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Loci Location Project

This tool is intended to retrieve physical locus positions from various sources. New sources can be extended for by making use of a plugin architecture. Currently supported sources are:
  • Plain ascii files from ldb (now more or less obsolete)
  • EMBL gene symbols (queried online)
Plans are to support online queries to NCBI.

Documentation

  • Installing the ENSEMBL API (required to retrieve from ENSEMBL)

Example

Change to the tools directory in the coloredChromosomes package dir and issue: 
./lociLocations.pl --retrieveLoci 'BRCA2 HD HLA-DRB1 Huntingtin HLA SHGC-4397'
The following output should result (some diagnostic output is ommitted): 
lociLocations.pl[26833]: List of unknown genes:
HLA-DRB1
Huntingtin
HLA
SHGC-4397
{ BRCA2 = { p = "0.278489c13"; }; HD = { p = "0.016266c4"; }; }
You can redirect just the location list by issuing, say: 
./lociLocations.pl --retrieveLoci 'BRCA2 HD HLA-DRB1 Huntingtin HLA SHGC-4397' > ~/myLoci.plist
which would produce the 'myLoci.plist' file in your home directory.

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