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#!/usr/bin/env python
__author__ = "Jesse Zaneveld"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jesse Zaneveld"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Jesse Zaneveld"
__email__ = "zaneveld@gmail.com"
__status__ = "Production"
"""
Test code for kegg_fasta.py in cogent.parse.
"""
from cogent.util.unit_test import TestCase, main
from cogent.parse.kegg_fasta import kegg_label_fields, parse_fasta
class ParseKeggFastaTests(TestCase):
def test_kegg_label_fields(self):
"""kegg_label_fields should return fields from line"""
# Format is species:gene_id [optional gene_name]; description.
# Note that the '>' should already be stripped by the Fasta Parser
test1 = \
"""stm:STM0001 thrL; thr operon leader peptide ; K08278 thr operon leader peptide"""
test2 = \
"""stm:STM0002 thrA; bifunctional aspartokinase I/homeserine dehydrogenase I (EC:2.7.2.4 1.1.1.13); K00003 homoserine dehydrogenase [EC:1.1.1.3]; K00928 aspartate kinase [EC:2.7.2.4]"""
obs = kegg_label_fields(test1)
exp = ('stm:STM0001','stm','STM0001',\
'thrL','thr operon leader peptide ; K08278 thr operon leader peptide')
self.assertEqual(obs,exp)
obs = kegg_label_fields(test2)
exp = ('stm:STM0002', 'stm', 'STM0002', 'thrA', \
'bifunctional aspartokinase I/homeserine dehydrogenase I (EC:2.7.2.4 1.1.1.13); K00003 homoserine dehydrogenase [EC:1.1.1.3]; K00928 aspartate kinase [EC:2.7.2.4]')
self.assertEqual(obs,exp)
def test_parse_fasta(self):
"""parse_fasta should parse KEGG FASTA lines"""
obs = parse_fasta(TEST_KEGG_FASTA_LINES)
exp = EXP_RESULT
for i,entry in enumerate(obs):
self.assertEqual(entry, exp[i])
TEST_KEGG_FASTA_LINES = \
[">stm:STM0001 thrL; thr operon leader peptide; K08278 thr operon leader peptide",\
"atgaaccgcatcagcaccaccaccattaccaccatcaccattaccacaggtaacggtgcgggctga",\
">stm:STM0002 thrA; bifunctional aspartokinase I/homeserine dehydrogenase I (EC:2.7.2.4 1.1.1.13); K12524 bifunctional aspartokinase/homoserine dehydrogenase 1 [EC:2.7.2.4 1.1.1.3]",\
"atgcgagtgttgaagttcggcggtacatcagtggcaaatgcagaacgttttctgcgtgtt",\
"gccgatattctggaaagcaatgccaggcaagggcaggtagcgaccgtactttccgccccc"]
EXP_RESULT = \
["\t".join(["stm:STM0001","stm","STM0001",\
"thrL","thr operon leader peptide; K08278 thr operon leader peptide","atgaaccgcatcagcaccaccaccattaccaccatcaccattaccacaggtaacggtgcgggctga","\n"]),\
"\t".join(["stm:STM0002","stm","STM0002",\
"thrA","bifunctional aspartokinase I/homeserine dehydrogenase I (EC:2.7.2.4 1.1.1.13); K12524 bifunctional aspartokinase/homoserine dehydrogenase 1 [EC:2.7.2.4 1.1.1.3]",\
"atgcgagtgttgaagttcggcggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgccaggcaagggcaggtagcgaccgtactttccgccccc","\n"])]
if __name__=="__main__":
main()
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