#!/usr/bin/env python
import os
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def cuffmerge_miRNA(step, cuffmerge_miRNA_flag):
'''Runs cuffmerge to merge .gtf files from Cufflinks.
input:
assembly_GTF_list.txt
output:
merged.gtf
citation:
Trapnell C, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology doi:10.1038/nbt.1621
link:
http://cufflinks.cbcb.umd.edu/
parameters from parameters file:
CUFFMERGE_RESULTS:
miRNA_GTF:
GENOME:
CUFFMERGE_OPTIONS:
CUFFLINKS_VERSION:
'''
check_create_dir(p.CUFFMERGE_RESULTS)
f = open(p.CUFFMERGE_RESULTS + '/assembly_GTF_list.txt', 'w')
for sample in p.SAMPLE_LIST:
f.write(p.CUFFLINKS_RESULTS + "/" + sample + "/transcripts.gtf\n")
f.close()
gtf_list = p.CUFFMERGE_RESULTS + '/assembly_GTF_list.txt'
spawn_job(jobname = 'cuffmerge_miRNA', SAMPLE = step, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "120:00:00", queue = p.QUEUE, nodes = 1, ppn = 8, memory = "15gb", script = "/cuffmerge_drmaa.sh", args_list = [gtf_list,p.CUFFMERGE_RESULTS,p.miRNA_GTF,p.GENOME,p.CUFFMERGE_OPTIONS,p.CUFFLINKS_VERSION])
job_status(jobname = 'cuffmerge_miRNA', resultspath = p.CUFFMERGE_RESULTS, SAMPLE = step, outputfilename = "merged.gtf", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
cuffmerge_miRNA(step, cuffmerge_miRNA_flag)
sys.exit(0)