def test_readgroup_to_sam():
'It test that we can add the readgroup the and the header to a bam'
sam_value = '''@SQ SN:SGN-U576692 LN:1714
@SQ SN:SGN-U572743 LN:833
SGN-E221403 0 SGN-U576692 1416 207 168M * 0 0 AGCCTGATAAAGGTCTGCCTACGTGTTTTAAGTGGAATCCGTTTCCCCATGTCCAAACCTTCTAAATAGTTTTTTGTGTTAGTTCTTGTATGCCACATACAAAAATTAACAAACTCTTTTGCCACATATGTTCCAGCACGTCAAAGCAACATGTATTTGAGCTACTTT 558<///035EB@;550300094>>FBF>>88>BBB200>@FFMMMJJ@@755225889>0..14444::FMF@@764444448@;;84444<//,4,.,<<QFBB;::/,,,.69FBB>9:2/.409;@@>88.7,//55;BDK@11,,093777777884241<:7 AS:i:160 XS:i:0 XF:i:3 XE:i:4 XN:i:0
SGN-E221664 0 SGN-U572743 317 226 254M24S * 0 0 GGATGATCTTAGAGCTGCCATTCAAAAGATGTTAGACACTCCTGGGCCATACTTGTTGGATGTGATTGTACCTCATCAGGAGCATGTTCTACCGATGATTCCCAGTGGCGGTGCTTTCAAAAATGTGATTACGGAGGGTGATGGGAGACGTTCCTATTGACTTTGAGAAGCTACATAACTAGTTCAAGGCATTGTATTATCTAAAATAAACTTAATATTTATGTTTACTTAAAAGTTTTTCATTGTGTGAAGGAAAAAAAAAAAAAAAAAAAAAAAAA 999@7<22-2***-,206433>:?9<,,,66:>00066=??EEAAA?B200002<<@@@=DB99777864:..0::@833099???<@488>></...<:B<<.,,8881288@BBDDBD885@@;;9:/9.,,,99B99233885558=?DKKKDDAA??DKBB=440/0<8?DEDFBB??6@152@@FBMFIIDDDDDDKKKOK@@@@DD:N688BBDDDBBBKKDEDDBN977?<9<111:<??==BKMPKKBB==99>QQYYYYYYYYYYYYQQ AS:i:250 XS:i:0 XF:i:0 XE:i:7 XN:i:0
'''
insam = NamedTemporaryFile(prefix='lb_group1.', suffix='.sam')
insam.write(sam_value)
outsam = NamedTemporaryFile()
add_header_and_tags_to_sam(insam, outsam)
out_content = open(outsam.name).read()
assert 'RG:Z:group1' in out_content
assert 'SM:group1' in out_content
insam = NamedTemporaryFile(prefix='sm_sample1.lb_group1.', suffix='.sam')
insam.write(sam_value)
outsam = NamedTemporaryFile()
add_header_and_tags_to_sam(insam, outsam)
out_content = open(outsam.name).read()
#print out_content
assert 'RG:Z:sample1_group1' in out_content
assert 'SM:sample1' in out_content
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 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})
