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#!/usr/bin/env python
from os import getcwd, remove, rmdir, mkdir, path
import tempfile, shutil
from cogent.app.cdbfasta import cdbfasta, index_fasta, index_fastq, cdbyank, \
query_indexed_seqs
from cogent.util.unit_test import TestCase, main
from shutil import rmtree
__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Daniel McDonald"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Daniel McDonald"
__email__ = "mcdonadt@colorado.edu"
__status__ = "Development"
class GeneralTests(TestCase):
def setUp(self):
"""cdbfasta/cdbyank setUp method for all tests"""
self.temp_dir = tempfile.mkdtemp()
self.seqs_fasta = path.join(self.temp_dir, 'seqs.fasta')
self.seqs_fastq = path.join(self.temp_dir, 'seqs.fastq')
f = open(self.seqs_fasta,'w')
self.fasta_seqs = {'ABC 567':'AATTGGCC','XYZ':'TTGGTT','123':'CCCC'}
f.write(''.join([">%s\n%s\n"%(k,v) for k,v in self.fasta_seqs.items()]))
f.close()
f = open(self.seqs_fastq,'w')
self.fastq_seqs = {'ABC 567':'AATTGGCC', 'XYZ':'TTGGTT','123':'CCCC'}
self.fastq_qual = {'ABC 567':'12345678', 'XYZ':'333333','123':'9876'}
for k in self.fastq_seqs:
f.write("@%s\n%s\n+\n%s\n" % (k, self.fastq_seqs[k],
self.fastq_qual[k]))
f.close()
def tearDown(self):
rmtree(self.temp_dir)
class cdbfastaTests(GeneralTests):
def test_index_fasta(self):
"""Index a fasta!"""
res = index_fasta(self.seqs_fasta)
self.assertEqual(res.rsplit('/')[-1], "seqs.fasta.cidx")
def test_index_fastq(self):
"""Index a fastq!!!"""
res = index_fastq(self.seqs_fastq)
self.assertEqual(res.rsplit('/')[-1], "seqs.fastq.cidx")
def test_version(self):
"""make sure the expected version string is produced"""
app = cdbfasta(SuppressStdout=False, params={'-v':True})
res = app(self.seqs_fasta)
self.assertEqual(res['StdOut'].read(),"cdbfasta version 0.99\n")
class cdbyankTests(GeneralTests):
def test_version(self):
"""make sure the expected version string is produced"""
app = cdbyank(SuppressStdout=False, params={'-v':True})
res = app(self.seqs_fasta)
self.assertEqual(res['StdOut'].read(),"cdbyank version 0.981\n")
def test_query_indexed_seqs_fasta(self):
"""pull out some sequences"""
idx = index_fasta(self.seqs_fasta)
seqs = query_indexed_seqs(['ABC','123'], idx)
exp = sorted([">ABC 567","AATTGGCC",">123","CCCC"])
obs = sorted(seqs.splitlines())
self.assertEqual(obs,exp)
def test_query_indexed_seqs_fastq(self):
"""pull out some sequences"""
idx = index_fastq(self.seqs_fastq)
seqs = query_indexed_seqs(['ABC','123'], idx)
exp = sorted(["@ABC 567","AATTGGCC","+","12345678",
"@123","CCCC","+","9876"])
obs = sorted(seqs.splitlines())
self.assertEqual(obs,exp)
if __name__ == '__main__':
main()
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