07-26-2012
Request to check
hi
Thanks for reply.
I have a first ile like this
Quote:
Gene Drug
ADRB2 (PA39) hydrochlorothiazide (PA449899)
WNK1 (PA33782) hydrochlorothiazide (PA449899)
ERCC1 (PA155) Platinum compounds (PA164713176)
ERCC1 (PA155) Platinum compounds (PA164713176)
NEDD4L (PA31534) hydrochlorothiazide (PA449899)
ADD1 (PA31) Antihypertensives (PA164712445)
ADD1 (PA31) Thiazides, plain (PA164713347)
CYP2C9 (PA126) simvastatin (PA45136
so gene name in one file has to match with gene name in other file but PA39 is actually not included in gene name only letter in caps are inlcuded in genen name in second file.
So it shuld match only with gene name not PA entries
if its same then before that common name there shuld be entry of scondm column of scond file and first file with no PA entries if possible
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LEARN ABOUT DEBIAN
ace::sequence::transcript
Ace::Sequence::Transcript(3pm) User Contributed Perl Documentation Ace::Sequence::Transcript(3pm)
NAME
Ace::Sequence::Transcript - Simple "Gene" Object
SYNOPSIS
# open database connection and get an Ace::Object sequence
use Ace::Sequence;
# get a megabase from the middle of chromosome I
$seq = Ace::Sequence->new(-name => 'CHROMOSOME_I,
-db => $db,
-offset => 3_000_000,
-length => 1_000_000);
# get all the transcripts
@genes = $seq->transcripts;
# get the exons from the first one
@exons = $genes[0]->exons;
# get the introns
@introns = $genes[0]->introns
# get the CDSs (NOT IMPLEMENTED YET!)
@cds = $genes[0]->cds;
DESCRIPTION
Ace::Sequence::Gene is a subclass of Ace::Sequence::Feature. It inherits all the methods of Ace::Sequence::Feature, but adds the ability
to retrieve the annotated introns and exons of the gene.
OBJECT CREATION
You will not ordinarily create an Ace::Sequence::Gene object directly. Instead, objects will be created in response to a transcripts()
call to an Ace::Sequence object.
OBJECT METHODS
Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported:
exons()
@exons = $gene->exons;
Return a list of Ace::Sequence::Feature objects corresponding to annotated exons.
introns()
@introns = $gene->introns;
Return a list of Ace::Sequence::Feature objects corresponding to annotated introns.
cds()
@cds = $gene->cds;
Return a list of Ace::Sequence::Feature objects corresponding to coding sequence. THIS IS NOT YET IMPLEMENTED.
relative()
$relative = $gene->relative;
$gene->relative(1);
This turns on and off relative coordinates. By default, the exons and intron features will be returned in the coordinate system used
by the gene. If relative() is set to a true value, then coordinates will be expressed as relative to the start of the gene. The first
exon will (usually) be 1.
SEE ALSO
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF
AUTHOR
Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>
Copyright (c) 1999, Lincoln D. Stein
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
POD ERRORS
Hey! The above document had some coding errors, which are explained below:
Around line 168:
You forgot a '=back' before '=head1'
perl v5.14.2 2001-05-22 Ace::Sequence::Transcript(3pm)