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|
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.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/biocore/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/biocore/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/biocore/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/biocore/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()
|
