mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
21b44bf348
using the following command: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 . ```
79 lines
2.4 KiB
Python
79 lines
2.4 KiB
Python
#!/usr/bin/env python
|
|
# Dan Blankenberg
|
|
"""
|
|
Read text output from FIMO and create an interval file.
|
|
"""
|
|
import os
|
|
import shutil
|
|
import subprocess
|
|
import sys
|
|
import tempfile
|
|
|
|
from galaxy_utils.sequence.transform import DNA_reverse_complement
|
|
|
|
buffsize = 1048576
|
|
|
|
|
|
def stop_err(msg):
|
|
sys.stderr.write(msg)
|
|
sys.exit()
|
|
|
|
|
|
def main():
|
|
assert len(sys.argv) == 8, "Wrong number of arguments"
|
|
sys.argv.pop(0)
|
|
fimo_cmd = sys.argv.pop(0)
|
|
html_path = sys.argv.pop(0)
|
|
html_out = sys.argv.pop(0)
|
|
interval_out = sys.argv.pop(0)
|
|
txt_out = sys.argv.pop(0)
|
|
xml_out = sys.argv.pop(0)
|
|
gff_out = sys.argv.pop(0)
|
|
|
|
# run fimo
|
|
try:
|
|
tmp_stderr = tempfile.NamedTemporaryFile()
|
|
proc = subprocess.Popen(args=fimo_cmd, shell=True, stderr=tmp_stderr)
|
|
returncode = proc.wait()
|
|
tmp_stderr.seek(0)
|
|
stderr = ''
|
|
try:
|
|
while True:
|
|
stderr += tmp_stderr.read(buffsize)
|
|
if not stderr or len(stderr) % buffsize != 0:
|
|
break
|
|
except OverflowError:
|
|
pass
|
|
|
|
if returncode != 0:
|
|
raise Exception(stderr)
|
|
except Exception as e:
|
|
raise Exception('Error running FIMO:\n' + str(e))
|
|
|
|
shutil.move(os.path.join(html_path, 'fimo.txt'), txt_out)
|
|
shutil.move(os.path.join(html_path, 'fimo.gff'), gff_out)
|
|
shutil.move(os.path.join(html_path, 'fimo.xml'), xml_out)
|
|
shutil.move(os.path.join(html_path, 'fimo.html'), html_out)
|
|
|
|
out_file = open(interval_out, 'wb')
|
|
out_file.write("#%s\n" % "\t".join(("chr", "start", "end", "pattern name", "score", "strand", "matched sequence", "p-value", "q-value")))
|
|
for line in open(txt_out):
|
|
if line.startswith('#'):
|
|
continue
|
|
fields = line.rstrip("\n\r").split("\t")
|
|
start, end = int(fields[2]), int(fields[3])
|
|
sequence = fields[7]
|
|
if start > end:
|
|
start, end = end, start # flip start and end, and set strand
|
|
strand = "-"
|
|
sequence = DNA_reverse_complement(sequence) # we want sequences relative to strand; FIMO always provides + stranded sequence
|
|
else:
|
|
strand = "+"
|
|
start -= 1 # make 0-based start position
|
|
out_file.write("%s\n" % "\t".join([fields[1], str(start), str(end), fields[0], fields[4], strand, sequence, fields[5], fields[6]]))
|
|
out_file.close()
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|