SeekGeneRecommender

Usage

Basic Usage

 SeekGeneRecommender -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>

Detailed Usage

package "SeekGeneRecommender"
version "1.0"
purpose "Preprocess datasets for Seek"

section "Mode"
option  "pcl"               e   "PCL mode, suitable for dataset gene variance calculation"
                                flag    off

section "PCL mode"
option  "pcl_list"          V   "PCL list"
                                string typestr="filename"
option  "pcl_dir"           F   "PCL directory"
                                string typestr="directory"

section "Input"
option  "input"             i   "Gene mapping file"
                                string typestr="filename"   yes
option  "query"             q   "Query file"
                                string typestr="filename"   yes

section "Output"
option  "dir_out"           D   "Output directory"
                                string typestr="directory"

Flag	Default	Type	Description
-i	stdin	Text file	Tab-delimited text file containing two columns, numerical gene IDs (one-based) and unique gene names (matching those in the input DAT/DAB files).
-d	.	Directory	Input directory containing DB files
-D	.	Directory	Output directory in which database files will be stored.
-x	.	Text file	Input file containing list of CDatabaselets to combine