#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def cuffdiff_miRNA(step, cuffdiff_miRNA_flag):
'''Runs Cuffdiff to perform differential expression. Runs after Cufflinks. Part of Tuxedo Suite.
input:
.bam files
output:
differential expression results
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:
CUFFDIFF_RESULTS:
GENOME:
CUFFDIFF_OPTIONS:
CUFFMERGE_RESULTS:
CUFFDIFF_INPUT_LIST_COND1:
CUFFDIFF_INPUT_LIST_COND2:
CUFFLINKS_VERSION:
'''
spawn_job(jobname = 'cuffdiff_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 = "/cuffdiff_drmaa.sh", args_list = [p.CUFFDIFF_RESULTS,p.GENOME,p.CUFFDIFF_OPTIONS,p.CUFFMERGE_RESULTS, p.CUFFDIFF_INPUT_LIST_COND1, p.CUFFDIFF_INPUT_LIST_COND2, p.CUFFLINKS_VERSION])
job_status(jobname = 'cuffdiff_miRNA', resultspath = p.CUFFDIFF_RESULTS, SAMPLE = step, outputfilename = "gene_exp.diff", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
cuffdiff_miRNA(step, cuffdiff_miRNA_flag)
sys.exit(0)