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_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
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()
def testsam2bam():
'It test sam2bam function'
bampath = os.path.join(TEST_DATA_DIR, 'seq.bam')
sampath = NamedTemporaryFile(suffix='.sam').name
bam2sam(bampath, sampath, header=True)
assert 'SN:SGN-U572743' in open(sampath).readline()
newbam = NamedTemporaryFile(suffix='.bam')
sam2bam(sampath, newbam.name)
newsam = NamedTemporaryFile(suffix='.sam')
bam2sam(newbam.name, newsam.name, header=True)
newsam_content = open(newsam.name).read()
oldsam_content = open(sampath).read()
assert newsam_content == oldsam_content
def test_sample_bam():
'it tests sample bam function'
sam = NamedTemporaryFile(suffix='.sam')
sam.write(SAM)
sam.flush()
bam_fhand = NamedTemporaryFile()
sam2bam(sam.name, bam_fhand.name)
bam_fhand.flush()
out_bam = NamedTemporaryFile(suffix='.bam')
sample_bam(bam_fhand, out_bam, 2)
out_sam = NamedTemporaryFile(suffix='.sam')
bam2sam(out_bam.name, out_sam.name, header=True)
sam = open(out_sam.name).read().splitlines()
assert len(sam) == 6
def test_sam_creator():
'It test sam creator'
alignement = '''ref\taggttttataaaacAAAAaattaagtctacagag-caacta
sample\taggttttataaaacAAA-aattaagtctacagagtcaacta
read\taggttttataaaacAA-Aaattaagtctacagagtcaacta
read\taggttttataaaacA-AAaattaagtctacagagtcaacta
read\taggttttataaaac-AAAaattaagtctacagagtcaacta'''
fhand = StringIO(alignement)
out_bam_fhand = NamedTemporaryFile(suffix = '.bam')
out_ref_fhand = NamedTemporaryFile(suffix = '.fasta')
sam_creator(fhand, out_bam_fhand.name, out_ref_fhand.name)
ref = open(out_ref_fhand.name).read()
assert '>ref\naggttttataaaacAAAAaattaagtctacagagcaacta' in ref
out_sam_fhand = NamedTemporaryFile(suffix = '.sam')
bam2sam(out_bam_fhand.name, out_sam_fhand.name)
bam = open(out_sam_fhand.name).read()
assert '16M1D17M1I6M' in bam
assert '15M1D18M1I6M' in bam
assert '14M1D19M1I6M' in bam
alignement = '''ref\taggttttataaaac----aattaagtctacagagcaacta
sample\taggttttataaaacAAATaattaagtctacagagcaacta
read\taggttttataaaac****aaAtaa
read1\t ggttttataaaac****aaAtaaTt
read2\t ttataaaacAAATaattaagtctaca
read3\t CaaaT****aattaagtctacagagcaac
read4\t aaT****aattaagtctacagagcaact
read5\t T****aattaagtctacagagcaacta'''
fhand = StringIO(alignement)
out_bam_fhand = NamedTemporaryFile(suffix = '.bam')
out_ref_fhand = NamedTemporaryFile(suffix = '.fasta')
sam_creator(fhand, out_bam_fhand.name, out_ref_fhand.name)
out_sam_fhand = NamedTemporaryFile(suffix = '.sam')
bam2sam(out_bam_fhand.name, out_sam_fhand.name)
bam = open(out_sam_fhand.name).read()
assert 'AGGTTTTATAAAACAAATA' in bam
assert '20M' in bam
def add_header_and_tags_bams(work_dir, output_dir):
'it adds readgroupto bams and return added reaadgroups'
#add to each of the bams the readgroup_tag
for bam in os.listdir(work_dir):
if bam.endswith('.bam'):
#get the readgroup from the name:
prefix = ".".join(bam.split('.')[:-1])
sam = open(os.path.join(output_dir, prefix + '.sam'), 'w')
temp_sam = NamedTemporaryFile(prefix='%s.' % prefix , suffix='.sam')
bam2sam(os.path.join(work_dir, bam), temp_sam.name)
add_header_and_tags_to_sam(temp_sam, sam)
# close and remove temporal stuff
sam.close()
temp_sam.close()
def test_remove_unmapped_reads():
'Tests remove_unmapped_reads'
sam = NamedTemporaryFile(suffix='.sam')
sam.write(SAM)
sam.flush()
bam_fhand = NamedTemporaryFile()
sam2bam(sam.name, bam_fhand.name)
out_bam_fhand = NamedTemporaryFile()
out_removed_reads_fhand = NamedTemporaryFile()
remove_unmapped_reads(bam_fhand, out_bam_fhand, out_removed_reads_fhand)
reads = open(out_removed_reads_fhand.name).read()
assert '@SGN-E221406' in reads
assert 'FFMMMJJ@@755225889>0.' in reads
out_sam = NamedTemporaryFile(suffix='.sam')
bam2sam(out_bam_fhand.name, out_sam.name, header=True)
sam_out = open(out_sam.name).read()
assert 'SGN-U572743' in sam_out
assert 'SGN-E221403' in sam_out
def testbam2sam():
'It test bam2sam function'
bampath = os.path.join(TEST_DATA_DIR, 'seq.bam')
sampath = NamedTemporaryFile(suffix='.sam').name
bam2sam(bampath, sampath, header=True)
assert 'SN:SGN-U572743' in open(sampath).readline()
def run(self):
'''It runs the analysis.'''
self._log({'analysis_started':True})
settings = self._project_settings
project_path = settings['General_settings']['project_path']
tmp_dir = settings['General_settings']['tmpdir']
inputs = self._get_input_fpaths()
bam_paths = inputs['bams']
reference_path = inputs['reference']
output_dir = self._create_output_dirs()['result']
merged_bam_path = VersionedPath(os.path.join(output_dir,
BACKBONE_BASENAMES['merged_bam']))
merged_bam_fpath = merged_bam_path.next_version
#Do we have to add the default qualities to the sam file?
#do we have characters different from ACTGN?
add_qualities = settings['Sam_processing']['add_default_qualities']
#memory for the java programs
java_mem = settings['Other_settings']['java_memory']
picard_path = settings['Other_settings']['picard_path']
if add_qualities:
default_sanger_quality = settings['Other_settings']['default_sanger_quality']
default_sanger_quality = int(default_sanger_quality)
else:
default_sanger_quality = None
temp_dir = NamedTemporaryDir()
for bam_path in bam_paths:
bam_basename = bam_path.basename
temp_sam = NamedTemporaryFile(prefix='%s.' % bam_basename,
suffix='.sam')
sam_fpath = os.path.join(temp_dir.name, bam_basename + '.sam')
bam2sam(bam_path.last_version, temp_sam.name)
sam_fhand = open(sam_fpath, 'w')
# First we need to create the sam with added tags and headers
add_header_and_tags_to_sam(temp_sam, sam_fhand)
temp_sam.close()
sam_fhand.close()
#the standardization
temp_sam2 = NamedTemporaryFile(prefix='%s.' % bam_basename,
suffix='.sam', delete=False)
standardize_sam(open(sam_fhand.name), temp_sam2,
default_sanger_quality,
add_def_qual=add_qualities,
only_std_char=True)
temp_sam2.flush()
shutil.move(temp_sam2.name, sam_fhand.name)
temp_sam2.close()
get_sam_fpaths = lambda dir_: [os.path.join(dir_, fname) for fname in os.listdir(dir_) if fname.endswith('.sam')]
# Once the headers are ready we are going to merge
sams = get_sam_fpaths(temp_dir.name)
sams = [open(sam) for sam in sams]
temp_sam = NamedTemporaryFile(suffix='.sam')
reference_fhand = open(reference_path.last_version)
try:
merge_sam(sams, temp_sam, reference_fhand)
except Exception:
if os.path.exists(merged_bam_fpath):
os.remove(merged_bam_fpath)
raise
reference_fhand.close()
# close files
for sam in sams:
sam.close()
# Convert sam into a bam,(Temporary)
temp_bam = NamedTemporaryFile(suffix='.bam')
sam2bam(temp_sam.name, temp_bam.name)
# finally we need to order the bam
#print 'unsorted.bam', temp_bam.name
#raw_input()
sort_bam_sam(temp_bam.name, merged_bam_fpath,
java_conf={'java_memory':java_mem,
'picard_path':picard_path}, tmp_dir=tmp_dir )
temp_bam.close()
temp_sam.close()
create_bam_index(merged_bam_fpath)
self._log({'analysis_finished':True})
