Usage
Basic Usage
SeekReader -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
Detailed Usage
package "SeekReader"
version "1.0"
purpose "Reads db files"
section "Diagnosis"
option "databaselet" D "Display values from databaselet(s)"
flag off
option "dataset" A "Check which datasets contain query of interest, based on .gpres file"
flag off
option "weight" W "Test dataset weights"
flag off
option "weight2" U "Test dataset weights 2"
flag off
option "comp_ranking" C "Compare two rankings (*.gscore files)"
flag off
option "convert_aracne" J "Convert Aracne output (.txt) to DAB file"
flag off
option "convert_dab" k "Convert DAB to matrix"
flag off
option "limit_hub" Y "Limit genes in the DAB to those that are hubby"
flag off
section "Limit Hub"
option "dabinput" y "DAB input file"
string typestr="filename" default="NA"
option "hub_dab_output" Z "DAB output file"
string typestr="filename" default="NA"
section "Convert Aracne"
option "aracne_file" K "Aracne .txt output file"
string typestr="filename" default="NA"
option "output_dab_file" L "DAB file"
string typestr="filename" default="NA"
section "Convert DAB to matrix"
option "dab_file" f "DAB file"
string typestr="filename" default="NA"
option "output_matrix" m "Output matrix filename"
string typestr="filename" default="NA"
section "Weight"
option "dweight_dir" E "Dataset weight directory"
string typestr="directory" default="NA"
option "dweight_num" n "Number of .dweight files"
int default="1000"
option "dweight_map" M "Dataset mapping file"
string typestr="filename" default="NA"
option "dweight_test_dir" F "Test dataset weight directory"
string typestr="directory" default="NA"
option "dweight_test_num" G "Test number of .dweight files"
int default="1000"
section "Compare Rankings"
option "gscore_dir1" H "Gene score directory 1"
string typestr="directory" default="NA"
option "gscore_dir2" h "Gene score directory 2"
string typestr="directory" default="NA"
option "gscore_num1" I "Number of .gscore files"
int default="1000"
section "Main"
option "order_stat_single_gene_query" O "Order statistics mode (single-gene query)"
flag off
option "db" x "Input dataset-platform definition"
string typestr="filename"
option "dset_list" X "Input a set of datasets"
string typestr="filename"
option "input" i "Input gene mapping"
string typestr="filename"
option "single_query" q "Query gene list"
string typestr="filename"
option "dir_in" d "Database directory"
string typestr="directory"
option "dir_prep_in" p "Prep directory (containing .gavg, .gpres files)"
string typestr="directory"
option "dir_gvar_in" r "Prep directory (containing .gexpvar files)"
string typestr="directory" default="NA"
option "dir_sinfo_in" s "Sinfo directory (containing .sinfo files)"
string typestr="directory" default="NA"
option "is_nibble" N "Whether the input DB is nibble type"
flag off
option "platform_dir" P "Platform directory"
string typestr="directory"
option "gvar_cutoff" v "Query gene's variance in the dataset cutoff"
float default="-1"
option "multi_query" Q "File containing multiple queries"
string typestr="filename" default="NA"
option "output_file" o "Output file"
string typestr="filename" default="NA"
| 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 |
