def bamsam_converter(input_fhand, output_fhand, java_conf=None):
'Converts between sam and bam'
picard_path = guess_jar_dir('SortSam.jar', java_conf)
picard_jar = os.path.join(picard_path, 'SamFormatConverter.jar')
cmd = java_cmd(java_conf)
cmd.extend(['-jar', picard_jar, 'INPUT=' + input_fhand,
'OUTPUT=' + output_fhand])
call(cmd, raise_on_error=True, add_ext_dir=False)
def realign_bam(bam_fpath, reference_fpath, out_bam_fpath, java_conf=None,
threads=False, tmp_dir=None):
'It realigns the bam using GATK Local realignment around indels'
#reference sam index
create_sam_reference_index(reference_fpath)
#reference picard dict
create_picard_dict(reference_fpath, java_conf=java_conf)
#bam index
create_bam_index(bam_fpath)
#the intervals to realign
gatk_path = guess_jar_dir('GenomeAnalysisTK.jar', java_conf)
gatk_jar = os.path.join(gatk_path, 'GenomeAnalysisTK.jar')
intervals_fhand = tempfile.NamedTemporaryFile(suffix='.intervals')
cmd = java_cmd(java_conf=java_conf)
cmd.extend(['-jar', gatk_jar, '-T', 'RealignerTargetCreator',
'-I', bam_fpath, '-R', reference_fpath, '-o', intervals_fhand.name])
#according to GATK this is experimental, so it might be a good idea to
#do it in just one thread. In version 1.0.4498. This options is removed
# so parallel = False
parallel = False
if parallel and threads and threads > 1:
cmd.extend(['-nt', str(get_num_threads(threads))])
call(cmd, raise_on_error=True, add_ext_dir=False)
#the realignment itself
unsorted_bam = NamedTemporaryFile(suffix='.bam')
cmd = java_cmd(java_conf=java_conf)
cmd.extend(['-Djava.io.tmpdir=%s' % tempfile.gettempdir(),
'-jar', gatk_jar, '-I', bam_fpath, '-R', reference_fpath,
'-T', 'IndelRealigner', '-targetIntervals', intervals_fhand.name,
'-o', unsorted_bam.name])
if parallel and threads and threads > 1:
cmd.extend(['-nt', str(get_num_threads(threads))])
call(cmd, raise_on_error=True, add_ext_dir=False)
# now we have to realign the bam
sort_bam_sam(unsorted_bam.name, out_bam_fpath, java_conf=java_conf,
tmp_dir=tmp_dir)
def sort_bam_sam(in_fpath, out_fpath, sort_method='coordinate',
java_conf=None, tmp_dir=None, strict_validation=True):
'It sorts a bam file using picard'
picard_path = guess_jar_dir('SortSam.jar', java_conf)
picard_sort_jar = os.path.join(picard_path, 'SortSam.jar')
java_cmd_ = java_cmd(java_conf)
java_cmd_.extend(['-jar', picard_sort_jar, 'INPUT=' + in_fpath,
'OUTPUT=' + out_fpath, 'SORT_ORDER=' + sort_method])
if not strict_validation:
java_cmd_.append('VALIDATION_STRINGENCY=LENIENT')
if tmp_dir:
java_cmd_.append('TMP_DIR=%s' % tmp_dir)
stdout, stderr, retcode = call(java_cmd_, raise_on_error=False, add_ext_dir=False)
err_msg = 'No space left on device'
if retcode and (err_msg in stdout or err_msg in stderr):
raise RuntimeError('Picard sort consumed all space in device.' + stderr)
elif retcode:
msg = 'Error running picard: %s\n stderr: %s\n stdout: %s' % \
(' '.join(java_cmd_), stderr,
stdout)
raise RuntimeError(msg)