Difference between revisions of "Converting Coordinates between releases"

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(Removed description of unmap_gff_between_releases.pl)
 
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== Description ==
 
== Description ==
  
Some scripts to map GFF files between various Wormbase releases
+
A script to map GFF files between various Wormbase releases
 
   
 
   
 
  remap_gff_between_releases.pl - map forwards e.g. from version 150 to 160
 
  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
 
  CHROMOSOME_DIFFERENCES/ - directory of mapping data files
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  remap_gff_between_releases.pl -gff test.gff -out test.out -release1 150 -release2 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.
 
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.

Latest revision as of 12:02, 19 July 2018

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

A script to map GFF files between various Wormbase releases

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

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

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.