Contexter

Contexter calculates gene/context association weights, either from a database and (X)DSL files on an as-needed basis (like BNServer) or from a given pre-calculated global functional relationship network (DAT/DAB file) and context files.

Usage

Basic Usage

 Contexter -i <contexts.txt> -d <database_dir> -c <contexts_genes.txt> -e <context>
        -g <genes.txt> -n <contexts_dir> -b <global.xdsl>

Output (to standard output) the specific association score for each gene in the genome to context number context, using (as with BNServer) the context ID/name mappings in contexts.txt, the context/gene mappings in contexts_genes.txt, the gene ID/name mappings in genes.txt, the Sleipnir::CDatabase in database_dir, the context-specific Bayesian classifiers in contexts_dir, and the global Bayesian classifier global.xdsl.

 Contexter -t -i <network.dab> -g <genes.txt> -c <contexts_genes.txt>

Output the specific association score for each gene in the genome to context number context, using the context/gene mappings in contexts_genes.txt, the gene ID/name mappings in genes.txt, and the pre-computed interaction network network.dab.

Detailed Usage

package "Contexter"
version "1.0"
purpose "Calculate gene/context association ratios"

section "Main"
option  "input"         i   "DAT/DAB file or context IDs and names"
                            string  typestr="filename"

section "Input"
option  "dat"           t   "Use DAT/DAB file input rather than Bayes nets"
                            flag    off
option  "database"      d   "Database directory"
                            string  typestr="directory" default="."
option  "contexts"      c   "Context/gene mapping"
                            string  typestr="filename"  yes
option  "context"       e   "Context ID to process"
                            int yes
option  "genes"         g   "Gene ID to name mapping"
                            string  typestr="filename"
option  "is_nibble"     N   "Define whether the database is nibble type."
                            int default="1"

section "Bayes nets"
option  "networks"      n   "Bayes net directory"
                            string  typestr="directory" default="."
option  "default"       b   "Bayes net for no context"
                            string  typestr="filename"
option  "xdsl"          x   "Use XDSL files instead of DSL"
                            flag    on
option  "minimal_in"    m   "Read stored contexts and minimal Bayes nets"
                            flag    off
option  "minimal_out"   M   "Store contexts and minimal Bayes nets"
                            string  typestr="filename"

section "Options"
option  "lookup"        l   "Gene name to lookup"
                            string
option  "memmap"        p   "Memory map input"
                            flag    off
option  "verbosity"     v   "Message verbosity"
                            int default="5"

Flag	Default	Type	Description
-i	None	DAT/DAB file or text file	When -t is on, an input DAT/DAB file containing a global predicted functional relationship network. When -t is off, a tab-delimited text file from which context indices, names, and string IDs are read.
-t	off	Flag	If on, read a global functional relationship network from -i; if off, read a context ID file (along with additional context/gene information from other arguments).
-d	.	Directory	When -t is off, directory from which Sleipnir::CDatabase data files are read.
-c	None	Text file	Tab-delimited text file containing two columns, context IDs and gene IDs (both one-based).
-e	None	Integer	Context ID (one-based) for which gene associations should be calculated.
-g	None	Text file	When -t is on, tab-delimited text file containing two columns, gene IDs (one-based) and unique gene names (matching those in the DAT/DAB file).
-n	.	Directory	Directory from which context-specific Bayesian classifiers ((X)DSL files) are read.
-b	None	(X)DSL file	Bayesian classifier for the default (global) context.
-x	on	Flag	If on, assume XDSL files will be used instead of DSL files.
-m	off	Flag	If on, read binary stored Bayesian classifiers from a file specified by -n; if off, assume -n specifies a directory of (X)DSL files.
-M	None	Binary file	If given, store Bayesian classifiers in a custom binary format in the given filename. Cannot be used with -m on. Loading the classifiers from a binary file can be faster than loading several hundred separate (X)DSLs. If your classifiers aren't changing, you can load them from (X)DSL files once, leaving -m off and saving them with -M, then on subsequent runs turn -M off and load the binary file with -m on.
-l	None	String	If given, calculate only the association weight for the given gene name rather than for the entire genome.
-p	off	Flag	If given, memory map the input files when possible. DAT and PCL inputs cannot be memmapped.