comparison blast2html.py @ 108:b3b5ee557170 draft

update test

107:a22c909c9b57

def main():
    default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja')

    parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
                                     usage="{0} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))
    input_group = parser.add_mutually_exclusive_group(required=True)
    input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
                             help='The input Blast XML file, same as -i/--input')
    input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'), 
                             help='The input Blast XML file')

    # care too much.
    parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template,
                        help='The template file to use. Defaults to blast_html.html.jinja')
    
    dblink_group = parser.add_mutually_exclusive_group()
    dblink_group.add_argument('--genelink-template', default='http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign',
                              help="""A link template to link hits to a gene bank webpage. The template string is a 
                              Python format string. It can contain the following replacement elements: {id[N]}, {fullid}, 
                              {defline[N]}, {fulldefline}, {accession}, where N is a number. id[N] and defline[N] will be 
                              replaced by the Nth element of the id or defline, where '|' is the field separator. 

    if args.input == None:
        parser.error('no input specified')

    if six.PY2:
        # The argparse.FileType wrapper doesn't support an encoding
        # argument or such, so for python 2 we need to wrap or reopen
        # the output. The input files are already read as utf-8 by the
        # respective libraries.

        # One option is using codecs, but the codecs' writelines()
        # method doesn't support streaming but collects all output and
        # writes at once. On the other hand the io module is slower
        # (though not significantly).

        # args.output = codecs.getwriter('utf-8')(args.output)
        args.output = io.open(args.output.name, 'w')
    
    templatedir, templatename = path.split(args.template.name)

108:b3b5ee557170

def main():
    default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja')

    parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
                                     usage="{0} [-i] INPUT [-o OUTPUT] [--genelink-template URL_TEMPLATE]".format(sys.argv[0]))
    input_group = parser.add_mutually_exclusive_group(required=True)
    input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
                             help='The input Blast XML file, same as -i/--input')
    input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'), 
                             help='The input Blast XML file')

    # care too much.
    parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template,
                        help='The template file to use. Defaults to blast_html.html.jinja')
    
    dblink_group = parser.add_mutually_exclusive_group()
    dblink_group.add_argument('--genelink-template', metavar='URL_TEMPLATE',
                              default='http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign',
                              help="""A link template to link hits to a gene bank webpage. The template string is a 
                              Python format string. It can contain the following replacement elements: {id[N]}, {fullid}, 
                              {defline[N]}, {fulldefline}, {accession}, where N is a number. id[N] and defline[N] will be 
                              replaced by the Nth element of the id or defline, where '|' is the field separator. 

    if args.input == None:
        parser.error('no input specified')

    if six.PY2:
        # The argparse.FileType wrapper doesn't support an encoding
        # argument, so for python 2 we need to wrap or reopen the
        # output. The input files are already read as utf-8 by the
        # respective libraries.

        # One option is using codecs, but the codecs' writelines()
        # method doesn't support streaming but collects all output and
        # writes at once (see Python issues #5445 and #21910). On the
        # other hand the io module is slower (though not
        # significantly).

        # args.output = codecs.getwriter('utf-8')(args.output)
        args.output = io.open(args.output.name, 'w')
    
    templatedir, templatename = path.split(args.template.name)