| |
|
|
| import sys |
| import math |
| import os.path |
|
|
| import Script |
|
|
| |
|
|
| def usage(): |
| progname = os.path.split(sys.argv[0])[1] |
| sys.stderr.write("""{} - Analyze intron retention. |
| |
| Usage: {} [options] intronsdb |
| |
| Options: |
| -i1 FILE | Name of BED file for introns in sample 1 (required) |
| -i2 FILE | Name of BED file for introns in sample 2 (required) |
| -j1 FILE | Name of BED file for junctions in sample 1 |
| -j2 FILE | Name of BED file for junctions in sample 2 |
| -o FILE | Set output file to FILE (default: stdout) |
| -fc F | Set fold change threshold to F (default: {}) |
| -t T | Set coverage threshold to T (default: {}) |
| |
| """.format(progname, progname, Params.fc, Params.thr)) |
|
|
| P = Script.Script("compareIntrons", version="1.0", usage=usage) |
|
|
| def readBEDfile(bedfile): |
| dict = {} |
| sys.stderr.write("Reading `{}'... ".format(bedfile)) |
| with open(bedfile, "r") as f: |
| for line in f: |
| parsed = line.rstrip("\r\n").split("\t") |
| dict[parsed[3]] = float(parsed[7]) |
| sys.stderr.write("done, {} entries.\n".format(len(dict))) |
| return dict |
|
|
| def dget(key, dict): |
| if key in dict: |
| return dict[key] |
| else: |
| return 0.0 |
|
|
| class Params(): |
| bedfile = None |
| introns1file = None |
| juncs1file = None |
| introns2file = None |
| juncs2file = None |
| outfile = None |
| fc = 1 |
| thr = 0.00001 |
| intr1 = {} |
| junc1 = {} |
| intr2 = {} |
| junc2 = {} |
|
|
| def __init__(self): |
| self.intr1 = {} |
| self.junc1 = {} |
| self.intr2 = {} |
| self.junc2 = {} |
|
|
| def parseArgs(self, args): |
| P.standardOpts(args) |
| next = "" |
| for a in args: |
| if next == "-i1": |
| self.introns1file = P.isFile(a) |
| next = "" |
| elif next == "-j1": |
| self.juncs1file = P.isFile(a) |
| next = "" |
| elif next == "-i2": |
| self.introns2file = P.isFile(a) |
| next = "" |
| elif next == "-j2": |
| self.juncs2file = P.isFile(a) |
| next = "" |
| elif next == "-o": |
| self.outfile = a |
| next = "" |
| elif next == "-fc": |
| self.fc = P.toFloat(a) |
| next = "" |
| elif next == "-t": |
| self.thr = P.toFloat(a) |
| next = "" |
| elif a in ["-i1", "-j1", "-i2", "-j2", "-fc", "-o", "-t"]: |
| next = a |
| else: |
| self.bedfile = a |
| if self.bedfile == None or self.introns1file == None or self.introns2file == None: |
| P.errmsg(P.NOFILE) |
| |
| def readFiles(self): |
| self.intr1 = readBEDfile(self.introns1file) |
| if self.juncs1file != None: |
| self.juncs1 = readBEDfile(self.juncs1file) |
| self.intr2 = readBEDfile(self.introns2file) |
| if self.juncs2file != None: |
| self.juncs2 = readBEDfile(self.juncs2file) |
|
|
| def compare(self, out): |
| nin = 0 |
| nup = 0 |
| ndown = 0 |
| maxup = 0 |
| maxdn = 0 |
| with open(self.bedfile, "r") as f: |
| for line in f: |
| nin += 1 |
| parsed = line.rstrip("\r\n").split("\t") |
| intron = parsed[3] |
| gene = parsed[4] |
| sp = intron.split("_") |
| tx = sp[0] |
| intid = sp[1] |
| iv1 = dget(intron, self.intr1) |
| iv2 = dget(intron, self.intr2) |
| if self.juncs1file: |
| iv1 = (iv1 + dget(intron + "_a", self.juncs1) + dget(intron + "_b", self.juncs1)) / 3.0 |
| if self.juncs2file: |
| iv2 = (iv2 + dget(intron + "_a", self.juncs2) + dget(intron + "_b", self.juncs2)) / 3.0 |
|
|
| if iv1 == 0 and iv2 == 0: |
| pass |
| elif iv1 == 0: |
| if iv2 >= self.thr: |
| out.write("{}\t{}\t{}\t{}\t{}\t{}\n".format(gene, tx, intid, iv1, iv2, "+inf")) |
| elif iv2 == 0: |
| if iv1 >= self.thr: |
| out.write("{}\t{}\t{}\t{}\t{}\t{}\n".format(gene, tx, intid, iv1, iv2, "-inf")) |
| else: |
| l2fc = math.log(iv2/iv1, 2) |
| if abs(l2fc) > self.fc: |
| out.write("{}\t{}\t{}\t{}\t{}\t{}\n".format(gene, tx, intid, iv1, iv2, l2fc)) |
| if l2fc > 0: |
| nup += 1 |
| if l2fc > maxup: |
| maxup = l2fc |
| else: |
| ndown += 1 |
| if l2fc < maxdn: |
| maxdn = l2fc |
| return (nin, nup, ndown, maxup, maxdn) |
|
|
| if __name__ == "__main__": |
| PA = Params() |
| PA.parseArgs(sys.argv[1:]) |
| PA.readFiles() |
| if PA.outfile: |
| with open(PA.outfile, "w") as out: |
| (nin, nup, ndown, maxup, maxdn) = PA.compare(out) |
| else: |
| (nin, nup, ndown, maxup, maxdn) = PA.compare(sys.stdout) |
|
|
| sys.stderr.write("{}\t{}\t{}\t{}\t{}\n".format(nin, nup, ndown, maxup, maxdn)) |
|
|
