def macs2_call_chipseq_peak_job(signal_samples, control_samples, output_dir,
name):
"""
Call ChIP-seq peaks with MACS2 in a slurm job.
:param list signal_samples: Signal Sample objects.
:param list control_samples: Background Sample objects.
:param list output_dir: Parent directory where MACS2 outputs will be stored.
:param str name: Name of the MACS2 comparison being performed.
"""
from pypiper.ngstk import NGSTk
import textwrap
tk = NGSTk()
output_path = os.path.join(output_dir, name)
if not os.path.exists(output_path):
os.mkdir(output_path)
job_name = "macs2_{}".format(name)
# Build job script
# slurm header
cmd = tk.slurm_header(job_name,
os.path.join(output_path, job_name + ".log"),
cpus_per_task=4)
# load macs2
cmd += """
\t\t/home/arendeiro/.local/bin/macs2 callpeak -t {0} -c {1} -n {2} --outdir {3}
""".format(" ".join([s.mapped for s in signal_samples]),
" ".join([s.mapped for s in control_samples]), name, output_path)
# Slurm footer
cmd += "\t\t" + tk.slurm_footer() + "\n"
# Write job to file
job_file = os.path.join(output_path, name + ".sh")
with open(job_file, "w") as handle:
handle.write(textwrap.dedent(cmd))
# Submit
tk.slurm_submit_job(job_file)
def homer_call_chipseq_peak_job(signal_samples, control_samples, output_dir,
name):
"""
Call ChIP-seq peaks with MACS2 in a slurm job.
:param list signal_samples: Signal Sample objects.
:param list control_samples: Background Sample objects.
:param list output_dir: Parent directory where MACS2 outputs will be stored.
:param str name: Name of the MACS2 comparison being performed.
"""
from pypiper.ngstk import NGSTk
import textwrap
tk = NGSTk()
output_path = os.path.join(output_dir, name)
if not os.path.exists(output_path):
os.mkdir(output_path)
job_name = "homer_findPeaks_{}".format(name)
# Build job script
# slurm header
cmd = tk.slurm_header(job_name,
os.path.join(output_path, job_name + ".log"),
cpus_per_task=4)
# make tag directory for the signal samples
signal_tag_directory = os.path.join(output_dir,
"homer_tag_dir_" + name + "_signal")
cmd += """
\t\tmakeTagDirectory {0} {1}
""".format(signal_tag_directory,
" ".join([s.filtered for s in signal_samples]))
# make tag directory for the background samples
background_tag_directory = os.path.join(
output_dir, "homer_tag_dir_" + name + "_background")
cmd += """
\t\tmakeTagDirectory {0} {1}
""".format(background_tag_directory,
" ".join([s.filtered for s in control_samples]))
# call peaks
output_file = os.path.join(output_dir, name,
name + "_homer_peaks.factor.narrowPeak")
if not os.path.exists(os.path.join(output_dir, name)):
os.makedirs(os.path.join(output_dir, name))
cmd += """
\t\tfindPeaks {signal} -style factor -o {output_file} -i {background}
""".format(output_file=output_file,
background=background_tag_directory,
signal=signal_tag_directory)
output_file = os.path.join(output_dir, name,
name + "_homer_peaks.histone.narrowPeak")
if not os.path.exists(os.path.join(output_dir, name)):
os.makedirs(os.path.join(output_dir, name))
cmd += """
\t\tfindPeaks {signal} -style histone -o {output_file} -i {background}
""".format(output_file=output_file,
background=background_tag_directory,
signal=signal_tag_directory)
# Slurm footer
cmd += "\t\t" + tk.slurm_footer() + "\n"
# Write job to file
job_file = os.path.join(output_path, name + ".sh")
with open(job_file, "w") as handle:
handle.write(textwrap.dedent(cmd))
# Submit
tk.slurm_submit_job(job_file)