def _annotate(input, mirbase):
output = "mirbase.bed"
cmd = ("bedtools intersect -bed -wo -s -f 0.80 -a"
" {input} -b {mirbase} >| {output}")
if not is_there(output):
do.run(cmd.format(**locals()), "")
return full(output)
def _annotate(input, mirbase):
output = "mirbase.bed"
cmd = ("bedtools intersect -bed -wo -s -f 0.80 -a"
" {input} -b {mirbase} >| {output}")
if not is_there(output):
do.run(cmd.format(**locals()), "")
return full(output)
def _tailor(input, index, mirbase):
safe_makedir("tailor")
with ch_directory("tailor"):
output = "tailor_map.bam"
cmd = ("tailor -l 15 map -p {index}" " -i {input}" " -o hits.sam")
cmd_bam = "samtools view -Sbh hits.sam >| {output}"
if not is_there("hits.sam"):
do.run(cmd.format(**locals()), "")
if not is_there(output):
do.run(cmd_bam.format(**locals()), "")
mirbase_output = _annotate(output, mirbase)
return (mirbase_output, full(output))
def _hisat(input, index, mirbase):
safe_makedir("hisat")
with ch_directory("hisat"):
output = "hisat_map.bam"
cmd = ("hisat -f -k 50 -L 18 -x {index}" " -U {input}" " >| hits.sam")
cmd_bam = "samtools view -Sbh hits.sam >| {output}"
if not is_there("hits.sam"):
do.run(cmd.format(**locals()), "")
if not is_there(output):
do.run(cmd_bam.format(**locals()), "")
mirbase_output = _annotate(output, mirbase)
return (mirbase_output, full(output))
def _tailor(input, index, mirbase):
safe_makedir("tailor")
with ch_directory("tailor"):
output = "tailor_map.bam"
cmd = ("tailor -l 15 map -p {index}"
" -i {input}"
" -o hits.sam")
cmd_bam = "samtools view -Sbh hits.sam >| {output}"
if not is_there("hits.sam"):
do.run(cmd.format(**locals()), "")
if not is_there(output):
do.run(cmd_bam.format(**locals()), "")
mirbase_output = _annotate(output, mirbase)
return (mirbase_output, full(output))
def _hisat(input, index, mirbase):
safe_makedir("hisat")
with ch_directory("hisat"):
output = "hisat_map.bam"
cmd = ("hisat -f -k 50 -L 18 -x {index}"
" -U {input}"
" >| hits.sam")
cmd_bam = "samtools view -Sbh hits.sam >| {output}"
if not is_there("hits.sam"):
do.run(cmd.format(**locals()), "")
if not is_there(output):
do.run(cmd_bam.format(**locals()), "")
mirbase_output = _annotate(output, mirbase)
return (mirbase_output, full(output))
def _star(input, index, mirbase):
safe_makedir("star")
with ch_directory("star"):
output = "star_map.bam"
cmd = ("STAR --genomeDir {index} --readFilesIN {input}"
" --outFilterMultimapNmax 50"
" --outSAMattributes NH HI NM"
" --alignIntronMax 1")
cmd_bam = "samtools view -Sbh Aligned.out.sam >| {output}"
if not is_there("Aligned.out.sam"):
do.run(cmd.format(**locals()), "")
if not is_there(output):
do.run(cmd_bam.format(**locals()), "")
mirbase_output = _annotate(output, mirbase)
return (mirbase_output, full(output))
def _star(input, index, mirbase):
safe_makedir("star")
with ch_directory("star"):
output = "star_map.bam"
cmd = ("STAR --genomeDir {index} --readFilesIN {input}"
" --outFilterMultimapNmax 50"
" --outSAMattributes NH HI NM"
" --alignIntronMax 1")
cmd_bam = "samtools view -Sbh Aligned.out.sam >| {output}"
if not is_there("Aligned.out.sam"):
do.run(cmd.format(**locals()), "")
if not is_there(output):
do.run(cmd_bam.format(**locals()), "")
mirbase_output = _annotate(output, mirbase)
return (mirbase_output, full(output))
def _srnamapper(input, index, mirbase):
safe_makedir("srnamapper")
with ch_directory("srnamapper"):
output = "srnamapper_map.bed"
cmd = ("sRNAmapper.pl -i {input} -g {index}"
" -s 10 -n 3 -o hits.eland")
if not is_there("hits.eland"):
do.run(cmd.format(**locals()), "")
if not is_there(output):
with open(output, 'w') as out_handle:
with open("hits.eland") as in_handle:
for line in in_handle:
cols = line.strip().split('\t')
print >>out_handle, "%s\t%s\t%s\t%s\t1\t%s\t1\t1\t1\t1\t1\t1" % (cols[0], cols[1], int(cols[1]) + len(cols[2]), cols[3], cols[6])
mirbase_output = _annotate(output, mirbase)
return (mirbase_output, full(output))
def _srnamapper(input, index, mirbase):
safe_makedir("srnamapper")
with ch_directory("srnamapper"):
output = "srnamapper_map.bed"
cmd = ("sRNAmapper.pl -i {input} -g {index}"
" -s 10 -n 3 -o hits.eland")
if not is_there("hits.eland"):
do.run(cmd.format(**locals()), "")
if not is_there(output):
with open(output, 'w') as out_handle:
with open("hits.eland") as in_handle:
for line in in_handle:
cols = line.strip().split('\t')
print >> out_handle, "%s\t%s\t%s\t%s\t1\t%s\t1\t1\t1\t1\t1\t1" % (
cols[0], cols[1], int(cols[1]) + len(cols[2]),
cols[3], cols[6])
mirbase_output = _annotate(output, mirbase)
return (mirbase_output, full(output))
if __name__ == "__main__":
parser = ArgumentParser(description="Run different tools in simulated fasta file")
parser.add_argument("--fasta", required=True, help="short reads")
parser.add_argument("--mirbase", required=True, help="bed file with mirbase annotation")
parser.add_argument("--star", help="star index")
parser.add_argument("--bowtie2", help="bowtie2 index")
parser.add_argument("--hisat", help="hisat index")
parser.add_argument("--tailor", help="tailor index")
parser.add_argument("--bwa_aln", help="bwa_aln index")
parser.add_argument("--srnamapper", help="srnamapper index")
args = parser.parse_args()
outputs = {}
if args.star:
print "doing STAR"
outputs.update({"star": _star(full(args.fasta), full(args.star), full(args.mirbase))})
if args.bowtie2:
print "doing bowtie2"
outputs.update({"bowtie2": _bowtie2(full(args.fasta), full(args.bowtie2), full(args.mirbase))})
if args.hisat:
print "doing hisat"
outputs.update({"hisat": _hisat(full(args.fasta), full(args.hisat), full(args.mirbase))})
if args.tailor:
print "doing tailor"
outputs.update({"tailor": _tailor(full(args.fasta), full(args.tailor), full(args.mirbase))})
if args.bwa_aln:
print "doing bwa_aln"
outputs.update({"bwa_aln": _bwa_aln(full(args.fasta), full(args.bwa_aln), full(args.mirbase))})
required=True,
help="bed file with mirbase annotation")
parser.add_argument("--star", help="star index")
parser.add_argument("--bowtie2", help="bowtie2 index")
parser.add_argument("--hisat", help="hisat index")
parser.add_argument("--tailor", help="tailor index")
parser.add_argument("--bwa_aln", help="bwa_aln index")
parser.add_argument("--srnamapper", help="srnamapper index")
args = parser.parse_args()
outputs = {}
if args.star:
print "doing STAR"
outputs.update({
"star":
_star(full(args.fasta), full(args.star), full(args.mirbase))
})
if args.bowtie2:
print "doing bowtie2"
outputs.update({
"bowtie2":
_bowtie2(full(args.fasta), full(args.bowtie2), full(args.mirbase))
})
if args.hisat:
print "doing hisat"
outputs.update({
"hisat":
_hisat(full(args.fasta), full(args.hisat), full(args.mirbase))
})
if args.tailor:
mirbase_output = _annotate(output, mirbase)
return mirbase_output
if __name__ == "__main__":
parser = ArgumentParser(description="Run different tools in simulated fasta file")
parser.add_argument("--fasta", required=True, help="short reads")
parser.add_argument("--mirbase", required=True, help="bed file with mirbase annotation")
parser.add_argument("--star", help="star index")
parser.add_argument("--bowtie2", help="bowtie2 index")
parser.add_argument("--hisat", help="hisat index")
args = parser.parse_args()
outputs = {}
if args.star:
print "doing STAR"
outputs.update({"star": _star(full(args.fasta), full(args.star), full(args.mirbase))})
if args.bowtie2:
print "doing bowtie2"
outputs.update({"bowtie2": _bowtie2(full(args.fasta), full(args.bowtie2), full(args.mirbase))})
if args.hisat:
print "doing hisat"
outputs.update({"hisat": _hisat(full(args.fasta), full(args.hisat), full(args.mirbase))})
os.remove("summary.tsv") if os.path.exists("summary.tsv") else None
with open("summary.tsv", 'w') as out_handle:
out_handle.write(res.H + "\n")
for tool, stat in outputs.items():
stat_file = _stats(stat, args.fasta, tool)
do.run("cat %s >> summary.tsv" % stat_file, "merging %s" % tool)
