#!/usr/local/bin/python # collect RPKM values across the supplied tissues and store in a table import pseudogenes import sys, getopt root = "/zhang/ptonner/pseudo_rp/" tissueLocation = root + "tables/rpkm/" opts, args = getopt.getopt(sys.argv[1:], "") tissues = args[0].split(",") genes = pseudogenes.load_all() geneDict = {} table = {} for tissue in tissues: ifile = open(tissueLocation + tissue + ".rpkm.txt") for line in ifile.readlines(): split = line.split() ident = split[3] rpkm = split[6] if ident not in table: table[ident] = dict() table[ident][tissue] = float(rpkm) for gene in genes: geneDict[gene.pseudogeneID] = gene
from fileconversion import efficientFileRead from bash import runCommand from samtools import samtoolsViewRegions from pseudogenes import load_all if __name__ == "__main__": inSam = False outSam = False opts, args = getopt(sys.argv[1:], "sS") if len(args) < 2: print "usage: samtoolsViewPseudogenes.py infile outfile" sys.exit() filename = args[0] outfile = args[1] for opt, val in opts: if opt == "-s": inSam = True elif opt == "-S": outSam = True pseudogenes = load_all() viewString = "" for pseudogene in pseudogenes: viewString += pseudogene.chrom + ":" + str(pseudogene.start) + "-" + str(pseudogene.end) + " " viewString = viewString[:-1] samtoolsViewRegions(filename, outfile, viewString)