# ---------------------------------------------------------------------------- # Copyright (c) 2013--, scikit-bio development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file LICENSE.txt, distributed with this software. # ---------------------------------------------------------------------------- import io from unittest import TestCase, main import skbio.io from skbio import DNA, RNA, Sequence, Protein from skbio.metadata import IntervalMetadata from skbio.util import get_data_path # Module specific execption and functions from skbio.io import EMBLFormatError from skbio.io.format.embl import ( _embl_sniffer, _parse_id, _parse_reference, _embl_to_generator, _get_embl_section, _embl_to_sequence, _embl_to_dna, _embl_to_rna, _embl_to_protein, _generator_to_embl, _sequence_to_embl, _protein_to_embl, _rna_to_embl, _dna_to_embl, _serialize_id, _parse_assembly, _embl_parse_section_default, _serialize_dbsource) class SnifferTests(TestCase): def setUp(self): self.positive_fps = list(map(get_data_path, [ 'embl_single_record', 'embl_multi_records'])) self.negative_fps = list(map(get_data_path, [ 'empty', 'whitespace_only', 'embl_uniprot_record', 'embl_w_beginning_whitespace'])) def test_positives(self): for fp in self.positive_fps: self.assertEqual(_embl_sniffer(fp), (True, {})) def test_negatives(self): for fp in self.negative_fps: self.assertEqual(_embl_sniffer(fp), (False, {})) # Boilerplate for EMBL IO tests # TODO: implements all setUp needed class EMBLIOTests(TestCase): def setUp(self): # to test ID line self.id = ( # This is a derived record (non-coding, rRNA and spacer records) # (feature level record: # http://www.ebi.ac.uk/ena/browse/feature-level-products # TODO: a Uniprot record? (['ID AB000684.1:1..275:rRNA; SV 1; linear; ' 'genomic DNA; STD; ENV; 275 BP.'], {'division': 'ENV', 'mol_type': 'genomic DNA', 'shape': 'linear', 'locus_name': 'AB000684.1:1..275:rRNA', 'unit': 'bp', 'size': 275, 'version': 1, 'class': 'STD', 'date': None}), # A standard record (['ID M14399; SV 1; linear; mRNA; STD; PRO; 63 BP.'], {'division': 'PRO', 'mol_type': 'mRNA', 'shape': 'linear', 'locus_name': 'M14399', 'unit': 'bp', 'size': 63, 'version': 1, 'class': 'STD', 'date': None})) # define a single DNA record (with no interval metadata) # M14399; SV 1; linear; mRNA; STD; PRO; 63 BP. self.single = ( 'gtgaaacaaagcactattgcactggctgtcttaccgttactgtttacccctgtgacaaaagcc', {'LOCUS': {'locus_name': 'M14399', 'class': 'STD', 'division': 'PRO', 'mol_type': 'mRNA', 'shape': 'linear', 'size': 63, 'unit': 'bp', 'version': 1, 'date': None}}, None, DNA) # define a single protein record (uniprot) self.protein = ( 'MAFSAEDVLKEYDRRRRMEALLLSLYYPNDRKLLDYKEWSPPRVQVECPKAPVEWNNPPSEKG' 'LIVGHFSGIKYKGEKAQASEVDVNKMCCWVSKFKDAMRRYQGIQTCKIPGKVLSDLDAKIKAY' 'NLTVEGVEGFVRYSRVTKQHVAAFLKELRHSKQYENVNLIHYILTDKRVDIQHLEKDLVKDFK' 'ALVESAHRMRQGHMINVKYILYQLLKKHGHGPDGPDILTVKTGSKGVLYDDSFRKIYTDLGWK' 'FTPL', {'LOCUS': {'locus_name': '001R_FRG3G', 'status': 'Reviewed', 'size': 256, 'unit': 'aa'}}, None, Protein) # define a single DNA record uppercase (filepath) self.single_upper_fp = get_data_path('embl_single_record_upper') # define a single RNA record lower self.single_lower_fp = get_data_path('embl_single_record_lower') # define a single RNA record file path self.single_rna_fp = get_data_path('embl_single_record') # define a http://www.ebi.ac.uk/ena/browse/feature-level-products self.feature_level_fp = get_data_path("embl_feature_level_record") # define a interval metadata (see skbio.metadata.IntervalMetadata) imd = IntervalMetadata(63) # then add interval object to interval metadata. Add source imd.add([(0, 63)], [(False, False)], {'db_xref': '"taxon:562"', 'mol_type': '"mRNA"', 'organism': '"Escherichia coli"', 'type': 'source', 'strand': '+', '__location': '1..63'}) imd.add([(0, 63)], # the second True is beacause exact location is not known [(False, True)], {'phase': 0, 'db_xref': ['"GOA:P00634"', '"InterPro:IPR001952"', '"InterPro:IPR017849"', '"InterPro:IPR017850"', '"InterPro:IPR018299"', '"PDB:1AJA"', '"PDB:1AJB"', '"PDB:1AJC"', '"PDB:1AJD"', '"PDB:1ALH"', '"PDB:1ALI"', '"PDB:1ALJ"', '"PDB:1ALK"', '"PDB:1ANI"', '"PDB:1ANJ"', '"PDB:1B8J"', '"PDB:1ED8"', '"PDB:1ED9"', '"PDB:1ELX"', '"PDB:1ELY"', '"PDB:1ELZ"', '"PDB:1EW8"', '"PDB:1EW9"', '"PDB:1HJK"', '"PDB:1HQA"', '"PDB:1KH4"', '"PDB:1KH5"', '"PDB:1KH7"', '"PDB:1KH9"', '"PDB:1KHJ"', '"PDB:1KHK"', '"PDB:1KHL"', '"PDB:1KHN"', '"PDB:1URA"', '"PDB:1URB"', '"PDB:1Y6V"', '"PDB:1Y7A"', '"PDB:2ANH"', '"PDB:2G9Y"', '"PDB:2GA3"', '"PDB:2MLX"', '"PDB:2MLY"', '"PDB:2MLZ"', '"PDB:3BDF"', '"PDB:3BDG"', '"PDB:3BDH"', '"PDB:3CMR"', '"PDB:3DPC"', '"PDB:3DYC"', '"PDB:3TG0"', '"PDB:4KM4"', '"PDB:4YR1"', '"PDB:5C66"', '"PDB:5GAD"', '"PDB:5GAF"', '"PDB:5GAG"', '"PDB:5GAH"', '"PDB:5JTL"', '"PDB:5JTM"', '"PDB:5JTN"', '"PDB:5JTO"', '"PDB:5JTP"', '"UniProtKB/Swiss-Prot:P00634"'], '__location': '1..>63', 'strand': '+', 'note': '"alkaline phosphatase signal peptide"', 'protein_id': '"AAA23431.1"', 'transl_table': '11', 'translation': '"MKQSTIALAVLPLLFTPVTKA"', 'type': 'CDS'}) self.single_rna = ( 'gugaaacaaagcacuauugcacuggcugucuuaccguuacuguuuaccccugugacaaaagcc', {'LOCUS': {'locus_name': 'M14399', 'class': 'STD', 'division': 'PRO', 'mol_type': 'mRNA', 'shape': 'linear', 'size': 63, 'unit': 'bp', 'version': 1, 'date': '02-SEP-1999'}, 'ACCESSION': 'M14399;', # accessions (could be more than one) 'VERSION': 'M14399.1', # a genbank like version 'DATE': ["16-JUL-1988 (Rel. 16, Created)", "02-SEP-1999 (Rel. 60, Last updated, Version 3)"], 'DBSOURCE': 'MD5; c9b40131b8622946b5aafdf5473b3d43.', 'DEFINITION': "E.coli alkaline phosphatase signal mRNA, 5' end.", 'KEYWORDS': "alkaline phosphatase; signal peptide.", 'SOURCE': {"ORGANISM": "Escherichia coli", 'taxonomy': "Bacteria; Proteobacteria; " "Gammaproteobacteria; Enterobacterales; " "Enterobacteriaceae; Escherichia."}, 'REFERENCE': [{'AUTHORS': 'Gray G.L., Baldridge J.S., ' 'McKeown K.S., Heyneker H.L., ' 'Chang C.N.;', 'JOURNAL': 'Gene 39(2-3):247-254(1985).', 'REFERENCE': '1 (bases 1 to 63)', 'TITLE': '"Periplasmic production of correctly ' 'processed human growth hormone in ' 'Escherichia coli: natural and bacterial ' 'signal sequences are ' 'interchangeable";', 'PUBMED': '3912261'}], 'CROSS_REFERENCE': ['DOI; 10.1016/0378-1119(85)' '90319-1. PUBMED; 3912261.']}, imd, RNA) # define a multi record. File path self.multi_fp = get_data_path('embl_multi_records') # define interval metadata (as single metadata) imd1 = imd # define interal metadata for multi 2 imd2 = IntervalMetadata(743) # then add interval object to interval metadata. Add source imd2.add([(0, 743)], [(False, False)], {'organism': '"Ruditapes philippinarum"', 'type': 'source', '__location': '1..743', 'strand': '+', 'mol_type': '"mRNA"', 'db_xref': '"taxon:129788"'}) imd2.add([(57, 444)], [(False, False)], {'translation': '"MPGGKAGKDSGKAKAKAVSRSARAGLQFPVGRIHRHLKNRT' 'TSHG RVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRI' 'TPRHLQLAIRGDEELDSLIKAT IAGGGVIPHIHKSLIGKKG' 'GQQAK"', 'type': 'CDS', '__location': '58..444', 'protein_id': '"APY18893.1"', 'strand': '+', 'phase': 0, 'product': '"histone"'}) # multi object self.multi = ( ('GTGAAACAAAGCACTATTGCACTGGCTGTCTTACCGTTACTGTTTACCCCTGTGACAAAAGCC', {'LOCUS': {'locus_name': 'M14399', 'class': 'STD', 'division': 'PRO', 'mol_type': 'mRNA', 'shape': 'linear', 'size': 63, 'unit': 'bp', 'version': 1, 'date': '02-SEP-1999'}, 'ACCESSION': 'M14399;', # accessions (could be more than one) 'VERSION': 'M14399.1', # a genbank like version 'DATE': ["16-JUL-1988 (Rel. 16, Created)", "02-SEP-1999 (Rel. 60, Last updated, Version 3)"], 'DBSOURCE': 'MD5; c9b40131b8622946b5aafdf5473b3d43.', 'DEFINITION': "E.coli alkaline phosphatase signal mRNA, 5' end.", 'KEYWORDS': "alkaline phosphatase; signal peptide.", 'SOURCE': {"ORGANISM": "Escherichia coli", 'taxonomy': "Bacteria; Proteobacteria; " "Gammaproteobacteria; Enterobacterales; " "Enterobacteriaceae; Escherichia."}, 'REFERENCE': [{'AUTHORS': 'Gray G.L., Baldridge J.S., ' 'McKeown K.S., Heyneker H.L., ' 'Chang C.N.;', 'JOURNAL': 'Gene 39(2-3):247-254(1985).', 'REFERENCE': '1 (bases 1 to 63)', 'TITLE': '"Periplasmic production of correctly ' 'processed human growth hormone in ' 'Escherichia coli: natural and ' 'bacterial signal sequences are ' 'interchangeable";', 'PUBMED': '3912261'}], 'CROSS_REFERENCE': ['DOI; 10.1016/0378-1119(85)' '90319-1. PUBMED; 3912261.']}, imd1, DNA), ('TGTGCACAGTCTACGCGTCATCTTGAAAGAAAGAACTACACTACTCCAAAAATAATCATGCC' 'TGGTGGAAAAGCTGGTAAAGATTCCGGAAAGGCCAAGGCTAAGGCAGTGTCAAGGTCCGCAA' 'GAGCTGGCTTACAGTTTCCAGTCGGACGTATTCACAGGCATTTGAAGAACAGAACCACTAGC' 'CACGGTCGTGTTGGAGCTACAGCAGCCGTTTACAGTGCAGCAATCCTTGAATACCTGACCGC' 'CGAAGTGCTTGAGTTGGCTGGAAACGCAAGTAAAGATCTCAAAGTAAAGAGAATCACCCCAC' 'GTCACTTGCAGTTGGCAATCAGAGGAGATGAAGAGTTGGATTCCCTAATTAAAGCCACAATC' 'GCTGGTGGTGGTGTTATTCCACATATCCACAAGTCACTTATTGGCAAGAAGGGAGGTCAGCA' 'AGCCAAATAAATTGGACATACTCATTCATCAGGGAACAATGTGTAGTGAATGTGTTAAAAAG' 'AACAATCTCATTGTGTAGCTCTTTAGTTTTATATGAATGTGTTAACATGGTCATTCACATCG' 'TATGACTCATAGAATCATCTGTGTATCATTTCATCCTCTCATTTTATAGCTCCTCATTTTCC' 'TTAGACTCATTAAAATTTTTATCTCGGAAAAATGTTTTTTCTACAATTTTAGCATTCATTTA' 'TCTTCATCTTGCTTTTATGTTTAATAAAACGAACTTATAATACCAAAAAAAAAAAAAAAAA', {'ACCESSION': 'KX454487;', 'VERSION': 'KX454487.1', 'COMMENT': '##Assembly-Data-START##\nSequencing Technology ' ':: Sanger dideoxy sequencing\n##Assembly-Data-END##', 'DATE': ['02-FEB-2017 (Rel. 131, Created)', '02-FEB-2017 (Rel. 131, Last updated, Version 1)'], 'DBSOURCE': 'MD5; cbc730cf7a8d694b50fb7dd6b993ae0d.', 'DEFINITION': 'Ruditapes philippinarum histone mRNA, ' 'complete cds.', 'KEYWORDS': '.', 'LOCUS': {'locus_name': 'KX454487', 'class': 'STD', 'division': 'INV', 'mol_type': 'mRNA', 'shape': 'linear', 'size': 743, 'unit': 'bp', 'version': 1, 'date': '02-FEB-2017'}, 'REFERENCE': [ {'AUTHORS': 'Yang D., Zhao J., Wang Q.;', 'JOURNAL': 'Submitted (27-JUN-2016) to the INSDC. Key ' 'Laboratory of Coastal Zone Environment Processes ' 'and Ecological Remediation, Yantai Institute ' 'of Coastal Zone Research (YIC), Chinese Academy ' 'of Sciences (CAS), 17 Chunhui Road, Laishan ' 'District, Yantai, Shandong 264003, China', 'REFERENCE': '1 (bases 1 to 743)', 'TITLE': ';'}], 'CROSS_REFERENCE': [None], 'SOURCE': { 'ORGANISM': 'Ruditapes philippinarum', 'taxonomy': 'Eukaryota; Metazoa; Lophotrochozoa; Mollusca; ' 'Bivalvia; Heteroconchia; Euheterodonta; ' 'Veneroida; Veneroidea; Veneridae; Ruditapes.'}}, imd2, DNA)) # define the feature level product obj self.feature_level = ( 'AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUC' 'GAGCGGCAGCACAGAGGAACUUGUUCCUUGGGUGGCGAGCGGCGGACGGGUGAGUAAUGCCU' 'AGGAAAUUGCCCUGAUGUGGGGGAUAACCAUUGGAAACGAUGGCUAAUACCGCAUGAUGCCU' 'ACGGGCCAAAGAGGGGGACCUUCUGGCCUCUCGCGUCAGGAUAUGCCUAGGUGGGAUUAGCU' 'AGUUGGUGAGGUAAUGGCUCACCAAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGAUCAGC' 'CACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACA' 'AUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUA' 'CUUUCAGUCGUGAGGAAGGUGGUGUUGUUAAUAGCAGCAUCAUUUGACGUUAGCGACAGAAG' 'AAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCGAGCGUUAAUCGGA' 'AUUACUGGGCGUAAAGCGCAUGCAGGUGGUGGAUUAAGUCAGAUGUGAAAGCCCGGGGCUCA' 'ACCUCGGAACCGCAUUUGAAACUGGUUCACUAGAGUACUGUAGAGGGGGGUAGAAUUUCAGG' 'UGUAGCGGUGAAAUGCGUAGAGAUCUGAAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACA' 'GAUACUGACACUCAGAUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCA' 'CGCCGUAAACGAUGUCUACUUGGAGGUUGUGGCCUUGAGCCGUGGCUUUCGGAGCUAACGCG' 'UUAAGUAGACCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAUGAAUUGACGGGGGCC' 'CGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUACUCUUG' 'ACAUCCAGAGAAGCCAGCGGAGACGCAGGUGUGCCUUCGGGAGCUCUGAGACAGGUGCUGCA' 'UGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUA' 'UCCUUGUUUGCCAGCGAGUCAUGUCGGGAACUCCAGGGAGACUGCCGGUGAUAAACCGGAGG' 'AAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAU' 'GGCGCAUACAGAGGGCAGCAAGCUAGCGAUAGUGAGCGAAUCCCAAAAAGUGCGUCGUAGUC' 'CGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUAGAUCAGAAU' 'GCUACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGCUG' 'CAAAAGAAGUGGGUAGUUUAACCUUUCGGGGAGGACGCUCACCACUUUGUGGUUCAUGACUG' 'GGGUGAAGUCGUAACAAGGUAGCGCUAGGGGAACCUGGCGCUGGAUCACCUCCUUA', {'DATE': ['02-JUN-2014 (Rel. 121, Created)', '04-FEB-2016 (Rel. 127, Last updated, Version 5)'], 'DBSOURCE': 'SILVA-LSU; LK021130. SILVA-SSU; LK021130. MD5; ' 'afd116bf2c1a13acbf40d63d82f0218c. BioSample; ' 'SAMEA3865288.', 'DEFINITION': 'Vibrio anguillarum 16S rRNA', 'KEYWORDS': '.', 'LOCUS': {'locus_name': 'LK021130.1:74067..75610:rRNA', 'class': 'STD', 'division': 'PRO', 'mol_type': 'genomic DNA', 'shape': 'linear', 'size': 1544, 'unit': 'bp', 'version': 1, 'date': '04-FEB-2016'}, 'PARENT_ACCESSION': 'LK021130.1', 'VERSION': 'LK021130.1', 'PROJECT_IDENTIFIER': 'Project:PRJEB5701;', 'REFERENCE': [ {'AUTHORS': 'Holm K.;', 'JOURNAL': 'Submitted (26-MAR-2014) to the INSDC. ' 'Norstruct, Dept of Chemistry, University of ' 'Tromso, Science Park 3, NO-9037 Tromso, NORWAY.', 'TITLE': ';', 'REFERENCE': '1'}, {'AUTHORS': 'Holm K.O., Nilsson K., Hjerde E., Willassen ' 'N.P., Milton D.L.;', 'JOURNAL': 'Stand Genomic Sci. 10:60-60(2015).', 'TITLE': '"Complete genome sequence of Vibrio anguillarum ' 'strain NB10, a virulent isolate from the Gulf ' 'of Bothnia";', 'REFERENCE': '2', 'PUBMED': '26380645'}], 'CROSS_REFERENCE': [ None, 'DOI; 10.1186/s40793-015-0060-7. PUBMED; 26380645.'], 'SOURCE': { 'ORGANISM': 'Vibrio anguillarum', 'taxonomy': 'Bacteria; Proteobacteria; Gammaproteobacteria; ' 'Vibrionales; Vibrionaceae; Vibrio.'}}, None, RNA) # get the feature level file without FT self.feature_level_fp = get_data_path( "embl_feature_level_record_no_FT") # get a genbank file in order to to file conversion self.genbank_fp = get_data_path('genbank_single_record') # a embl constructed sequence file path self.embl_constructed_fp = get_data_path("embl_constructed") # a simple embl version to perform embl->gb->embl conversion self.single_rna_simple_fp = get_data_path( "embl_single_record_simple") class ReaderTests(EMBLIOTests): """Implements test for reading EMBL data""" def test_parse_id(self): """Parse ID record (first line of embl format)""" for serialized, parsed in self.id: self.assertEqual(_parse_id(serialized), parsed) def test_parse_id_invalid(self): lines = [ # uniprot line (should this module handle it?) ['ID 001R_FRG3G Reviewed; 256 AA.'], # missing unit ['ID M14399; SV 1; linear; mRNA; STD; PRO; 63'], # missing division ['ID M14399; SV 1; linear; mRNA; STD; 63 BP.']] for line in lines: with self.assertRaisesRegex(EMBLFormatError, r'Could not parse the ID line:.*'): _parse_id(line) # current status of protein support is described in issue-1499 # https://github.com/scikit-bio/scikit-bio/issues/1499 def test_no_protein_support(self): """Testing no protein support for embl""" # TODO: add protein support # a fake protein line. handle = io.StringIO('ID M14399; SV 1; linear; mRNA; STD; ' 'PRO; 63 AA.\n//\n') with self.assertRaisesRegex(EMBLFormatError, r"There's no protein support for EMBL " "record"): # read a protein record Protein.read(handle) # return to 0 handle.seek(0) with self.assertRaisesRegex(EMBLFormatError, r"There's no protein support for EMBL " "record"): # read a generic record skbio.io.read(handle, format='embl') def test_parse_reference(self): lines = ''' RP 1-63 RX DOI; 10.1016/0378-1119(85)90319-1. RX PUBMED; 3912261. RA Gray G.L., Baldridge J.S., McKeown K.S., Heyneker H.L., Chang C.N.; RT "Periplasmic production of correctly processed human growth hormone in RT Escherichia coli: natural and bacterial signal sequences are RT interchangeable"; RL Gene 39(2-3):247-254(1985).'''.split('\n') # DNA, Sequence and RNA data contain newlines lines = [line+"\n" for line in lines if line != ''] exp = {'AUTHORS': 'Gray G.L., Baldridge J.S., ' 'McKeown K.S., Heyneker H.L., Chang C.N.;', 'JOURNAL': 'Gene 39(2-3):247-254(1985).', 'CROSS_REFERENCE': 'DOI; 10.1016/0378-1119(85)90319-1. ' 'PUBMED; 3912261.', 'REFERENCE': '(bases 1 to 63)', 'TITLE': '"Periplasmic production of correctly processed ' 'human growth hormone in Escherichia coli: ' 'natural and bacterial signal sequences are ' 'interchangeable";', 'PUBMED': '3912261' } # read reference obs = _parse_reference(lines) # See all differences self.maxDiff = None self.assertEqual(obs, exp) def test_parse_assembly(self): lines = """ AH LOCAL_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP AS 1-426 AC004528.1 18665-19090 AS 427-526 AC001234.2 1-100 c AS 527-1000 TI55475028 not_available """.split('\n') # DNA, Sequence and RNA data contain newlines lines = [line+"\n" for line in lines if line != ''] exp = [ { 'local_span': '1-426', 'primary_identifier': 'AC004528.1', 'primary_span': '18665-19090', 'comp': '' }, { 'local_span': '427-526', 'primary_identifier': 'AC001234.2', 'primary_span': '1-100', 'comp': 'c' }, { 'local_span': '527-1000', 'primary_identifier': 'TI55475028', 'primary_span': 'not_available', 'comp': '' } ] # read reference obs = _parse_assembly(lines) # See all differences self.maxDiff = None self.assertEqual(obs, exp) def test_parse_bad_assembly(self): """test for a wrong assembly line""" lines = """ AH LOCAL_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP AS 1-426 AC004528.1 """.split("\n") # DNA, Sequence and RNA data contain newlines lines = [line+"\n" for line in lines if line != ''] with self.assertRaisesRegex(EMBLFormatError, r"Can't parse assembly line"): # read a malformed assembly record _parse_assembly(lines) def test_embl_to_generator_single(self): # test single record and uppercase sequence for c in [Sequence, DNA]: obs = next(_embl_to_generator( self.single_upper_fp, constructor=c)) exp = c(self.single[0], metadata=self.single[1], positional_metadata=self.single[2], lowercase=True) self.assertEqual(exp, obs) def test_get_embl_section(self): """Verify to have a section for each embl ID""" with open(self.single_rna_fp) as fh: for line in fh: if line.startswith("//"): continue # test that this function doesn't raise exceptions try: _get_embl_section(line) except KeyError as err: raise EMBLFormatError("Key {0} isn't defined in embl." "KEYS_2_SECTIONS".format(err)) def test_embl_to_generator(self): for i, obs in enumerate(_embl_to_generator(self.multi_fp)): seq, md, imd, constructor = self.multi[i] exp = constructor(seq, metadata=md, lowercase=True, interval_metadata=imd) self.assertEqual(exp, obs) def test_embl_to_sequence(self): for i, exp in enumerate(self.multi): obs = _embl_to_sequence(self.multi_fp, seq_num=i+1) exp = Sequence(exp[0], metadata=exp[1], lowercase=True, interval_metadata=exp[2]) self.assertEqual(exp, obs) def test_embl_to_rna(self): seq, md, imd, constructor = self.single_rna obs = _embl_to_rna(self.single_rna_fp) exp = constructor(seq, metadata=md, lowercase=True, interval_metadata=imd) self.assertEqual(exp, obs) def test_embl_to_dna(self): i = 1 exp = self.multi[i] obs = _embl_to_dna(self.multi_fp, seq_num=i+1) exp = DNA(exp[0], metadata=exp[1], lowercase=True, interval_metadata=exp[2]) self.assertEqual(exp, obs) # current status of protein support is described in issue-1499 # https://github.com/scikit-bio/scikit-bio/issues/1499 def test_embl_to_protein(self): # TODO: add protein support i = 0 # there is no support for protein at the moment # when protein support will be added, this code must work # exp = self.multi[i] # obs = _embl_to_protein(self.multi_fp, seq_num=i+1) # exp = Protein(exp[0], metadata=exp[1], # lowercase=True, interval_metadata=exp[2]) # self.assertEqual(exp, obs) with self.assertRaisesRegex(EMBLFormatError, r"There's no protein support for EMBL " "record"): # read a generic record _embl_to_protein(self.multi_fp, seq_num=i+1) # deal with feature-level-products: ignore feature table def test_feature_level_products(self): seq, md, imd, constructor = self.feature_level obs = _embl_to_rna(self.feature_level_fp) exp = constructor(seq, metadata=md, lowercase=True, interval_metadata=imd) self.assertEqual(obs, exp) # deal with constructed sequences: ignore interval metadata def test_constructed_sequences(self): with self.assertRaisesRegex( EMBLFormatError, r"There's no support for embl CON record"): _embl_to_dna(self.embl_constructed_fp) class WriterTests(EMBLIOTests): def test_serialize_id(self): for serialized, parsed in self.id: self.assertEqual( _serialize_id('ID', parsed), serialized[0] + '\n') def test_serialize_dbsource(self): """Serialize a complex dbsource entry""" # test with a complex uniprot dbsource exp = """DR EMBL; AY548484; AAT09660.1; -; Genomic_DNA. DR RefSeq; YP_031579.1; NC_005946.1. DR ProteinModelPortal; Q6GZX4; -. DR SwissPalm; Q6GZX4; -. DR GeneID; 2947773; -. DR KEGG; vg:2947773; -. DR Proteomes; UP000008770; Genome. """ # split by lines lines = [line+"\n" for line in exp.split("\n") if line != ''] # parse objects parsed = _embl_parse_section_default(lines) # now serialize them obs = _serialize_dbsource("DR", parsed) # test objects self.assertEqual(obs, exp) def test_generator_to_embl(self): seq, md, imd, constructor = self.single obj = constructor(seq, md, interval_metadata=imd, lowercase=True) with io.StringIO() as fh: _generator_to_embl([obj], fh) obs = fh.getvalue() with open(self.single_lower_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_sequence_to_embl(self): with io.StringIO() as fh: for i, (seq, md, imd, constructor) in enumerate(self.multi): obj = Sequence(seq, md, interval_metadata=imd) _sequence_to_embl(obj, fh) obs = fh.getvalue() with open(self.multi_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_dna_to_embl(self): with io.StringIO() as fh: for i, (seq, md, imd, constructor) in enumerate(self.multi): obj = constructor( seq, md, interval_metadata=imd, lowercase=True) _dna_to_embl(obj, fh) # read all records written obs = fh.getvalue() with open(self.multi_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) # TODO: add support for protein # current status of protein support is described in issue-1499 # https://github.com/scikit-bio/scikit-bio/issues/1499 def test_protein_to_embl(self): seq, md, imd, constructor = self.protein obj = constructor(seq, md, interval_metadata=imd) with io.StringIO() as fh: self.assertRaisesRegex(EMBLFormatError, r"There's no protein support for EMBL " "record", _protein_to_embl, [obj], fh) def test_rna_to_embl(self): with io.StringIO() as fh: seq, md, imd, constructor = self.single_rna obj = constructor(seq, md, interval_metadata=imd, lowercase=True) _rna_to_embl(obj, fh) obs = fh.getvalue() with open(self.single_rna_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_rna_to_embl_flp(self): """Test writing feature level products""" with io.StringIO() as fh: seq, md, imd, constructor = self.feature_level obj = constructor(seq, md, interval_metadata=imd, lowercase=True) _rna_to_embl(obj, fh) obs = fh.getvalue() with open(self.feature_level_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) class RoundtripTests(EMBLIOTests): def test_roundtrip_generator(self): with io.StringIO() as fh: _generator_to_embl(_embl_to_generator(self.multi_fp), fh) obs = fh.getvalue() with open(self.multi_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_roundtrip_rna(self): with io.StringIO() as fh: _rna_to_embl(_embl_to_rna(self.single_rna_fp), fh) obs = fh.getvalue() with open(self.single_rna_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_roundtrip_dna(self): with io.StringIO() as fh: _dna_to_embl(_embl_to_dna(self.single_rna_fp), fh) obs = fh.getvalue() with open(self.single_rna_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) # TODO: test_roundtrip_protein # current status of protein support is described in issue-1499 # https://github.com/scikit-bio/scikit-bio/issues/1499 def test_roundtrip_sequence(self): with io.StringIO() as fh: _sequence_to_embl(_embl_to_sequence(self.single_rna_fp), fh) obs = fh.getvalue() with open(self.single_rna_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) class Convertertest(EMBLIOTests): def test_gb_to_embl(self): genbank = DNA.read(self.genbank_fp, format="genbank") with io.StringIO() as fh: DNA.write(genbank, format="embl", file=fh) # EMBL can't deal with genbank version (ie M14399.1 GI:145229) # read embl data and write to gb fh.seek(0) embl = DNA.read(fh, format="embl") with io.StringIO() as fh: DNA.write(embl, format="genbank", file=fh) # read gb data obs = fh.getvalue() with open(self.genbank_fp) as fh: exp = fh.read() self.assertEqual(exp, obs) def test_embl_to_gb(self): # EMBL records have more features than genbank, (ex more than one date, # embl class, DOI cross references) so I can't convert an embl to gb # and then to embl keeping all those data. But I can start from # genbank record # do embl file -> embl object -> gb file -> gb object -> # embl file. Ensure that first and last files are identical embl = DNA.read(self.single_rna_simple_fp, format="embl") # "write" genbank record in a embl file with io.StringIO() as fh: DNA.write(embl, format="genbank", file=fh) # read genbank file fh.seek(0) genbank = DNA.read(fh, format="genbank") # "write" genbank record in a embl file with io.StringIO() as fh: DNA.write(genbank, format="embl", file=fh) # read file object obs = fh.getvalue() # test objects with open(self.single_rna_simple_fp) as fh: exp = fh.read() self.assertEqual(exp, obs) if __name__ == '__main__': main()