GMODTools 1.2b bulkfiles to dump gff3 from Chado

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

GMODTools 1.2b bulkfiles to dump gff3 from Chado

Sanjay Chellapilla
Hello,

I am trying to use GMODTools bulkfiles script to dump gff3 from a Chado-1.22
database. I downloaded GMODTools-1.2b.zip from http://eugenes.org/gmod/GMODTools/
and installed the sample sgdlite Chado database. There were a few errors as below,
when loading the sample sgdlite database.

psql:<stdin>:1320464: ERROR:  insert or update on table "arraydesign" violates foreign key constraint "$1"
DETAIL:  Key (manufacturer_id)=(25) is not present in table "contact".
psql:<stdin>:1320545: ERROR:  insert or update on table "assay" violates foreign key constraint "$3"
DETAIL:  Key (operator_id)=(3) is not present in table "contact".

And then trying to dump gff3 from it using bulkfiles, using the following command

perl -Ilib bin/bulkfiles.pl -format gff -conf conf/sgdtest.xml -make \
-showconfig -debug >& gmodtools-bulkfiles-debug-sgdtest.log

I see the following errors in the log file.

Can't use string ("32/64") as a HASH ref while "strict refs" in use at lib/Bio/GMOD/Bulkfiles/BulkWriter.pm line 96.
no writer module for fff
# feature_table org=scer species=Saccharomyces_cerevisiae path=data/genomes/Saccharomyces_cerevisiae/scer_2012-11-13_16_22_54/tmp/featdump
# feature_table files=chadofeat-scersum.tsv
read feature tables= sum
Can't call method "makeFiles" without a package or object reference at lib/Bio/GMOD/Bulkfiles.pm line 1517.

I get the same errors when using conf/bulkfiles/sgdbulk.xml too.
Please could you help resolve the errors - am I missing something.
Thank you.

Sanjay.

------------------------------------------------------------------------------
Monitor your physical, virtual and cloud infrastructure from a single
web console. Get in-depth insight into apps, servers, databases, vmware,
SAP, cloud infrastructure, etc. Download 30-day Free Trial.
Pricing starts from $795 for 25 servers or applications!
http://p.sf.net/sfu/zoho_dev2dev_nov
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema