def collect_and_write_peak_summary_stats(
peaks, motifs, fasta,
chipseq_reads,
atacseq_reads, histone_mark_reads,
frag_len, ofname):
proc_queue = multiprocessing.Queue()
for pk in peaks: proc_queue.put(pk)
# process a single peak so that we know what to name the columns
region = proc_queue.get()
peak = load_peak_region(
fasta,
region[0], max(0, region[1]-2*frag_len), region[2]+2*frag_len,
atacseq_reads, histone_mark_reads,
motifs,
chipseq_reads,
frag_len)
header, vals = peak.calc_summary_stats()
ofp = ProcessSafeOPStream(open(ofname, "w"))
args = [proc_queue, ofp, motifs, fasta,
chipseq_reads, atacseq_reads, histone_mark_reads, frag_len]
ofp.write("\t".join(header) + "\n")
ofp.write("\t".join(map(str, vals)) + "\n")
fork_and_wait(NTHREADS, process_peaks_worker, args)
# let the printing catch up
time.sleep(0.1)
ofp.close()
def main():
motifs, fasta, peaks = parse_arguments()
peak_cntr = Counter()
#output_fname = 'predictors.E116_E117_E118.CTCF_REST.txt'
#output_fname = 'SELEX.output.txt'
output_fname = 'SELEX.predictors.YY1.txt'
header, stats = load_summary_stats(peaks[100][1], fasta, motifs)
with ThreadSafeFile(output_fname, 'w') as ofp:
ofp.write("\t".join(header) + "\n")
fork_and_wait(NTHREADS, extract_data_worker, (ofp, peak_cntr, motifs, fasta, peaks))
def score_regions(ofp, genome, regions, motifs):
ofp.write("region".ljust(30) + " " + " ".join(
(motif.tf_name + "_" + motif.tf_species[0]).ljust(15)
for motif in motifs) + "\n")
regions_queue = multiprocessing.Queue()
regions_queue.cancel_join_thread()
for region in regions:
regions_queue.put(region)
fork_and_wait(36, score_regions_worker, (ofp, genome, regions_queue, motifs))
regions_queue.close()
def main():
genes = load_gtf(sys.argv[1])
reads = MergedReads([
RNAseqReads(fname).init(reads_are_stranded=False)
for fname in sys.argv[2:]
])
fl_dists = build_fl_dists_from_annotation(genes, reads)
genes_queue = multiprocessing.Queue()
for gene in genes:
genes_queue.put(gene)
with ThreadSafeFile("bins.gtf", "w") as ofp:
ofp.write("track type=gtf name=bin_expresion_test\n")
args = [genes_queue, reads, fl_dists, ofp]
fork_and_wait(24, build_transcripts_lines_worker, args)
return