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
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.