Helpers to handle canonical forms of genes about cruzdb

[brentp]

Do you know about knownCanonical?

http://genome.ucsc.edu/cgi-bin/hgTables?hgta_doSchemaDb=hg19&hgta_doSchemaTable=knownCanonical

[brentp]

ping @lbeltrame : does knownCanonical do what you need?

[lbeltrame]

In data martedì 8 ottobre 2013 07:10:06, Brent Pedersen - Bioinformatics ha
scritto:

ping @lbeltrame : does knownCanonical do what you need?

It does, through a rather convoluted query, but it does.

[brentp]

can you post the query? maybe we can make it simpler. probably related to #9

On Tue, Oct 8, 2013 at 8:13 AM, Luca Beltrame [email protected]:

In data martedì 8 ottobre 2013 07:10:06, Brent Pedersen - Bioinformatics
ha
scritto:

ping @lbeltrame : does knownCanonical do what you need?

It does, through a rather convoluted query, but it does.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/11#issuecomment-25893218
.

[lbeltrame]

can you post the query? maybe we can make it simpler. probably related to #9

It is something like this (apologies, I can't format it via replies through
email):

query(
ucsc.kgXref.geneSymbol, ucsc.knownCanonical.chromStart,
ucsc.knownCanonical.chromEnd,ucsc.refFlat.strand).filter(
(ucsc.kgXref.geneSymbol.in_(genes.values)) &
(ucsc.kgXref.kgID == ucsc.knownCanonical.transcript) &
(ucsc.refFlat.geneName == ucsc.kgXref.geneSymbol)
).distinct()

Where "ucsc" is my Genome instance, "genes" is a list of genes I'm interested
in and "query" is just an alias for "ucsc.session.query".

[brentp]

cheers. I'll make that simpler soon.

On Tue, Oct 8, 2013 at 8:36 AM, Luca Beltrame [email protected]:

can you post the query? maybe we can make it simpler. probably related
to #9

It is something like this (apologies, I can't format it via replies
through
email):

query(
ucsc.kgXref.geneSymbol, ucsc.knownCanonical.chromStart,
ucsc.knownCanonical.chromEnd,ucsc.refFlat.strand).filter(
(ucsc.kgXref.geneSymbol.in_(genes.values)) &
(ucsc.kgXref.kgID == ucsc.knownCanonical.transcript) &
(ucsc.refFlat.geneName == ucsc.kgXref.geneSymbol)
).distinct()

Where "ucsc" is my Genome instance, "genes" is a list of genes I'm
interested
in and "query" is just an alias for "ucsc.session.query".

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/11#issuecomment-25895238
.