def test_gmap_without_mapping_output():
'''It test that the gmap doesn't map anything'''
mappers_dir = join(TEST_DATA_DIR, 'mappers')
cmap_dir = join(TEST_DATA_DIR, 'mappers', 'gmap')
work_dir = NamedTemporaryDir()
temp_genome = join(work_dir.name, 'genome.fa')
os.symlink(join(mappers_dir, 'genome.fa'), temp_genome)
reads_fhand = NamedTemporaryFile()
reads_fhand.write('>seq\natgtgatagat\n')
reads_fhand.flush()
out_bam_fhand = NamedTemporaryFile()
out_bam_fpath = out_bam_fhand.name
out_bam_fhand.close()
parameters = {'threads':None, 'kmer':13}
map_reads_with_gmap(temp_genome, reads_fhand.name, out_bam_fpath,
parameters)
reads_fhand.close()
temp_sam_fhand = NamedTemporaryFile(suffix='.sam')
bam2sam(out_bam_fpath, temp_sam_fhand.name, True)
result = open(temp_sam_fhand.name).read()
assert 'seq\t4\t*\t0\t0' in result
def test_gmap_mapper():
'It test the gmap mapper'
mappers_dir = join(TEST_DATA_DIR, 'mappers')
gmap_dir = join(TEST_DATA_DIR, 'mappers', 'gmap')
work_dir = NamedTemporaryDir()
temp_genome = join(work_dir.name, 'genome.fa')
os.symlink(join(mappers_dir, 'genome.fa'), temp_genome)
reads_fpath = join(gmap_dir, 'lb_lib1.pl_sanger.sm_sam1.fa')
out_bam_fhand = NamedTemporaryFile(suffix='.bam')
parameters = {'threads':None, 'kmer':13}
map_reads_with_gmap(temp_genome, reads_fpath, out_bam_fhand.name,
parameters)
sam_fhand = NamedTemporaryFile(suffix='.sam')
bam2sam(out_bam_fhand.name, sam_fhand.name, header=True)
result = open(sam_fhand.name).read()
assert exists(out_bam_fhand.name)
assert '36M2I204M' in result
assert 'SN:SL2.30ch00' in result
assert 'seq9_rev_MOD' in result
work_dir.close()
out_bam_fhand.close()
sam_fhand.close()
work_dir = NamedTemporaryDir()
temp_genome = join(work_dir.name, 'genome.fa')
os.symlink(join(mappers_dir, 'genome.fa'), temp_genome)
reads_fpath = join(gmap_dir, 'lb_lib1.pl_sanger.sm_sam1.sfastq')
out_bam_fhand = NamedTemporaryFile(suffix='.bam')
unmapped_fhand = StringIO.StringIO()
parameters = {'threads':None, 'kmer':13,
'unmapped_fhand':unmapped_fhand}
map_reads_with_gmap(temp_genome, reads_fpath, out_bam_fhand.name,
parameters)
sam_fhand = NamedTemporaryFile(suffix='.sam')
bam2sam(out_bam_fhand.name, sam_fhand.name, header=True)
result = open(sam_fhand.name).read()
assert exists(out_bam_fhand.name)
assert '36M2I204M' in result
assert 'SN:SL2.30ch00' in result
assert 'seq9_rev_MOD' in result
assert '?????????????????' in result
work_dir.close()
out_bam_fhand.close()
sam_fhand.close()