Velvet Galaxy Composite Dataset

#!/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__()