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
bio::tools::geneid
Bio::Tools::Geneid(3pm) User Contributed Perl Documentation Bio::Tools::Geneid(3pm)
NAME
Bio::Tools::Geneid - Results of one geneid run
SYNOPSIS
use Bio::Tools::Geneid;
my $gid = Bio::Tools::Geneid(-file => "geneid.out");
while (my $gene = $gid->next_prediction)
{
my @transcripts = $gene->transcripts;
foreach my $t (@transcripts)
{
my @exons = $t->exons;
foreach my $e (@exons)
{
printf("Exon %d..%d
", $e->start, $e->end);
}
}
}
DESCRIPTION
This is the parser for the output of geneid by Enrique Blanco and Roderic Guigo (IMIM-UPF). See http://www1.imim.es/software/geneid. It
relies on native geneid output format internally and will work with geneid versions 1.0 and 1.1. Currently this module supports only the
default mode of operation which is to predict exons and assemble an optimal gene prediction.
It takes either a file handle or a file name and returns a Bio::SeqFeature::Gene::GeneStructure object.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Keith James
Email: kdj@sanger.ac.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : $obj->new(-file = "<geneid.out");
$obj->new(-fh => *GI);
Function: Constructor for geneid wrapper. Takes either a file
: or filehandle
Returns : L<Bio::Tools::Geneid>
next_prediction
Title : next_prediction
Usage : while($gene = $geneid->next_prediction)
{
# do something
}
Function: Returns the gene structure prediction of the geneid result
file. Call this method repeatedly until FALSE is returned.
Returns : A Bio::SeqFeature::Gene::GeneStructure object
Args : None
_add_exon
Title : _add_exon
Usage : $obj->_add_exon($gene, $transcript, ... exon data ...)
Function: Adds a new exon to both gene and transcript from the data
: supplied as args
Example :
Returns : Nothing
_set_strand
Title : _set_strand
Usage : $obj->_set_strand($gene)
Function: Sets the overall gene strand to the same strand as all
: the exons if they are all on the same strand, or to strand 0
: if the exons are on different strands.
Example :
Returns : Nothing
_target_id
Title : _target_id
Usage : $obj->_target_id
Function: get/set for genomic sequence id
Example :
Returns : A target ID
perl v5.14.2 2012-03-02 Bio::Tools::Geneid(3pm)