./affyprobeset2ensg

SYNOPSIS

affyprobeset2ensg --man --help --verbose --version

affyprobeset2ensg --ensdb --enshost --user --affydb fileofaffyids.tab

Determine the genes whose transcripts are selected for by Ensembl'e Affy probe mapping.

OPTIONS

Options are specified on the command line. Their case is ignored, and they may be abbreviated to uniqueness (i.e. --h instead of --help).

--ensdb, --enshost, --user, --affydb: Read the description!
--help: Display command line usage with options.
--man: Display complete manual page and exit.
--verbose: Provides a trace of processing on STDERR.
--version: Display the scripts version number and exit.

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DESCRIPTION

Determine the genes whose transcripts are selected for by Ensembl'e Affy probe mapping, as found in the ensemble database --ensdb (default: mus_musculus_core_36_34d) hosted by mysql instance on --enshost (default: ensembldb.ensembl.org) connecting as --user (default: anonymous) with --password (default: NONE). Probeset names appear on STDIN (one per line), and must all be from the same --affydb (defaulting to AFFY_Mouse430_2).

Note that these results are for Ensembl's own precomputed Affy probe map, produced using process documented at http://www.ensembl.org/info/software/java/affy_probeset_to_transcript_mapping.html

Also note that this is pretty easily accomplished using Ensembl's BioMart.

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EXAMPLES

echo "1425308_at" | ./affyprobeset2ensg --enshost=ensembldb.ensembl.org --user anonymous --ensdb mus_musculus_core_36_34d --affydb AFFY_Mouse430_2 --verb

 PREPARED QUERY: 
 
 SELECT distinct x.dbprimary_acc, gs.stable_id
 FROM gene g, transcript t, object_xref o, xref x, external_db e, gene_stable_id gs
 WHERE x.xref_id           = o.xref_id
 AND g.gene_id             = t.gene_id
 AND e.external_db_id      = x.external_db_id
 AND o.ensembl_object_type = 'Transcript'
 AND o.ensembl_id          = t.transcript_id
 AND gs.gene_id            = g.gene_id
 AND e.db_name             = ?
 AND x.dbprimary_acc       = ?;
 
 
 
 RUNNING QUERY ON: AFFY_Mouse430_2, 1425308_at
 1425308_at     ENSMUSG00000058063

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VERSION

$Revision: 0.01$

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AUTHOR

Malcolm Cook (mec@stowers-institute.org)

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DEPENDENCIES

perl, DBI, DBD::mysql

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AVAILABILITY

Email the author for sources.

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./affyprobeset2ensg