This is the new server for GMOD.org. Please let us know if you notice anything weird while it's getting broken in.
Load GenBank into Chado
- Install prerequisites: latest versions of Chado and GBrowse
- Fetch Genbank genome/chromosomes
- Run genbank2gff3 script from BioPerl (Important: use a version of the script created April 2007 or later)
- Run gmod_bulk_load_gff3.pl script (from GMOD)
- View genome(s) with GBrowse (see an example at eugenes.org).
In summary, to load Saccharomyces chromosome X to Chado database 'mychado', from a Unix command-line, do:
curl ftp://ftp.ncbi.nih.gov/genomes/Saccharomyces_cerevisiae/CHR_X/NC_001142.gbk \ | perl bp_genbank2gff3.pl -noCDS -in stdin -out stdout \ | perl gmod_bulk_load_gff3.pl -dbname mychado -organism fromdata
Fetch Genbank Genome Files
mkdir data; cd data
Fetch from NCBI, or this Indiana mirror
curl ftp://bio-mirror.net/biomirror/ncbigenomes/ curl -RO ftp://bio-mirror.net/biomirror/ncbigenomes/Saccharomyces_cerevisiae/CHR_X/NC_001142.gbk.gz
Other sample genomes of interest:
Create GFF3 from the Genbank Files
-noCDS flag is required for this. Use
-s flag to summarize features found.
bp_genbank2gff3.pl -noCDS -s -o . data/NC_001142.gbk.gz
Load GFF3 into Chado
Use the GMOD script
gmod_bulk_load_gff3.pl for this. Note that
gmod_bulk_load_gff3 will only handle one organism at a time. Chose the best --dbxref per organism (WormBase, SGD, MGI, FLYBASE), depending on contents of GenBank annotations. The 'GeneID' dbxref is standard for most GenBank genomes.
gmod_bulk_load_gff3.pl --dbname dev_chado_01c --dbxref GeneID --organism fromdata --gff data/NC_004353.gbk.gz.gff
psql -d dev_chado_01c -c 'select count(f.*), \ (select common_name from organism where organism_id = f.organism_id) as species \ from feature f group by f.organism_id;' psql -d dev_chado_01c -c 'select count(f.*), \ (select common_name from organism where organism_id = f.organism_id) as species \ from feature f where f.seqlen>0 group by f.organism_id;'
It's possible that you'll run into some errors coming from the input data itself. Some of the errors, and their fixes, are described below.
couldn't open /var/lib/gmod/conf directory for reading:No such file or directory
Make sure the environmental variable GMOD_ROOT is set to where gmod was installed, for example:
setenv GMOD_ROOT /usr/local/gmod/ # tcsh
set GMOD_ROOT=/usr/local/gmod/ # bash
Your GFF3 file uses a tag called <term>, but this term is not already in the cvterm and dbxref tables so that its value can be inserted into the featureprop table
Solution: This error message will be followed by SQL statements that insert the term in the correct way - execute them. By the way, one explanation for this error is that the source sequence was curated but not with terms from the Sequence Ontology.
DBD::Pg::db pg_endcopy failed: ERROR: duplicate key violates unique constraint "featureprop_c1"
CONTEXT: COPY featureprop, line ...
Solution: The CONTEXT line above is telling you what the offending data is. This error probably means that there are 2 features sharing the same name or ID and feature type in the GFF3 file. Correct these errors by hand and reload.