#!/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)
