from gtfIO import GTFReader, GTFWriter
from optparse import OptionParser
parser = OptionParser()
parser.add_option("--input",
dest="input",
help="A gtf file containing the RepeatMasked gtf annotation")
parser.add_option("--minlen", dest="minleng", help="minimum length")
parser.add_option("--output", dest="output", help="A gtf output file")
parser.add_option("--maxdiv",
dest="maxdiv",
help="minimum length",
default=99999999999999999)
(options, args) = parser.parse_args()
minleng = int(options.minleng)
w = GTFWriter(options.output)
for e in GTFReader(options.input):
leng = (e.end - e.start) + 1
if (leng >= minleng):
if (e.score < float(options.maxdiv)):
w.write(e)
w.close()
help="A gtf file containing the reference annotation")
parser.add_option(
"--totest",
dest="totest",
help="A gtf file containing the annotation that should be tested")
parser.add_option(
"--output",
dest="output",
help=
"The output file containing novel TE insertions not in the reference genome"
)
(options, args) = parser.parse_args()
# chromosomes with incomplete reference annotation: 2L, 2R, 3L
# fine: 3R, X, 4
rawref = GTFReader.readall(options.reference)
rawtotest = GTFReader.readall(options.totest)
chref = convert_chrhash(rawref)
chtotest = convert_chrhash(rawtotest)
ofh = GTFWriter(options.output)
for chr in ["X", "2L", "2R", "3L", "3R", "4"]:
cref = chref[chr]
ctotest = chtotest[chr]
ne = novelentries(cref, ctotest)
for n in ne:
ofh.write(n)
ofh.close()
from gtfIO import GTFReader,GTFWriter;
import sys
import random
from optparse import OptionParser, OptionGroup
import collections
parser = OptionParser()
parser.add_option("--input",dest="input",help="A gtf file containing the RepeatMasked gtf annotation")
parser.add_option("--min-leng",dest="minleng",help="minimum length")
parser.add_option("--output",dest="output",help="A gtf output file")
(options, args) = parser.parse_args()
minleng=int(options.minleng)
w=GTFWriter(options.output)
for e in GTFReader(options.input):
leng=(e.end-e.start)+1
if(leng>=minleng):
w.write(e)
w.close()
# chromosomes with incomplete reference annotation: 2L, 2R, 3L # fine: 3R, X, 4 rawref=GTFReader.readall(options.reference) rawtotest=GTFReader.readall(options.totest) chref=convert_chrhash(rawref) chtotest=convert_chrhash(rawtotest) ofh=GTFWriter(options.output) for chr in ["X","2L","2R","3L","3R","4"]: cref=chref[chr] ctotest=chtotest[chr] ne=novelentries(cref,ctotest) for n in ne: ofh.write(n) ofh.close()
