Difference between revisions of "Load RefSeq Into Chado"

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m (Convert Genbank to GFF)
m (Add an Entry for Your Organism)
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You will need to have an entry for your species in the Chado organism table.  See
 
You will need to have an entry for your species in the Chado organism table.  See
  
   load/bin/load_gff3.pl -h
+
   >load/bin/load_gff3.pl -h
  
 
for details. This script is found in the scripts/Bio-DB-GFF/ directory of [http://www.bioperl.org BioPerl].
 
for details. This script is found in the scripts/Bio-DB-GFF/ directory of [http://www.bioperl.org BioPerl].
 
  
 
==Load the GFF==
 
==Load the GFF==

Revision as of 02:56, 8 February 2007

Abstract

This HOWTO describes a method for loading the sequence data in Genbank files into the Chado database.


Authors


Copyright

This document is copyright Scott Cain, 2007. For reproduction other than personal use please contact <cain@cshl.org>


Revision History

Revision 1.0 2007-02-07 BIO First version


Download the Sequence Files

Download the Genbank genome record of interest. A good source for Genbank files is NCBI's FTP site (ftp://ftp.ncbi.nih.gov/genomes/), look for the *.gbk files, they will probably be compressed (*.gbk.gz).


Convert Genbank to GFF

Use the BioPerl script genbank2gff3.pl, found in scripts/Bio-DB-GFF/genbank2gff3.PLS within the BioPerl distribution.

 >load/bin/genbank2gff3.pl <filename>

This will convert the Genbank file to GFF version 3. It may give several warnings about unrecognized feature types. If the feature types are not part of SOFA, you will have to hand edit the resulting GFF file to change the feature type. Any skipped features will be printed at the end. If you want those to be part of the GFF file, you will have to add those manually as well, fixing any non-SOFA feature types.

Add an Entry for Your Organism

You will need to have an entry for your species in the Chado organism table. See

  >load/bin/load_gff3.pl -h

for details. This script is found in the scripts/Bio-DB-GFF/ directory of BioPerl.

Load the GFF

Run the load_gff3.pl script:

  >load/bin/load_gff3.pl --organism <your org>  --srcdb DB:genbank --gfffile <your gfffile>

This will load your data to chado. Note that if there are non-SOFA feature types remaining in the GFF file the load will fail when they are encountered. If that happens, edit the file to fix the incorrect term and load again. Only the previously unloaded data will load (ie, you won't have duplicate rows.


More Information

Please send questions to the GMOD developers list:

gmod-devel@lists.sourceforge.net