comparison region_motif_intersect.r @ 35:4ce22698acb0 draft

Uploaded

34:fe8a884363df

# 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
# Email: [e-mail]
# Date: 15/02/04
# 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

# Auxiliary function to concatenate multiple strings

  return(paste(input_list, sep="", collapse=""))
}

# Retrive motif database path
args <- commandArgs()
motifDB_bgz = args[7]
motifDB_tbi = args[8]

# Set input and reference files, comment to toggle commmand line arguments
inBed = args[9]
outTab = args[10]

35:4ce22698acb0

# 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
# Email: [e-mail]
# 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

# Auxiliary function to concatenate multiple strings

  return(paste(input_list, sep="", collapse=""))
}

# Retrive motif database path
args <- commandArgs()
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]
outTab = args[10]