Mercurial > repos > greg > cwpair2

changeset 9:6469dda597d6 draft

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Uploaded
author greg
date Wed, 02 Dec 2015 16:13:59 -0500
parents 1fc26b8e618d
children b52d6705aed0
files cwpair2.py
diffstat 1 files changed, 4 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/cwpair2.py	Wed Dec 02 16:13:51 2015 -0500
+++ b/cwpair2.py	Wed Dec 02 16:13:59 2015 -0500
@@ -8,7 +8,7 @@
 Input: list of one or more gff format files
 
 Output: files produced for each input/mode combination:
-S (simple), D (detailed), O (orphans), P (frequency preview plot), F (final frequency plot),
+MP (matched_pair), D (details), O (orphans), P (frequency preview plot), F (frequency final plot),
 C (statistics graph), statistics.tabular
 """
 
@@ -26,12 +26,11 @@
     parser.add_argument('--threshold_format', dest='threshold_format', help='Percentage to filter the 95th percentile.')
     parser.add_argument('--relative_threshold', dest='relative_threshold', type=float, default=0.0, help='Percentage to filter the 95th percentile.')
     parser.add_argument('--absolute_threshold', dest='absolute_threshold', type=float, default=0.0, help='Absolute value to filter.')
-    parser.add_argument('--output_files', dest='output_files', default='simple', help='Restrict output dataset collections.')
-    parser.add_argument('--sort_score', dest='sort_score', default='no', help='Sort output by score.')
+    parser.add_argument('--output_files', dest='output_files', default='matched_pair', help='Restrict output dataset collections.')
     parser.add_argument('--statistics_output', dest='statistics_output', help='Statistics output file.')
     args = parser.parse_args()
 
-    cwpair2_util.create_directories(args.method)
+    cwpair2_util.create_directories()
 
     statistics = []
     if args.absolute_threshold > 0:
@@ -48,8 +47,7 @@
                                           args.up_distance,
                                           args.down_distance,
                                           args.binsize,
-                                          args.output_files,
-                                          args.sort_score)
+                                          args.output_files)
         statistics.extend(stats)
     # Accumulate statistics.
     by_file = {}