Source code for omics_pipe.modules.RNAseq_QC

#!/usr/bin/env python

from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)

[docs]def RNAseq_QC(sample, RNAseq_QC_flag): '''Runs rseqc to determine insert size as QC for alignment. input: .bam output: pdf plot link: http://rseqc.sourceforge.net/ parameters from parameters file: STAR_RESULTS: QC_PATH: BAM_FILE_NAME: RSEQC_REF: RSEQC_VERSION: TEMP_DIR: PICARD_VERSION: ''' spawn_job(jobname = 'RNAseq_QC', SAMPLE = sample, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, walltime = "240:00:00", queue = p.QUEUE, nodes = 1, ppn = 8, memory = "16gb", script = "/RNAseq_QC.sh", args_list = [p.STAR_RESULTS, p.QC_PATH, p.BAM_FILE_NAME, p.RSEQC_REF, p.RSEQC_VERSION, p.TEMP_DIR, sample, p.PICARD_VERSION]) job_status(jobname = 'RNAseq_QC', resultspath = p.QC_PATH, SAMPLE = sample, outputfilename = sample + "/insert_size.inner_distance_plot.pdf", FLAG_PATH = p.FLAG_PATH) return
if __name__ == '__main__': RNAseq_QC(sample, RNAseq_QC_flag) sys.exit(0)