Converting Coordinates between releases

From WormBaseWiki
Jump to: navigation, search

GFF coordinate conversion

A tool written in Perl for converting GFF files between the different releases of the C.elegans genome.

The needed files are available from the Sanger FTP server.

remap.tar.bz2 contains all of the data files as well as the scripts etc.

The data files are updated every release.

Description

Some scripts to map GFF files between various Wormbase releases

remap_gff_between_releases.pl - map forwards e.g. from version 150 to 160
unmap_gff_between_releases.pl - map backwards e.g. from version 160 back to 150

CHROMOSOME_DIFFERENCES/ - directory of mapping data files
test.gff - example input GFF file
test.out - example output GFF file

Usage

To map from 150 to 160:

remap_gff_between_releases.pl -gff test.gff -out test.out -release1 150 -release2 160

To map from 160 back to 150:

unmap_gff_between_releases.pl -gff test.gff -out test.out -release1 150 -release2 160

If an object specified in the GFF file has a genomic change within it, then the changed line is written to the screen, the object will probably have an erroneous structure now and should be investigated.

Only genomic changes which insert or delete bases are held in this set of data.