def run(name, chip_bam, input_bam, genome_build, out_dir, method, resources,
data):
"""
Run macs2 for chip and input samples avoiding
errors due to samples.
"""
# output file name need to have the caller name
config = dd.get_config(data)
out_file = os.path.join(out_dir, name + "_peaks_macs2.xls")
macs2_file = os.path.join(out_dir, name + "_peaks.xls")
if utils.file_exists(out_file):
_compress_and_sort_bdg_files(out_dir, data)
return _get_output_files(out_dir)
macs2 = config_utils.get_program("macs2", config)
antibody = dd.get_antibody(data)
if antibody:
antibody = antibody.lower()
if antibody not in antibodies.SUPPORTED_ANTIBODIES:
logger.error(
f"{antibody} specified, but not listed as a supported antibody. Valid antibodies are {antibodies.SUPPORTED_ANTIBODIES}. If you know your antibody "
f"should be called with narrow or broad peaks, supply 'narrow' or 'broad' as the antibody."
f"It will run 'narrow' if the antibody is not supported.")
antibody = 'narrow'
antibody = antibodies.ANTIBODIES[antibody]
logger.info(
f"{antibody.name} specified, using {antibody.peaktype} peak settings."
)
peaksettings = select_peak_parameters(antibody)
elif method == "atac":
logger.info(f"ATAC-seq specified, using narrow peak settings.")
peaksettings = " "
else:
peaksettings = " "
options = " ".join(resources.get("macs2", {}).get("options", ""))
genome_size = bam.fasta.total_sequence_length(dd.get_ref_file(data))
genome_size = "" if options.find("-g") > -1 else "-g %s" % genome_size
paired = "-f BAMPE" if bam.is_paired(chip_bam) else ""
with utils.chdir(out_dir):
cmd = _macs2_cmd(data)
cmd += peaksettings
try:
do.run(cmd.format(**locals()), "macs2 for %s" % name)
utils.move_safe(macs2_file, out_file)
except subprocess.CalledProcessError:
raise RuntimeWarning(
"macs2 terminated with an error. "
"Please, check the message and report "
"error if it is related to bcbio. "
"You can add specific options for the sample "
"setting resources as explained in docs: "
"https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#sample-specific-resources"
)
_compress_and_sort_bdg_files(out_dir, data)
return _get_output_files(out_dir)
def run(name, chip_bam, input_bam, genome_build, out_dir, method, resources,
data):
"""
Run macs2 for chip and input samples avoiding
errors due to samples.
"""
# output file name need to have the caller name
config = dd.get_config(data)
out_file = os.path.join(out_dir, name + "_peaks_macs2.xls")
macs2_file = os.path.join(out_dir, name + "_peaks.xls")
if utils.file_exists(out_file):
_compress_bdg_files(out_dir)
return _get_output_files(out_dir)
macs2 = config_utils.get_program("macs2", config)
antibody = antibodies.ANTIBODIES.get(dd.get_antibody(data).lower(), None)
if antibody:
logger.info(
f"{antibody.name} specified, using {antibody.peaktype} peak settings."
)
peaksettings = select_peak_parameters(antibody)
else:
peaksettings = ""
options = " ".join(resources.get("macs2", {}).get("options", ""))
genome_size = bam.fasta.total_sequence_length(dd.get_ref_file(data))
genome_size = "" if options.find("-g") > -1 else "-g %s" % genome_size
paired = "-f BAMPE" if bam.is_paired(chip_bam) else ""
with utils.chdir(out_dir):
cmd = _macs2_cmd(data)
cmd += peaksettings
try:
do.run(cmd.format(**locals()), "macs2 for %s" % name)
utils.move_safe(macs2_file, out_file)
except subprocess.CalledProcessError:
raise RuntimeWarning(
"macs2 terminated with an error.\n"
"Please, check the message and report "
"error if it is related to bcbio.\n"
"You can add specific options for the sample "
"setting resources as explained in docs: "
"https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#sample-specific-resources"
)
_compress_bdg_files(out_dir)
return _get_output_files(out_dir)