Mercurial > repos > artbio > mircounts

comparison mature_mir_gff_translation.py @ 10:de227b7307cf draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
author artbio
date Sun, 29 Apr 2018 18:57:13 -0400
parents 2a08a6eb471c
children b045c30fb768
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9:2a08a6eb471c 10:de227b7307cf
3 3
4 4
5 def Parser(): 5 def Parser():
6 the_parser = argparse.ArgumentParser() 6 the_parser = argparse.ArgumentParser()
7 the_parser.add_argument( 7 the_parser.add_argument(
8 '--input', action="store", type=str, help="input miRBase GFF3 file") 8 '--gff_path', action="store", type=str,
9 help="path to miRBase GFF3 file")
9 the_parser.add_argument( 10 the_parser.add_argument(
10 '--output', action="store", type=str, 11 '--output', action="store", type=str,
11 help="output GFF3 file with converted mature mir coordinates") 12 help="output GFF3 file with converted mature mir coordinates")
13 the_parser.add_argument(
14 '--basename', action="store", type=str,
15 help="basename of the parsed gff file returned")
12 args = the_parser.parse_args() 16 args = the_parser.parse_args()
13 return args 17 return args
14 18
15 19
16 def convert_and_print_gff(gff_input_file, output): 20 def convert_and_print_gff(gff_input_file, output):
93 output.write('%s' % get_gff_header(gff_input_file)) 97 output.write('%s' % get_gff_header(gff_input_file))
94 output.write('\n'.join(gff_list)) 98 output.write('\n'.join(gff_list))
95 output.write('\n') 99 output.write('\n')
96 100
97 101
98 def main(infile, outfile): 102 def main(gff_path, outfile):
99 convert_and_print_gff(infile, outfile) 103 convert_and_print_gff(gff_path, outfile)
100 104
101 105
102 if __name__ == "__main__": 106 if __name__ == "__main__":
103 args = Parser() 107 args = Parser()
104 main(args.input, args.output) 108 main(args.gff_path, args.output)