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#!/usr/bin/env python
from StringIO import StringIO
import xml.dom.minidom
from cogent.util.unit_test import TestCase, main
from cogent.parse.tinyseq import TinyseqParser
__author__ = "Matthew Wakefield"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Matthew Wakefield"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Matthew Wakefield"
__email__ = "wakefield@wehi.edu.au"
__status__ = "Production"
data = """<?xml version="1.0"?>
<!DOCTYPE TSeqSet PUBLIC "-//NCBI//NCBI TSeq/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd">
<TSeqSet>
<TSeq>
<TSeq_seqtype value="nucleotide"/>
<TSeq_gi>31322957</TSeq_gi>
<TSeq_accver>AY286018.1</TSeq_accver>
<TSeq_taxid>9315</TSeq_taxid>
<TSeq_orgname>Macropus eugenii</TSeq_orgname>
<TSeq_defline>Macropus eugenii medium wave-sensitive opsin 1 (OPN1MW) mRNA, complete cds</TSeq_defline>
<TSeq_length>99</TSeq_length>
<TSeq_sequence>GGCAGGGAAAGGGAAGAAAGTAAAGGGGCCATGACACAGGCATGGGACCCTGCAGGGTTCTTGGCTTGGCGGCGGGACGAGAACGAGGAGACGACTCGG</TSeq_sequence>
</TSeq>
</TSeqSet>
"""
sample_seq = ">AY286018.1\nGGCAGGGAAAGGGAAGAAAGTAAAGGGGCCATGACACAGGCATGGGACCCTGCAGGGTTCTTGGCTTGGCGGCGGGACGAGAACGAGGAGACGACTCGG"
sample_annotations = '[genbank_id "AY286018.1" at [0:99]/99, organism "Macropus eugenii" at [0:99]/99]'
class ParseTinyseq(TestCase):
def test_parse(self):
for name,seq in [TinyseqParser(data).next(),TinyseqParser(xml.dom.minidom.parseString(data)).next()]:
self.assertEqual(name, 'AY286018.1')
self.assertEqual(sample_seq, seq.toFasta())
self.assertEqual(str(seq.annotations), sample_annotations)
pass
if __name__ == "__main__":
main()
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