Difference between revisions of "GMODTools TestCase"
From GMOD
Dongilbert (Talk | contribs) (New page: This is an example test case for GMOD, loading a GenBank format genome (chromosome) to Chado database, then dumping it out, including GenBank submission format with GenBank output to test ...) |
Dongilbert (Talk | contribs) m (add output url) |
||
| Line 9: | Line 9: | ||
set dbname=anogam_x | set dbname=anogam_x | ||
$pg/bin/createdb -T chado_01_template $dbname | $pg/bin/createdb -T chado_01_template $dbname | ||
| − | + | ||
# fix Genbank FT to SO type map if needed | # fix Genbank FT to SO type map if needed | ||
vi lib/Bio/SeqFeature/Tools/TypeMapper.pm : add pseudogenic tRNA | vi lib/Bio/SeqFeature/Tools/TypeMapper.pm : add pseudogenic tRNA | ||
| − | + | ||
# load chromosome X to chado | # load chromosome X to chado | ||
gunzip -c NC_004818.gbk.gz |\ | gunzip -c NC_004818.gbk.gz |\ | ||
perl bin/bp_genbank2gff3.pl -noCDS -in stdin -out stdout |\ | perl bin/bp_genbank2gff3.pl -noCDS -in stdin -out stdout |\ | ||
| − | perl bin/gmod_bulk_load_gff3.pl -dbname $dbname -organism fromdata | + | perl bin/gmod_bulk_load_gff3.pl -dbname $dbname -organism fromdata |
| − | + | ||
# create GMOD Bulkfiles conf/bulkfiles/anogam.xml from template.xml : dbname, etc. edits | # create GMOD Bulkfiles conf/bulkfiles/anogam.xml from template.xml : dbname, etc. edits | ||
# see samples to create a new organism/project configuration | # see samples to create a new organism/project configuration | ||
| Line 23: | Line 23: | ||
# create standard Bulkfiles outputs for anogam_x | # create standard Bulkfiles outputs for anogam_x | ||
perl -Ilib bin/bulkfiles.pl -config=anogam -make >& log.anogam1 & | perl -Ilib bin/bulkfiles.pl -config=anogam -make >& log.anogam1 & | ||
| − | + | ||
# new in progress output, includes regurgitation of GenBank record to compare with original | # new in progress output, includes regurgitation of GenBank record to compare with original | ||
# you should check and edit conf/bulkfiles/genbanksubmit.xml before running this part | # you should check and edit conf/bulkfiles/genbanksubmit.xml before running this part | ||
| − | perl -Ilib bin/bulkfiles.pl -config=anogam -format=genbanktbl -make | + | perl -Ilib bin/bulkfiles.pl -config=anogam -format=genbanktbl -make |
| − | Outputs should include genbanksubmit/ folder with outputs of GMOD Bulkfiles: | + | Outputs should include genbanksubmit/ folder with outputs of GMOD Bulkfiles: |
anogam-all-anogam1.tbl : feature table ** new part | anogam-all-anogam1.tbl : feature table ** new part | ||
anogam-all-anogam1.fsa : genome dna == fasta/chromosome | anogam-all-anogam1.fsa : genome dna == fasta/chromosome | ||
| Line 37: | Line 37: | ||
anogam-all-anogam1.val : errors & warnings | anogam-all-anogam1.val : errors & warnings | ||
anogam-all-anogam1.gbf : Genbank format for review | anogam-all-anogam1.gbf : Genbank format for review | ||
| + | |||
| + | You will find these sample outputs here http://insects.eugenes.org/genome/Anopheles_gambiae_str._PEST/anogam_20080511/ | ||
There remain caveats on reproducing the original GenBank record this way. At this writing, the GenbankSubmit function is still in development, and the Genbank to GFF to Chado loading has some losses. | There remain caveats on reproducing the original GenBank record this way. At this writing, the GenbankSubmit function is still in development, and the Genbank to GFF to Chado loading has some losses. | ||
Latest revision as of 17:03, 20 June 2008
This is an example test case for GMOD, loading a GenBank format genome (chromosome) to Chado database, then dumping it out, including GenBank submission format with GenBank output to test round-trip agreement.
This is an abbreviated example, current as of May 2008. It uses a Chado-db template in Postgres, and assumes you have installed/tested GMOD components available.
# get AnoGam chrX and load to chado db curl -OR ftp://bio-mirror.net/biomirror/ncbigenomes/Anopheles_gambiae/CHR_X/NC_004818.gbk.gz or curl -OR ftp://ftp.ncbi.nih.gov/genomes/Anopheles_gambiae/CHR_X/NC_004818.gbk.gz
set dbname=anogam_x $pg/bin/createdb -T chado_01_template $dbname
# fix Genbank FT to SO type map if needed vi lib/Bio/SeqFeature/Tools/TypeMapper.pm : add pseudogenic tRNA
# load chromosome X to chado gunzip -c NC_004818.gbk.gz |\ perl bin/bp_genbank2gff3.pl -noCDS -in stdin -out stdout |\ perl bin/gmod_bulk_load_gff3.pl -dbname $dbname -organism fromdata
# create GMOD Bulkfiles conf/bulkfiles/anogam.xml from template.xml : dbname, etc. edits # see samples to create a new organism/project configuration
# create standard Bulkfiles outputs for anogam_x perl -Ilib bin/bulkfiles.pl -config=anogam -make >& log.anogam1 &
# new in progress output, includes regurgitation of GenBank record to compare with original # you should check and edit conf/bulkfiles/genbanksubmit.xml before running this part perl -Ilib bin/bulkfiles.pl -config=anogam -format=genbanktbl -make
Outputs should include genbanksubmit/ folder with outputs of GMOD Bulkfiles:
anogam-all-anogam1.tbl : feature table ** new part anogam-all-anogam1.fsa : genome dna == fasta/chromosome anogam-all-anogam1.pep : protein aa == fasta/translation
and outputs of NCBI tbl2asn:
anogam-all-anogam1.sqn : ASN.1 record to submit to NCBI anogam-all-anogam1.val : errors & warnings anogam-all-anogam1.gbf : Genbank format for review
You will find these sample outputs here http://insects.eugenes.org/genome/Anopheles_gambiae_str._PEST/anogam_20080511/
There remain caveats on reproducing the original GenBank record this way. At this writing, the GenbankSubmit function is still in development, and the Genbank to GFF to Chado loading has some losses.
