#!/usr/bin/env python
"""
Classes encapsulating decypher tool.
James E Johnson - University of Minnesota
"""
import os
import subprocess
import sys
assert sys.version_info[:2] >= (2, 4)
def __main__():
# Parse command line
html_file = sys.argv[1]
working_dir = sys.argv[2]
try: # for test - needs this done
os.makedirs(working_dir)
except Exception as e:
sys.exit("Error running velveth " + str(e))
hash_length = sys.argv[3]
inputs = " ".join(sys.argv[4:])
cmdline = "velveth %s %s %s > /dev/null" % (working_dir, hash_length, inputs)
try:
proc = subprocess.Popen(args=cmdline, shell=True, stderr=subprocess.PIPE)
returncode = proc.wait()
# get stderr, allowing for case where it's very large
stderr = b""
buffsize = 1048576
try:
while True:
stderr += proc.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:
sys.exit("Error running velveth " + str(e))
sequences_path = os.path.join(working_dir, "Sequences")
roadmaps_path = os.path.join(working_dir, "Roadmaps")
rval = ["<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>"]
rval.append("<div>%s<p/></div>" % (cmdline))
rval.append("<div>This composite dataset is composed of the following files:<p/><ul>")
rval.append('<li><a href="%s" type="text/plain">%s </a>%s</li>' % (sequences_path, "Sequences", "Sequences"))
rval.append('<li><a href="%s" type="text/plain">%s </a>%s</li>' % (roadmaps_path, "Roadmaps", "Roadmaps"))
rval.append("</ul></div></html>")
with open(html_file, "w") as f:
f.write("\n".join(rval))
f.write("\n")
if __name__ == "__main__":
__main__()