcca cttcaccaca
+      901 cctgccttag ttgtggaaaa ggatgccgtt tttatacctg caggctggga caatgaaaag
+      961 aaaatagcta ttttacatga aaattttaca accgtgaagc cggaagatgc atatgaagac
+     1021 tttattgtga aacctcccgt gagaaagctg gtccacgaca aagagttggc agcagaagat
+     1081 gagcaggtgt tcctaatgaa gcaacagtca ctccttgcca agcaaccagc cactcccacg
+     1141 agagcttctg aatctcctgc aagaggaccc tctggctctc caaggaccca gggtcgggga
+     1201 gggccagcca gtgtgcctag ctcctcccca ggcacgtcag taaaaaagcc ggacccaaac
+     1261 atcaaaaata atgcagcaag tgaaggggtg ttggccagct tcttcaacag tctgttgagt
+     1321 aaaaagacag gctctcctgg aagtcctggt gctggtgggg tgcagagcac agccaagaag
+     1381 tcaggacaaa agactgtgtt gtcaaatgtt caggaagaac tggatagaat gactcgaaag
+     1441 ccagactcta tggtaacaaa ctcttcaaca gaaaatgaag cctgaacctc cttaaaaagt
+     1501 gcatatgtcg aatgaccaaa taactatgta tattgatctg ctaagaccag gatttttctg
+     1561 atatggcaca tgctatcagt tttttggggc aggggagatg aactttaaaa aaaaaaaaaa
+     1621 aa
+//

Tests/test_GenBank.py

@@ -3444,6 +3444,114 @@ qualifiers:
                 """\
 type: CDS
 location: [6:1485](+)
+qualifiers:
+    Key: codon_start, Value: ['1']
+    Key: db_xref, Value: ['LocusID:1783', 'GI:5453634']
+    Key: gene, Value: ['DNCLI2']
+    Key: note, Value: ['similar to R. norvegicus and G. gallus dynein light intermediate chain 2, Swiss-Prot Accession Numbers Q62698 and Q90828, respectively']
+    Key: product, Value: ['dynein, cytoplasmic, light intermediate polypeptide 2']
+    Key: protein_id, Value: ['NP_006132.1']
+    Key: translation, Value: ['MAPVGVEKKLLLGPNGPAVAAAGDLTSEEEEGQSLWSSILSEVSTRARSKLPSGKNILVFGEDGSGKTTLMTKLQGAEHGKKGRGLEYLYLSVHDEDRDDHTRCNVWILDGDLYHKGLLKFAVSAESLPETLVIFVADMSRPWTVMESLQKWASVLREHIDKMKIPPEKMRELERKFVKDFQDYMEPEEGCQGSPQRRGPLTSGSDEENVALPLGDNVLTHNLGIPVLVVCTKCDAVSVLEKEHDYRDEHLDFIQSHLRRFCLQYGAALIYTSVKEEKNLDLLYKYIVHKTYGFHFTTPALVVEKDAVFIPAGWDNEKKIAILHENFTTVKPEDAYEDFIVKPPVRKLVHDKELAAEDEQVFLMKQQSLLAKQPATPTRASESPARGPSGSPRTQGRGGPASVPSSSPGTSVKKPDPNIKNNAASEGVLASFFNSLLSKKTGSPGSPGAGGVQSTAKKSGQKTVLSNVQEELDRMTRKPDSMVTNSSTENEA']
+""",
+                1,
+            ),
+        )
+        dbxrefs = []
+        self.perform_feature_parser_test(
+            record,
+            seq,
+            id,
+            name,
+            description,
+            annotations,
+            references,
+            features,
+            dbxrefs,
+        )
+
+    def test_feature_parser_date_warning(self):
+        path = "GenBank/noref_date_warning.gb"
+        with warnings.catch_warnings(record=True) as caught:
+            warnings.simplefilter("always")
+            with open(path) as handle:
+                records = GenBank.Iterator(handle, self.feat_parser)
+                record = next(records)
+            self.assertEqual(len(caught), 2)
+            self.assertEqual(caught[0].category, BiopythonParserWarning)
+            self.assertEqual(caught[1].category, BiopythonParserWarning)
+            self.assertEqual(
+                str(caught[0].message),
+                "LOCUS line does not contain - at position 65 in date:\n"
+                "LOCUS       NM_006141    1622 bp    mRNA            PRI       yyyy/mon/dd\n",
+            )
+            self.assertEqual(
+                str(caught[1].message),
+                "LOCUS line does not contain - at position 69 in date:\n"
+                "LOCUS       NM_006141    1622 bp    mRNA            PRI       yyyy/mon/dd\n",
+            )
+        seq = "GGCAAGATGGCGCCGGTGGGGGTGGAGAAGAAGCTGCTGCTAGGTCCCAACGGG...AAA"
+        id = "NM_006141.1"
+        name = "NM_006141"
+        description = (
+            "Homo sapiens dynein, cytoplasmic, light intermediate polypeptide 2"
+            " (DNCLI2), mRNA"
+        )
+        annotations = {
+            "accessions": ["NM_006141"],
+            "comment": """\
+PROVISIONAL REFSEQ: This record has not yet been subject to final
+NCBI review. The reference sequence was derived from AF035812.1.""",
+            "data_file_division": "PRI",
+            # "date": "01-NOV-2000", NB: no date
+            "gi": "5453633",
+            "keywords": [""],
+            "molecule_type": "mRNA",
+            "organism": "Homo sapiens",
+            "sequence_version": 1,
+            "source": "human",
+            "taxonomy": [
+                "Eukaryota",
+                "Metazoa",
+                "Chordata",
+                "Craniata",
+                "Vertebrata",
+                "Euteleostomi",
+                "Mammalia",
+                "Eutheria",
+                "Primates",
+                "Catarrhini",
+                "Hominidae",
+                "Homo",
+            ],
+        }
+        references = []
+        features = (
+            (
+                """\
+type: source
+location: [0:1622](+)
+qualifiers:
+    Key: db_xref, Value: ['taxon:9606']
+    Key: map, Value: ['16']
+    Key: organism, Value: ['Homo sapiens']
+""",
+                1,
+            ),
+            (
+                """\
+type: gene
+location: [0:1622](+)
+qualifiers:
+    Key: db_xref, Value: ['LocusID:1783']
+    Key: gene, Value: ['DNCLI2']
+    Key: note, Value: ['LIC2']
+""",
+                1,
+            ),
+            (
+                """\
+type: CDS
+location: [6:1485](+)
 qualifiers:
     Key: codon_start, Value: ['1']
     Key: db_xref, Value: ['LocusID:1783', 'GI:5453634']
@@ -8124,6 +8232,14 @@ class LineOneTests(unittest.TestCase):
                 "BCT",
                 None,
             ),
+            (
+                "LOCUS       AB070938                6497 bp    DNA     linear   BCT"
+                " 1-Oct-2001\n",
+                "linear",
+                "DNA",
+                "BCT",
+                [BiopythonParserWarning, BiopythonParserWarning],
+            ),
             (
                 "LOCUS       NC_005816               9609 bp    DNA     circular BCT"
                 " 21-JUL-2008",
@@ -8509,5 +8625,6 @@ class GenBankScannerTests(unittest.TestCase):
 
 
 if __name__ == "__main__":
+    os.chdir(os.path.dirname(__file__))
     runner = unittest.TextTestRunner(verbosity=2)
     unittest.main(testRunner=runner)