#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def find_motifs(step, find_motifs_flag):
'''Runs HOMER to find motifs from ChIPseq data.
input:
.txt peak file from Homer
output:
.txt file
citation:
Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432
link:
http://homer.salk.edu/homer/
parameters from parameters file:
PAIR_LIST:
HOMER_RESULTS:
HOMER_VERSION:
TEMP_DIR:
HOMER_GENOME:
HOMER_MOTIFS_OPTIONS:
'''
spawn_job(jobname = 'find_motifs', SAMPLE = step, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "240:00:00", queue = p.QUEUE, nodes = 1, ppn = 8, memory = "15gb", script = "/find_motifs.sh", args_list = [p.PAIR_LIST, p.HOMER_RESULTS, p.HOMER_VERSION, p.TEMP_DIR, p.HOMER_GENOME, p.HOMER_MOTIFS_OPTIONS])
job_status(jobname = 'find_motifs', resultspath = p.HOMER_RESULTS, SAMPLE = step, outputfilename = "*_MotifOutput/knownResults.txt", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
find_motifs(step, find_motifs_flag)
sys.exit(0)