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import xml.dom.minidom
from unittest import TestCase
from cogent3.parse.tinyseq import TinyseqParser
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\n"
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 [
next(TinyseqParser(data)),
next(TinyseqParser(xml.dom.minidom.parseString(data))),
]:
self.assertEqual(name, "AY286018.1")
self.assertEqual(sample_seq, seq.to_fasta(block_size=len(sample_seq)))
self.assertEqual(seq.annotation_db.num_matches(), 2)
pass
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