NAME
go-fetch-associations-by-terms.pl - queries db for associations to terms
SYNOPSIS
go-fetch-associations-by-terms.pl -d go -h localhost "cysteine*"
go-fetch-associations-by-terms.pl -d go -id GO:0008234 -id GO:003693
go-fetch-associations-by-term.pl -d go_load -denormalized -q type=biological_process -q "search=cysteine*"
go-fetch-associations-by-term.pl -d go_load -q "where=term.name like '%neuroderm%' or term.name like '%procephalic%'"DESCRIPTION
Queries db for associations to queried terms. Traverses DAG to get recursive associations
ARGUMENTS
Arguments are either connection arguments, generic to all go-db-perl scripts, and arguments specific to this script
CONNECTION ARGUMENTS
Specify db connect arguments first; these are:
- -dbname [or -d]
-
name of database; usually "go" but you may want point at a test/dvlp database
- -dbuser
-
name of user to connect to database as; optional
- -dbauth
-
password to connect to database with; optional
- -dbhost [or -h]
-
name of server where the database server lives; see http://www.godatabase.org/dev/database for details of which servers are active. or you can just specify "localhost" if you have go-mysql installed locally
SCRIPT ARGUMENTS
- -id ID
-
GO/OBO accession no; multiple can be passed on one line; eg
-id GO:0008234 -id GO:003693 - -q KEY=VAL
-
Pass in query constraints
See GO::AppHandle for full list, under get_terms() method
- -denormalized
-
Writes one row for every gene_product to term association (default will combine all terms for one gene product on one row)
- -use_property PROP
-
if the db has gene_product_property defined, this will fill in the specified propery value instead of summarising all properties. Multiple props can be passed.
OUTPUT
The default output produces tab-delimited rows with the following data:
- GeneProduct-dbname
- GeneProduct-accession
- GeneProduct-symbol
- GeneProduct-full_name
- GeneProduct-properties
- Terms
Only the terms that were in the initial query which are associated to that gene product are listed
With the -denormalized option each term is listed on its own row, with two additional columns (termacc and termname)