#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def read_density(sample, read_density_flag):
'''Runs HOMER to visualize read density from ChIPseq data.
input:
.bam file
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:
BOWTIE_RESULTS:
CHROM_SIZES:
HOMER_RESULTS:
HOMER_VERSION:
TEMP_DIR:
'''
spawn_job(jobname = 'read_density', SAMPLE = sample, 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 = "/read_density.sh", args_list = [sample, p.BOWTIE_RESULTS, p.CHROM_SIZES, p.HOMER_RESULTS, p.HOMER_VERSION, p.TEMP_DIR])
job_status(jobname = 'read_density', resultspath = p.HOMER_RESULTS, SAMPLE = sample, outputfilename = sample + "/" + sample + "_trackInfo.txt", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
read_density(sample, read_density_flag)
sys.exit(0)