Orthologer

Orthologer will read in a text-based orthology file containing orthologous clusters of functionally equivalent genes across multiple organisms. It will then "align" gold standards for those organisms in two ways. First, gene pairs from the same organism within an orthologous cluster will be assigned one weight (high) in the aligned standard. Next, gene pairs in from the same organism spanning different orthologous clusters that share a gene pair related in some organism will be assigned a second weight (low). Existing positive functional relationships in the input files are never overwritten.

Usage

Basic Usage

 Orthologer -i <orthology.txt> -w <weight1> -W <weight2> <answers.dab>*

Aligns (modifies) the organism-specific answer files answers.dab based on the orthologous clusters in orthology.txt, assigning score weight1 to previously unrelated genes sharing an orthologous cluster and weight2 to previously unrelated genes in different orthologous clusters spanned by a gene pair related in some organism.

Detailed Usage

package "Orthologer"
version "1.0"
purpose "Orthology-based DAT/DAB gold standard processing"

section "Main"
option  "input"     i   "Orthology file"
                        string  typestr="filename"
option  "weight1"   w   "Weight of in-cluster ortholog relationships"
                        double  default="1"
option  "weight2"   W   "Weight of cross-cluster ortholog relationships"
                        double  default="1"
option  "positives" p   "Expected fraction of positives"
                        double  default="1"

section "Optional"
option  "verbosity" v   "Message verbosity"
                        int default="5"

Flag	Default	Type	Description
None	None	DAT/DAB files	Input gold standard answer files for each organism within the orthology to be aligned.
-i	stdin	Orthology text file	Tab-delimited text file in which each line represents an orthologous cluster. Tab-separated tokens within each line should be of the form <organism id>|<gene id>, e.g. SCE|YAL001C or MMU|MGI:88064.
-w	1	Double	Weight inserted into aligned gold standards for genes in the same orthologous cluster.
-W	1	Double	Weight inserted into aligned gold standards for genes in different orthologous clusters spanned by a gene pair functionally related in at least one organism.
-m	off	Flag	If given, memory map the input files when possible. DAT and PCL inputs cannot be memmapped.