Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
diff readmap.py @ 23:d6b93af0da55 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
| author | mvdbeek |
|---|---|
| date | Sun, 24 Apr 2016 09:23:44 -0400 |
| parents | f75315939afe |
| children | bf7388df53cf |
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--- a/readmap.py Thu Feb 04 08:29:18 2016 -0500 +++ b/readmap.py Sun Apr 24 09:23:44 2016 -0400 @@ -23,7 +23,6 @@ the_parser.add_argument('--gff', type=str, help="GFF containing regions of interest") the_parser.add_argument('--minquery', type=int, help="Minimum readsize") the_parser.add_argument('--maxquery', type=int, help="Maximum readsize") - the_parser.add_argument('--rcode', type=str, help="R script") args = the_parser.parse_args() return args @@ -38,7 +37,6 @@ size_distribution_file=args.output_size_distribution minquery=args.minquery maxquery=args.maxquery -Rcode = args.rcode filePath=args.input fileExt=args.ext fileLabel=args.label @@ -154,10 +152,6 @@ item_downstream_coordinate = int(gff_fields[4]) item_polarity = gff_fields[6] for sample in readDict.keys(): -## this is not required anymore but test -# if not GFFinstanceDict.has_key(sample): -# GFFinstanceDict[sample]={} -#### subinstance=extractsubinstance(item_upstream_coordinate, item_downstream_coordinate, readDict[sample].instanceDict[chrom]) if item_polarity == '-': subinstance.readDict={key*-1:value for key, value in subinstance.readDict.iteritems()} @@ -172,8 +166,4 @@ write_readplot_dataframe(MasterListOfGenomes, readmap_file) write_size_distribution_dataframe(MasterListOfGenomes, size_distribution_file) - -R_command="Rscript "+ Rcode -process = subprocess.Popen(R_command.split()) -process.wait()