Mercurial > repos > jjohnson > mothur_toolsuite
diff mothur/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py @ 17:57df76d861e4
Modifications for ToolShed proprietary data types
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 17 Jan 2012 11:08:15 -0600 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py Tue Jan 17 11:08:15 2012 -0600 @@ -0,0 +1,31 @@ +#!/usr/bin/env python +""" +convert a ref.taxonommy file to a seq.taxonomy file +Usage: +%python ref_to_seq_taxonomy_converter.py <ref.taxonommy_filename> <seq.taxonomy_filename> +""" + +import sys, os, re +from math import * + +assert sys.version_info[:2] >= ( 2, 4 ) + +def stop_err( msg ): + sys.stderr.write( "%s" % msg ) + sys.exit() + +def __main__(): + infile_name = sys.argv[1] + outfile = open( sys.argv[2], 'w' ) + pat = '^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)]))*(;)?)$' + for i, line in enumerate( file( infile_name ) ): + line = line.rstrip() # eliminate trailing space and new line characters + if not line or line.startswith( '#' ): + continue + fields = line.split('\t') + # make sure the 2nd field (taxonomy) ends with a ; + outfile.write('%s\t%s;\n' % (fields[0], re.sub(';$','',fields[1]))) + + outfile.close() + +if __name__ == "__main__": __main__()