def test_bwa_mapping():
'''It test that the gmap doesn't map anything'''
reference = join(TEST_DATA_DIR, 'blast/arabidopsis_genes')
work_dir = NamedTemporaryDir()
reference_fpath = join(work_dir.name, 'arabidopsis_genes')
os.symlink(reference, reference_fpath)
reads_fhand = NamedTemporaryFile(suffix='.sfastq')
reads_fhand.write(SOLEXA)
reads_fhand.flush()
out_bam_fhand = NamedTemporaryFile()
out_bam_fpath = out_bam_fhand.name
out_bam_fhand.close()
parameters = {'colorspace': False, 'reads_length':'short',
'threads':None, 'java_conf':None}
map_reads_with_bwa(reference_fpath, reads_fhand.name, out_bam_fpath,
parameters)
test_sam_fhand = NamedTemporaryFile(suffix='sam')
bam2sam(out_bam_fpath, test_sam_fhand.name)
result = open(test_sam_fhand.name).read()
assert 'seq17' in result
unmapped_fhand = StringIO.StringIO()
parameters = {'colorspace': False, 'reads_length':'short',
'threads':None, 'java_conf':None,
'unmapped_fhand':unmapped_fhand}
map_reads_with_bwa(reference_fpath, reads_fhand.name, out_bam_fpath,
parameters)
assert 'seq17' in unmapped_fhand.getvalue()
test_sam_fhand = NamedTemporaryFile(suffix='sam')
bam2sam(out_bam_fpath, test_sam_fhand.name)
result = open(test_sam_fhand.name).read()
assert 'seq17' not in result
