def estimateCopyNumber(infiles, outfile): '''Estimate copy numbers based on standard curves constructed from the spike-ins''' P.submit(os.path.join(code_dir, "PipelineScRnaseq.py"), "estimateCopyNumber", infiles=infiles, outfiles=outfile, params=[code_dir])
def splitPooledBamfiles(infile, sentinel): infile = P.snip(infile, ".sentinel") + ".bam" outfile = P.snip(sentinel, ".sentinel") params = '2' try: module = P.snip(IDR.__file__, ".py") except ValueError: module = P.snip(IDR.__file__, ".pyc") P.submit(module, "splitBam", params, infile, outfile) P.touch(sentinel)
def findNPeaksForPooledPseudoreplicates(infiles, outfile): idr_thresh = PARAMS["idr_options_pooled_consistency_threshold"] try: module = P.snip(IDR.__file__, ".py") except ValueError: module = P.snip(IDR.__file__, ".pyc") P.submit(module, "findNPeaks", params=[str(idr_thresh), ], infiles=infiles, outfiles=outfile)
def findNPeaksForIndividualReplicates(infiles, outfile): idr_thresh = PARAMS["idr_options_inter_replicate_threshold"] try: module = P.snip(IDR.__file__, ".py") except ValueError: module = P.snip(IDR.__file__, ".pyc") P.submit(module, "findNPeaks", params=[str(idr_thresh), ], infiles=infiles, outfiles=outfile)
def splitBamfiles(infile, sentinel): """ For all tracks, split the filtered bamfile in two using pysam """ infile = P.snip(infile, ".sentinel") + ".bam" outfile = P.snip(sentinel, ".sentinel") params = '2' try: module = P.snip(IDR.__file__, ".py") except ValueError: module = P.snip(IDR.__file__, ".pyc") P.submit(module, "splitBam", params, infile, outfile) P.touch(sentinel)