Mercurial > repos > iuc > nanocompore_db
diff NanocomporeDB_process.py @ 2:d193d0e411bd draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
|---|---|
| date | Wed, 01 Sep 2021 07:47:15 +0000 |
| parents | 97a6b3f9a98d |
| children |
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--- a/NanocomporeDB_process.py Wed Jun 17 17:27:33 2020 +0000 +++ b/NanocomporeDB_process.py Wed Sep 01 07:47:15 2021 +0000 @@ -40,7 +40,7 @@ help='path to the annotations') parser.add_argument('--bedgraph', action="store_true", help='write output in BEDGRAPH format instead of BED') - parser.add_argument('--pvalue-threshold', default=1.0, + parser.add_argument('--pvalue-threshold', type=float, default=1.0, help='Maximum reported p-value.') parser.add_argument('--out-dir', default="./", type=is_valid_directory, help='path the plotting output directory.') @@ -52,9 +52,15 @@ print(db) print("DB read ids:", db.ref_id_list) + if args.bedgraph: + file_ext = 'bedgraph' + else: + file_ext = 'bed' + if args.annotation_bed: for pt in args.pvalue_types.split(','): - print("bedgraph output for p-value type:", pt) - db.save_to_bed(output_fn='{}/{}.bedgraph'.format(args.out_dir, pt), + out_path = '{}/{}.{}'.format(args.out_dir, pt, file_ext) + print("%s output for p-value type:" % out_path, pt) + db.save_to_bed(output_fn=out_path, pvalue_field=pt, pvalue_thr=args.pvalue_threshold, bedgraph=args.bedgraph)