def simulateReads(bed12, bed12Fasta, explv, bedReads, faReads, readLength, readCount, seqError):
#output = shell(getBinary("gensimreads.py") + " -l " + str(readLength) + " -e " + explv + " -n " + str(readCount) + " -b " + rNASeqReadSimulatorPath + "demo/input/sampleposbias.txt --stranded " + bed12 + " > " + bedReads)
output = shell(getBinary("gensimreads.py") + " -l " + str(readLength) + " -e " + explv + " -n " + str(readCount) + " --stranded " + bed12 + " 2> /dev/null > " + bedReads)
if len(output.strip()) > 5:
print(output)
output = shell(getBinary("getseqfrombed.py") + " -f -r " + str(seqError) + " -l " + str(readLength) + " " + bedReads + " " + bed12Fasta + " 2> /dev/null > " + faReads)
if len(output.strip()) > 5:
print(output)
def simulateReads(bed12, bed12Fasta, explv, bedReads, faReads, readLength,
readCount, seqError):
#output = shell(getBinary("gensimreads.py") + " -l " + str(readLength) + " -e " + explv + " -n " + str(readCount) + " -b " + rNASeqReadSimulatorPath + "demo/input/sampleposbias.txt --stranded " + bed12 + " > " + bedReads)
output = shell(
getBinary("gensimreads.py") + " -l " + str(readLength) + " -e " +
explv + " -n " + str(readCount) + " --stranded " + bed12 +
" 2> /dev/null > " + bedReads)
if len(output.strip()) > 5:
print(output)
output = shell(
getBinary("getseqfrombed.py") + " -f -r " + str(seqError) + " -l " +
str(readLength) + " " + bedReads + " " + bed12Fasta +
" 2> /dev/null > " + faReads)
if len(output.strip()) > 5:
print(output)
def prepareUTRs(bed, bed12, bed12Fasta, referenceFasta, readLength, polyALength, explv, snpRate, vcfFile):
# Read utrs from BED file
utrs = parseUtrBedFile(bed)
vcf = open(vcfFile, "w")
print("##fileformat=VCFv4.1", file=vcf)
print("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO", file=vcf)
bedFile = BedTool(bed)
bedFasta = bedFile.sequence(fi=referenceFasta, s=True, name=True)
bed12FastaFile = open(bed12Fasta, "w")
utrName = None
for line in bedFasta.print_sequence().splitlines():
if(line[0] == ">"):
print(line, file=bed12FastaFile)
utrName = line[1:]
else:
print(simulateUTR(line, utrs[utrName], polyALength, snpRate, vcf), file=bed12FastaFile)
bed12FastaFile.close()
vcf.close()
bed12File = open(bed12, "w")
totalLength = 0
minFragmentLength = 150
maxFragmentLength = 450
for utr in BedIterator(bed):
fragmentLength = random.randrange(minFragmentLength, maxFragmentLength, 1) #+ readLength
fragmentLength = min(fragmentLength, utr.getLength())
start = max(0, utr.getLength() - fragmentLength)
end = utr.getLength() #- readLength
totalLength += (end - start)
# min(utr.getLength() + readLength / 4, fragmentLength + readLength / 4)
print(utr.name, start, end, utr.name, utr.score, "+", start, end, "255,0,0", "1", (end - start), 0, sep="\t", file=bed12File)
bed12File.close()
output = shell(getBinary("genexplvprofile.py") + " --geometric 1 " + bed12 + " 2> /dev/null > " + explv)
if len(output.strip()) > 5:
print(output)
return totalLength
def prepareUTRs(bed, bed12, bed12Fasta, referenceFasta, readLength,
polyALength, explv, snpRate, vcfFile):
# Read utrs from BED file
utrs = parseUtrBedFile(bed)
vcf = open(vcfFile, "w")
print("##fileformat=VCFv4.1", file=vcf)
print("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO", file=vcf)
bedFile = BedTool(bed)
bedFasta = bedFile.sequence(fi=referenceFasta, s=True, name=True)
f = tempfile.NamedTemporaryFile(mode='w', delete=False)
for line in bedFasta.print_sequence().splitlines():
if (line[0] == ">"):
print(line.split("::")[0], file=f)
else:
print(line.rstrip(), file=f)
f.close()
bed12FastaFile = open(bed12Fasta, "w")
utrName = None
with open(f.name, 'r') as f:
for line in f:
if (line[0] == ">"):
print(line.rstrip(), file=bed12FastaFile)
utrName = line.rstrip()[1:]
else:
print(simulateUTR(line.rstrip(), utrs[utrName], polyALength,
snpRate, vcf).rstrip(),
file=bed12FastaFile)
bed12FastaFile.close()
vcf.close()
bed12File = open(bed12, "w")
totalLength = 0
minFragmentLength = 150
maxFragmentLength = 450
for utr in BedIterator(bed):
fragmentLength = random.randrange(minFragmentLength, maxFragmentLength,
1) #+ readLength
fragmentLength = min(fragmentLength, utr.getLength())
start = max(0, utr.getLength() - fragmentLength)
end = utr.getLength() #- readLength
totalLength += (end - start)
# min(utr.getLength() + readLength / 4, fragmentLength + readLength / 4)
print(utr.name,
start,
end,
utr.name,
utr.score,
"+",
start,
end,
"255,0,0",
"1", (end - start),
0,
sep="\t",
file=bed12File)
bed12File.close()
output = shell(
getRNASeqReadSimulator("genexplvprofile.py") + " --geometric 1 " +
bed12 + " 2> /dev/null > " + explv)
if len(output.strip()) > 5:
print(output)
return totalLength