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#!/usr/bin/env python
import xml.dom.minidom
from unittest import TestCase, main
from cogent3.parse.gbseq import GbSeqXmlParser
__author__ = "Matthew Wakefield"
__copyright__ = "Copyright 2007-2022, The Cogent Project"
__credits__ = ["Matthew Wakefield"]
__license__ = "BSD-3"
__version__ = "2023.2.12a1"
__maintainer__ = "Matthew Wakefield"
__email__ = "wakefield@wehi.edu.au"
__status__ = "Production"
data = """<?xml version="1.0"?>
<!DOCTYPE GBSet PUBLIC "-//NCBI//NCBI GBSeq/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.dtd">
<GBSet>
<GBSeq>
<GBSeq_locus>AY286018</GBSeq_locus>
<GBSeq_length>99</GBSeq_length>
<GBSeq_strandedness>single</GBSeq_strandedness>
<GBSeq_moltype>mRNA</GBSeq_moltype>
<GBSeq_topology>linear</GBSeq_topology>
<GBSeq_division>MAM</GBSeq_division>
<GBSeq_update-date>29-SEP-2003</GBSeq_update-date>
<GBSeq_create-date>01-JUN-2003</GBSeq_create-date>
<GBSeq_definition>Macropus eugenii medium wave-sensitive opsin 1 (OPN1MW) mRNA, complete cds</GBSeq_definition>
<GBSeq_primary-accession>AY286018</GBSeq_primary-accession>
<GBSeq_accession-version>AY286018.1</GBSeq_accession-version>
<GBSeq_other-seqids>
<GBSeqid>gb|AY286018.1|</GBSeqid>
<GBSeqid>gi|31322957</GBSeqid>
</GBSeq_other-seqids>
<GBSeq_source>Macropus eugenii (tammar wallaby)</GBSeq_source>
<GBSeq_organism>Macropus eugenii</GBSeq_organism>
<GBSeq_taxonomy>Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Metatheria; Diprotodontia; Macropodidae; Macropus</GBSeq_taxonomy>
<GBSeq_references>
<GBReference>
<GBReference_reference>1</GBReference_reference>
<GBReference_position>1..99</GBReference_position>
<GBReference_authors>
<GBAuthor>Deeb,S.S.</GBAuthor>
<GBAuthor>Wakefield,M.J.</GBAuthor>
<GBAuthor>Tada,T.</GBAuthor>
<GBAuthor>Marotte,L.</GBAuthor>
<GBAuthor>Yokoyama,S.</GBAuthor>
<GBAuthor>Marshall Graves,J.A.</GBAuthor>
</GBReference_authors>
<GBReference_title>The cone visual pigments of an Australian marsupial, the tammar wallaby (Macropus eugenii): sequence, spectral tuning, and evolution</GBReference_title>
<GBReference_journal>Mol. Biol. Evol. 20 (10), 1642-1649 (2003)</GBReference_journal>
<GBReference_xref>
<GBXref>
<GBXref_dbname>doi</GBXref_dbname>
<GBXref_id>10.1093/molbev/msg181</GBXref_id>
</GBXref>
</GBReference_xref>
<GBReference_pubmed>12885969</GBReference_pubmed>
</GBReference>
<GBReference>
<GBReference_reference>2</GBReference_reference>
<GBReference_position>1..99</GBReference_position>
<GBReference_authors>
<GBAuthor>Deeb,S.S.</GBAuthor>
<GBAuthor>Wakefield,M.J.</GBAuthor>
<GBAuthor>Tada,T.</GBAuthor>
<GBAuthor>Marotte,L.</GBAuthor>
<GBAuthor>Yokoyama,S.</GBAuthor>
<GBAuthor>Graves,J.A.M.</GBAuthor>
</GBReference_authors>
<GBReference_title>Direct Submission</GBReference_title>
<GBReference_journal>Submitted (29-APR-2003) RSBS, The Australian National University, Acton, ACT 0200, Australia</GBReference_journal>
</GBReference>
</GBSeq_references>
<GBSeq_feature-table>
<GBFeature>
<GBFeature_key>source</GBFeature_key>
<GBFeature_location>1..99</GBFeature_location>
<GBFeature_intervals>
<GBInterval>
<GBInterval_from>1</GBInterval_from>
<GBInterval_to>99</GBInterval_to>
<GBInterval_accession>AY286018.1</GBInterval_accession>
</GBInterval>
</GBFeature_intervals>
<GBFeature_quals>
<GBQualifier>
<GBQualifier_name>organism</GBQualifier_name>
<GBQualifier_value>Macropus eugenii</GBQualifier_value>
</GBQualifier>
<GBQualifier>
<GBQualifier_name>mol_type</GBQualifier_name>
<GBQualifier_value>mRNA</GBQualifier_value>
</GBQualifier>
<GBQualifier>
<GBQualifier_name>db_xref</GBQualifier_name>
<GBQualifier_value>taxon:9315</GBQualifier_value>
</GBQualifier>
<GBQualifier>
<GBQualifier_name>country</GBQualifier_name>
<GBQualifier_value>Australia: Kangaroo Island</GBQualifier_value>
</GBQualifier>
</GBFeature_quals>
</GBFeature>
<GBFeature>
<GBFeature_key>gene</GBFeature_key>
<GBFeature_location>1..99</GBFeature_location>
<GBFeature_intervals>
<GBInterval>
<GBInterval_from>1</GBInterval_from>
<GBInterval_to>99</GBInterval_to>
<GBInterval_accession>AY286018.1</GBInterval_accession>
</GBInterval>
</GBFeature_intervals>
<GBFeature_quals>
<GBQualifier>
<GBQualifier_name>gene</GBQualifier_name>
<GBQualifier_value>OPN1MW</GBQualifier_value>
</GBQualifier>
</GBFeature_quals>
</GBFeature>
<GBFeature>
<GBFeature_key>CDS</GBFeature_key>
<GBFeature_location>31..99</GBFeature_location>
<GBFeature_intervals>
<GBInterval>
<GBInterval_from>31</GBInterval_from>
<GBInterval_to>99</GBInterval_to>
<GBInterval_accession>AY286018.1</GBInterval_accession>
</GBInterval>
</GBFeature_intervals>
<GBFeature_quals>
<GBQualifier>
<GBQualifier_name>gene</GBQualifier_name>
<GBQualifier_value>OPN1MW</GBQualifier_value>
</GBQualifier>
<GBQualifier>
<GBQualifier_name>note</GBQualifier_name>
<GBQualifier_value>cone pigments</GBQualifier_value>
</GBQualifier>
<GBQualifier>
<GBQualifier_name>codon_start</GBQualifier_name>
<GBQualifier_value>1</GBQualifier_value>
</GBQualifier>
<GBQualifier>
<GBQualifier_name>transl_table</GBQualifier_name>
<GBQualifier_value>1</GBQualifier_value>
</GBQualifier>
<GBQualifier>
<GBQualifier_name>product</GBQualifier_name>
<GBQualifier_value>medium wave-sensitive opsin 1</GBQualifier_value>
</GBQualifier>
<GBQualifier>
<GBQualifier_name>protein_id</GBQualifier_name>
<GBQualifier_value>AAP37945.1</GBQualifier_value>
</GBQualifier>
<GBQualifier>
<GBQualifier_name>db_xref</GBQualifier_name>
<GBQualifier_value>GI:31322958</GBQualifier_value>
</GBQualifier>
<GBQualifier>
<GBQualifier_name>translation</GBQualifier_name>
<GBQualifier_value>MTQAWDPAGFLAWRRDENE</GBQualifier_value>
</GBQualifier>
</GBFeature_quals>
</GBFeature>
</GBSeq_feature-table>
<GBSeq_sequence>ggcagggaaagggaagaaagtaaaggggccatgacacaggcatgggaccctgcagggttcttggcttggcggcgggacgagaacgaggagacgactcgg</GBSeq_sequence>
</GBSeq>
</GBSet>
"""
sample_seq = ">AY286018.1\nGGCAGGGAAAGGGAAGAAAGTAAAGGGGCCATGACACAGGCATGGGACCCTGCAGGGTTCTTGGCTTGGCGGCGGGACGAGAACGAGGAGACGACTCGG\n"
sample_annotations = '[source "[0:99]/99 of AY286018.1" at [0:99]/99, organism "Macropus eugenii" at [0:99]/99, gene "OPN1MW" at [0:99]/99, CDS "OPN1MW" at [30:99]/99]'
class ParseGBseq(TestCase):
def test_parse(self):
for name, seq in [
next(GbSeqXmlParser(data)),
next(GbSeqXmlParser(xml.dom.minidom.parseString(data))),
]:
self.assertEqual(name, "AY286018.1")
self.assertEqual(sample_seq, seq.to_fasta(block_size=len(sample_seq)))
self.assertEqual(str(seq.annotations), sample_annotations)
pass
if __name__ == "__main__":
main()
|
