7 from cistematic.genomes import Genome
8 from commoncode import getMergedRegions, getFeaturesByChromDict
10 print "%s: version 1.1" % sys.argv[0]
18 print "usage: python %s genome [acceptFile] gid outfile\n" % argv[0]
27 acceptFileName = argv[2]
31 listGeneFeatures(genome, gid, outfile, acceptFileName)
34 def listGeneFeatures(genome, gid, outFileName, acceptFileName=""):
36 outfile = open(outFileName, "w")
38 additionalDict = getMergedRegions(acceptFileName, maxDist = 0, keepLabel = True, verbose = True)
42 featuresDict = getFeaturesByChromDict(hg, additionalDict, restrictList=[gid])
43 outfile.write('track name="LOC%s"\n' % gid)
45 senseDict = {"F": "+",
51 for chrom in featuresDict:
52 for (start, stop, fgid, sense, ftype) in featuresDict[chrom]:
53 outfile.write("chr%s\t%d\t%d\t%s\t0\t%s\n" % (chrom, start, stop, ftype, senseDict[sense]))
58 if __name__ == "__main__":