#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def cufflinks_ncRNA(sample, cufflinks_ncRNA_flag):
'''Runs cufflinks to assemble .bam files from TopHat. Takes parameters LNCRNA_GTF and NONCODE_FASTA.
input:
accepted_hits.bam
output:
transcripts.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:
TOPHAT_RESULTS:
CUFFLINKS_RESULTS:
LNCRNA_GTF:
NONCODE_FASTA:
CUFFLINKS_OPTIONS:
CUFFLINKS_VERSION:
'''
spawn_job(jobname = 'cufflinks_ncRNA', SAMPLE = sample, 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 = "/cufflinks_drmaa.sh", args_list = [sample,p.TOPHAT_RESULTS,p.CUFFLINKS_RESULTS,p.LNCRNA_GTF,p.NONCODE_FASTA,p.CUFFLINKS_OPTIONS,p.CUFFLINKS_VERSION])
job_status(jobname = 'cufflinks_ncRNA', resultspath = p.CUFFLINKS_RESULTS, SAMPLE = sample, outputfilename = sample + "/transcripts.gtf", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
cufflinks_ncRNA(sample, cufflinks_ncRNA_flag)
sys.exit(0)