#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def htseq_miRNA(sample, htseq_miRNA_flag):
'''Runs htseq-count to get raw count data from alignments.
input:
Aligned.out.sort.bam
output:
counts.txt
citation:
Simon Anders, EMBL
link:
http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
parameters from parameters file:
TOPHAT_RESULTS:
HTSEQ_OPTIONS:
miRNA_GFF:
HTSEQ_RESULTS:
TEMP_DIR:
SAMTOOLS_VERSION:
BAM_FILE_NAME:
'''
spawn_job(jobname = 'htseq_miRNA', 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 = "/htseq_drmaa.sh", args_list = [sample,p.TOPHAT_RESULTS,p.HTSEQ_OPTIONS,p.miRNA_GFF,p.HTSEQ_RESULTS,p.TEMP_DIR,p.SAMTOOLS_VERSION, p.BAM_FILE_NAME, p.PYTHON_VERSION])
job_status(jobname = 'htseq_miRNA', resultspath = p.HTSEQ_RESULTS, SAMPLE = sample, outputfilename = sample + "_counts.txt", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
htseq_miRNA(sample, htseq_miRNA_flag)
sys.exit(0)