mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-28 02:58:18 +08:00
58 lines
1.9 KiB
Python
58 lines
1.9 KiB
Python
#!/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__()
|