# Copyright 2013 by Kai Blin. # Revisions copyright 2015-2016 by Peter Cock. # 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. import unittest import warnings from os import path from Bio import BiopythonParserWarning from Bio import BiopythonWarning from Bio import GenBank from Bio import SeqIO from Bio.SeqRecord import SeqRecord from Bio.Seq import Seq from Bio.Alphabet import generic_dna from Bio._py3k import StringIO class GenBankTests(unittest.TestCase): """GenBank tests.""" def test_invalid_product_line_raises_value_error(self): """Parsing invalid product line.""" def parse_invalid_product_line(): rec = SeqIO.read(path.join('GenBank', 'invalid_product.gb'), 'genbank') self.assertRaises(ValueError, parse_invalid_product_line) def test_genbank_read(self): """GenBank.read(...) simple test.""" with open(path.join("GenBank", "NC_000932.gb")) as handle: record = GenBank.read(handle) self.assertEqual(['NC_000932'], record.accession) def test_genbank_read_multirecord(self): """GenBank.read(...) error on multiple record input.""" with open(path.join("GenBank", "cor6_6.gb")) as handle: self.assertRaises(ValueError, GenBank.read, handle) def test_genbank_read_invalid(self): """GenBank.read(...) error on invalid file (e.g. FASTA file).""" with open(path.join("GenBank", "NC_000932.faa")) as handle: self.assertRaises(ValueError, GenBank.read, handle) def test_genbank_read_no_origin_no_end(self): """GenBank.read(...) error on malformed file.""" with open(path.join("GenBank", "no_origin_no_end.gb")) as handle: self.assertRaises(ValueError, GenBank.read, handle) # Evil hack with 000 to manipulate sort order to ensure this is tested # first (otherwise something silences the warning) def test_000_genbank_bad_loc_wrap_warning(self): """Feature line wrapping warning.""" with warnings.catch_warnings(): warnings.simplefilter("error", BiopythonParserWarning) with open(path.join("GenBank", "bad_loc_wrap.gb")) as handle: # self.assertRaises(BiopythonParserWarning, GenBank.read, handle) try: record = GenBank.read(handle) except BiopythonParserWarning as e: self.assertEqual(str(e), "Non-standard feature line wrapping (didn't break on comma)?") else: self.assertTrue(False, "Expected specified BiopythonParserWarning here.") # Similar hack as we also want to catch that warning here def test_001_negative_location_warning(self): """Un-parsable feature location warning.""" with warnings.catch_warnings(): warnings.simplefilter("error", BiopythonParserWarning) try: SeqIO.read(path.join("GenBank", "negative_location.gb"), "genbank") except BiopythonParserWarning as e: self.assertEqual(str(e), "Couldn't parse feature location: '-2..492'") else: self.assertTrue(False, "Expected specified BiopythonParserWarning here.") def test_genbank_bad_loc_wrap_parsing(self): """Bad location wrapping.""" with warnings.catch_warnings(): warnings.simplefilter("ignore", BiopythonParserWarning) with open(path.join("GenBank", "bad_loc_wrap.gb")) as handle: record = GenBank.read(handle) self.assertEqual(1, len(record.features)) loc = record.features[0].location self.assertEqual(loc, "join(3462..3615,3698..3978,4077..4307,4408..4797,4876..5028,5141..5332)") def test_negative_location(self): """Negative feature locations.""" with warnings.catch_warnings(): warnings.simplefilter("ignore", BiopythonParserWarning) rec = SeqIO.read(path.join("GenBank", "negative_location.gb"), "genbank") self.assertEqual(None, rec.features[-1].location) def test_dot_lineage(self): """Missing taxonomy lineage.""" with warnings.catch_warnings(): warnings.simplefilter("ignore", BiopythonParserWarning) rec = SeqIO.read("GenBank/bad_loc_wrap.gb", "genbank") self.assertEqual(rec.annotations["organism"], ".") self.assertEqual(rec.annotations["taxonomy"], []) def test_dblink(self): """GenBank record with old DBLINK project entry.""" record = SeqIO.read("GenBank/NC_005816.gb", "gb") self.assertEqual(record.dbxrefs, ["Project:58037"]) embl = record.format("embl") self.assertTrue("XX\nPR Project:58037;\nXX\n" in embl, embl) def test_dblink_two(self): """GenBank record with old and new DBLINK project entries.""" record = SeqIO.read("GenBank/NP_416719.gbwithparts", "gb") self.assertEqual(record.dbxrefs, ["Project:57779", "BioProject:PRJNA57779"]) embl = record.format("embl") self.assertTrue("XX\nPR Project:PRJNA57779;\nXX\n" in embl, embl) def test_dbline_gb_embl(self): """GenBank / EMBL paired records with PR project entry: GenBank""" record = SeqIO.read("GenBank/DS830848.gb", "gb") self.assertTrue("BioProject:PRJNA16232" in record.dbxrefs, record.dbxrefs) gb = record.format("gb") self.assertTrue("\nDBLINK BioProject:PRJNA16232\n" in gb, gb) # Also check EMBL output embl = record.format("embl") self.assertTrue("XX\nPR Project:PRJNA16232;\nXX\n" in embl, embl) def test_dbline_embl_gb(self): """GenBank / EMBL paired records with PR project entry: EMBL""" record = SeqIO.read("EMBL/DS830848.embl", "embl") # TODO: Should we map this to BioProject:PRJNA16232 self.assertTrue("Project:PRJNA16232" in record.dbxrefs, record.dbxrefs) gb = record.format("gb") self.assertTrue("\nDBLINK Project:PRJNA16232\n" in gb, gb) embl = record.format("embl") self.assertTrue("XX\nPR Project:PRJNA16232;\nXX\n" in embl, embl) def test_structured_comment_parsing(self): """Structued comment parsing.""" # GISAID_EpiFlu(TM)Data, HM138502.gbk has both 'comment' and 'structured_comment' record = SeqIO.read(path.join('GenBank', 'HM138502.gbk'), 'genbank') self.assertEqual(record.annotations['comment'], "Swine influenza A (H1N1) virus isolated during human swine flu\noutbreak of 2009.") self.assertEqual(record.annotations['structured_comment']['GISAID_EpiFlu(TM)Data']['Lineage'], 'swl') self.assertEqual(len(record.annotations['structured_comment']['GISAID_EpiFlu(TM)Data']), 3) # FluData structured comment record = SeqIO.read(path.join('GenBank', 'EU851978.gbk'), 'genbank') self.assertEqual(record.annotations['structured_comment']['FluData']['LabID'], '2008704957') self.assertEqual(len(record.annotations['structured_comment']['FluData']), 5) # Assembly-Data structured comment record = SeqIO.read(path.join('GenBank', 'KF527485.gbk'), 'genbank') self.assertEqual(record.annotations['structured_comment']['Assembly-Data']['Assembly Method'], 'Lasergene v. 10') self.assertEqual(len(record.annotations['structured_comment']['Assembly-Data']), 2) # No structured comment in NC_000932.gb, just a regular comment record = SeqIO.read(path.join('GenBank', 'NC_000932.gb'), 'genbank') self.assertFalse("structured_comment" in record.annotations) self.assertEqual(record.annotations['comment'], 'REVIEWED REFSEQ: This record has been curated by NCBI staff. The\n' 'reference sequence was derived from AP000423.\n' 'COMPLETENESS: full length.') def test_locus_line_topogoly(self): """Test if chromosome topology is conserved""" record = SeqIO.read('GenBank/DS830848.gb', 'genbank') self.assertEqual(record.annotations['topology'], 'linear') out_handle = StringIO() SeqIO.write([record], out_handle, 'genbank') first_line = out_handle.getvalue().split('\n')[0] # TODO - Use self.assertIn once drop Python 2.6 # self.assertIn('linear', first_line) self.assertTrue(" linear " in first_line) with open('GenBank/DS830848.gb', 'r') as fh: orig_first_line = fh.readline().strip() self.assertEqual(first_line, orig_first_line) def test_long_names(self): """Various GenBank names which push the column based LOCUS line.""" original = SeqIO.read("GenBank/iro.gb", "gb") self.assertEqual(len(original), 1326) for name, seq_len, ok in [ ("short", 1, True), ("max_length_of_16", 1000, True), ("overly_long_at_17", 1000, True), ("excessively_long_at_22", 99999, True), ("excessively_long_at_22", 100000, False), ("pushing_the_limits_at_24", 999, True), ("pushing_the_limits_at_24", 1000, False), ("longest_possible_len_of_26", 10, False), # 2 digits ("longest_possible_len_of_26", 9, True), # 1 digit ]: # Make the length match the desired target record = original[:] # TODO - Implement Seq * int record.seq = Seq("N" * seq_len, original.seq.alphabet) # Set the identifer to the desired name record.id = record.name = name # Attempt to output the record... if not ok: # e.g. ValueError: Locus identifier 'excessively_long_at_22' is too long self.assertRaises(ValueError, record.format, "gb") continue with warnings.catch_warnings(): # e.g. BiopythonWarning: Stealing space from length field to # allow long name in LOCUS line warnings.simplefilter("ignore", BiopythonWarning) # output = record.format("gb") handle = StringIO() self.assertEqual(1, SeqIO.write(record, handle, "gb")) handle.seek(0) line = handle.readline() self.assertTrue(" %s " % name in line, line) self.assertTrue(" %i bp " % seq_len in line, line) name_and_length = line[12:40] self.assertEqual(name_and_length.split(), [name, str(seq_len)], line) handle.seek(0) with warnings.catch_warnings(): # e.g. BiopythonParserWarning: GenBank LOCUS line # identifier over 16 characters warnings.simplefilter("ignore", BiopythonWarning) new = SeqIO.read(handle, "gb") self.assertEqual(name, new.name) self.assertEqual(seq_len, len(new)) class OutputTests(unittest.TestCase): """GenBank output tests.""" def test_mad_dots(self): """Writing and reading back accesssion.version variants.""" for identifier in ["example", "example.1a", "example.1.2", "example.1-2", ]: old = SeqRecord(Seq("ACGT", generic_dna), id=identifier, name=identifier, description="mad dots") new = SeqIO.read(StringIO(old.format("gb")), "gb") self.assertEqual(old.id, new.id) self.assertEqual(old.name, new.name) self.assertEqual(old.description, new.description) self.assertEqual(old.seq, new.seq) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)