Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.py @ 12:a0bde9b84ca6 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07
author drosofff
date Wed, 09 Nov 2016 11:22:31 -0500
parents 5d82f9b15957
children
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11:88cdd6118bfe 12:a0bde9b84ca6
179 if args.index_from == "history": 179 if args.index_from == "history":
180 tmp_dir, index_path = bowtie_squash(args.index_source) 180 tmp_dir, index_path = bowtie_squash(args.index_source)
181 else: 181 else:
182 tmp_dir, index_path = "dummy/dymmy", args.index_source 182 tmp_dir, index_path = "dummy/dymmy", args.index_source
183 command_line = bowtieCommandLiner(args.method, args.v_mismatches, args.output_format, 183 command_line = bowtieCommandLiner(args.method, args.v_mismatches, args.output_format,
184 args.aligned, args.unaligned, args.input_format, args.input, 184 args.aligned, args.unaligned, args.input_format, args.input,
185 index_path, args.output, args.num_threads) 185 index_path, args.output, args.num_threads)
186 bowtie_alignment(command_line, flyPreIndexed=tmp_dir) 186 bowtie_alignment(command_line, flyPreIndexed=tmp_dir)
187 F.close() 187 F.close()
188 if __name__ == "__main__": 188 if __name__ == "__main__":
189 __main__() 189 __main__()