def test_merge_sam():
'It merges two sams'
reference = NamedTemporaryFile(suffix='.sam')
reference.write('''>SGN-U572743
atatata
>SGN-U576692
gcgc''')
sam1 = NamedTemporaryFile(suffix='.sam')
sam1.write('''@SQ SN:SGN-U576692 LN:1714
@SQ SN:SGN-U572743 LN:833
@RG ID:g1 LB:g1 SM:g1
@RG ID:g2 LB:g2 SM:g2
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 RG:Z:g2
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 RG:Z:g1
''')
sam1.flush()
sam2 = NamedTemporaryFile(suffix='.sam')
sam2.write('''@SQ SN:SGN-U576692 LN:1714
@SQ SN:SGN-U572743 LN:833
@RG ID:g1 LB:g1 SM:g1
@RG ID:g3 LB:g3 SM:g3
SGN-E200000 0 SGN-U572743 317 226 254M24S * 0 0 GGATGATCTTAGAGKTGCCATTCAAAAGATGTTAGACACTCCTGGGCCATACTTGTTGGATGTGATTGTACCTCATCAGGAGCATGTTCTACCGATGATTCCCAGTGGCGGTGCTTTCAAAAATGTGATTACGGAGGGTGATGGGAGACGTTCCTATTGACTTTGAGAAGCTACATAACTAGTTCAAGGCATTGTATTATCTAAAATAAACTTAATATTTATGTTTACTTAAAAGTTTTTCATTGTGTGAAGGAAAAAAAAAAAAAAAAAAAAAAAAA 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 RG:Z:g1
SGN-E40000 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 RG:Z:g3
''')
sam2.flush()
sam3 = NamedTemporaryFile(suffix='.sam')
merge_sam(infiles=[sam1, sam2], outfile=sam3, reference=reference)
sam3.seek(0)
sam3_content = sam3.read()
assert 'SN:SGN-U572743' in sam3_content
assert 'SGN-E200000' in sam3_content
assert 'SGN-E221664' in sam3_content
def main():
'The script itself'
#set parameters
work_dir, output, reference = set_parameters()
# make a working tempfir
temp_dir = NamedTemporaryDir()
# add readgroup tag to each alignment in bam
add_header_and_tags_bams(work_dir, temp_dir.name)
# Prepare files to merge
sams = get_opened_sams_from_dir(temp_dir.name)
temp_sam = NamedTemporaryFile()
# merge all the sam in one
merge_sam(sams, temp_sam, reference)
# 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
sort_bam_sam(temp_bam.name, output)
# and make and index of the bam
call(['samtools', 'index', output], raise_on_error=True)
temp_dir.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})
