Chris Mungall > go-db-perl-0.01 > go-fetch-associations-by-terms.pl

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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)

DOCUMENTATION

http://www.godatabase.org/dev

SEE ALSO

GO::AppHandle

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