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