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