Mercurial > repos > jeremyjliu > region_motif_enrichment
diff region_motif_intersect.r @ 35:4ce22698acb0 draft
Uploaded
| author | jeremyjliu |
|---|---|
| date | Thu, 26 Feb 2015 22:54:09 -0500 |
| parents | 0e031bf8c5b1 |
| children | b868314320e2 |
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--- a/region_motif_intersect.r Tue Feb 10 02:03:15 2015 -0500 +++ b/region_motif_intersect.r Thu Feb 26 22:54:09 2015 -0500 @@ -1,9 +1,9 @@ # Name: region_motif_intersect.r # Description: Takes a bed file of target regions and counts intersections # of each motif (in separately installed tabix database) and target regions. -# Author: Jeremy liu +# Author: Jeremy Liu # Email: jeremy.liu@yale.edu -# Date: 15/02/04 +# Date: 15/02/11 # Note: This script is meant to be invoked with the following command # R --slave --vanilla -f ./region_motif_intersect.r --args <db_bgz> <db_tbi> <inbed> <outtab> # Dependencies: region_motif_data_manager @@ -16,8 +16,8 @@ # Retrive motif database path args <- commandArgs() -motifDB_bgz = args[7] -motifDB_tbi = args[8] +motifDB_bgz = args[7].split(',')[0] # Handles duplicate entries in data table +motifDB_tbi = args[8].split(',')[0] # Just takes the first one # Set input and reference files, comment to toggle commmand line arguments inBed = args[9]