Example #1
0
    def usage_from_genbank_or_usage_file(self, method, **kwargs):
        genbank_file = kwargs.get('genbank_file', None)
        usage_file = kwargs.get('usage_file', None)

        if usage_file != None:
            usage = json.loads("\n".join(open(usage_file, 'r').readlines()))
            return usage
        elif genbank_file != None:
            ua = UsageAnalyzer(genbank_file)
            return ua.get_usage_with_method(method, **kwargs)
        else:
            raise "Neither usage nor genbank file specified. Cannot get usage from nothin."
Example #2
0
            output_file = a
        if o == '-m':
            method = a
        if o == '-a':
            get_absolute_values = True
        if o == '-x':
            exclude = a
        if o == '-c':
            cutoff = int(a)
        if o == '-h':
            show_help = True

    if (genbank_file == None) or (method == None) or (show_help == True):
        usage()

    ua = UsageAnalyzer(genbank_file)

    output = ua.get_usage_with_method(method, absolute_values=get_absolute_values, exclude=exclude, cutoff=cutoff)

    if output == None:
        print "Unknown method"
        usage()

    if output_file == None:
        print str(output)
    else:
        f = open(output_file, 'w')
        f.write(json.dumps(output))
        f.close()
    exit(0)