New task expandflag

sanger-pathogens · Jun 27, 2017 · 5de0da1 · 5de0da1
1 parent 92db92c
commit 5de0da1
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diff --git a/ariba/tasks/__init__.py b/ariba/tasks/__init__.py
@@ -1,5 +1,6 @@
 __all__ = [
     'aln2meta',
+    'expandflag',
     'flag',
     'getref',
     'micplot',

diff --git a/ariba/tasks/expandflag.py b/ariba/tasks/expandflag.py
@@ -0,0 +1,8 @@
+import argparse
+import sys
+import ariba
+
+def run(options):
+    expander = ariba.report_flag_expander.ReportFlagExpander(options.infile, options.outfile)
+    expander.run()
+
diff --git a/scripts/ariba b/scripts/ariba
@@ -29,6 +29,18 @@ subparser_aln2meta.add_argument('outprefix', help='Prefix of output filenames')
 subparser_aln2meta.set_defaults(func=ariba.tasks.aln2meta.run)
 
 
+#---------------------------- expandflag ------------------------------
+subparser_expandflag = subparsers.add_parser(
+    'expandflag',
+    help='Expands flag column of report file',
+    usage='ariba expandflag <in.report.tsv> <out.tsv',
+    description='Expands the flag column in a report file from number to comma-separated list of flag bits',
+)
+
+subparser_expandflag.add_argument('infile', help='Name of input report TSV file')
+subparser_expandflag.add_argument('outfile', help='Name of output report TSV file')
+subparser_expandflag.set_defaults(func=ariba.tasks.expandflag.run)
+
 
 #---------------------------- flag ------------------------------------
 subparser_flag = subparsers.add_parser(