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Top Forums Shell Programming and Scripting Convert rows to columns based on condition Post 302843770 by raj_k on Thursday 15th of August 2013 01:33:45 AM
Old 08-15-2013
Convert rows to columns based on condition

I have a file some thing like this:
Code:
GN   Name=YWHAB;
RC   TISSUE=Keratinocyte;
RC   TISSUE=Thymus;
CC   -!- FUNCTION: Adapter protein implicated in the regulation of a large
CC       spectrum of both general and specialized signaling pathways
GN   Name=YWHAE;
RC   TISSUE=Liver;
RC   TISSUE=Brain;
RC   TISSUE=Heart;
CC   -!- FUNCTION: Adapter protein implicated in the regulation of a large
CC       spectrum of both general and specialized signaling pathways. Binds
CC       to a large number of partners, usually by recognition of a
CC       phosphoserine or phosphothreonine motif. Binding generally results
CC       in the modulation of the activity of the binding partner.

I want to keep the information related to each entry column wise. each entry starts with GN (gene name) and ends with Function

Code:
GN	TISSUE	                 FUNCTION		
YWHAB	Keratinocyte;Thymus	Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways
YWHAE	Liver;Brain;Heart;	Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner.

 
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Bio::Matrix::PSM::InstanceSite(3pm)			User Contributed Perl Documentation		       Bio::Matrix::PSM::InstanceSite(3pm)

NAME
Bio::Matrix::PSM::InstanceSite - A PSM site occurance SYNOPSIS
use Bio::Matrix::PSM::InstanceSite; #You can get an InstanceSite object either from a file: my ($instances,$matrix)=$SomePSMFile->parse_next; #or from memory my %params=(seq=>'TATAAT', id=>"TATAbox1", accession=>'ENSG00000122304', mid=>'TB1', desc=>'TATA box, experimentally verified in PRM1 gene', -relpos=>-35, -anchor=>'CHR7', -start=>35000921, -end=>35000926); #Last 2 arguments are passed to create a Bio::LocatableSeq object #Anchor shows the coordinates system for the Bio::LocatableSeq object DESCRIPTION
Abstract interface to PSM site occurrence (PSM sequence match). InstanceSite objects may be used to describe a PSM (See Bio::Matrix::PSM::SiteMatrix) sequence matches. The usual characteristic of such a match is sequence coordinates, score, sequence and sequence (gene) identifier- accession number or other id. This object inherits from Bio::LocatableSeq (which defines the real sequence) and might hold a SiteMatrix object, used to detect the CRE (cis-regulatory element), or created from this CRE. While the documentation states that the motif id and gene id (accession) combination should be unique, this is not entirely true- there might be more than one occurrence of the same cis-regulatory element in the upstream region of the same gene. Therefore relpos would be the third element to create a really unique combination. 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/ Description Bio::Matrix::PSM::InstanceSiteI implementation AUTHOR - Stefan Kirov Email skirov@utk.edu APPENDIX
new Title : new Usage : my $isntance=Bio::Matrix::PSM::InstanceSite->new (-seq=>'TATAAT', -id=>"TATAbox1", -accession_number='ENSG00000122304', -mid=>'TB1', -desc=>'TATA box, experimentally verified in PRM1 gene', -relpos=>-35, -anchor=>'CHR7', -start=>35000921, -end=>35000926, strand=>1) Function: Creates an InstanceSite object from memory. Throws : Example : Returns : Bio::Matrix::PSM::InstanceSite object Args : hash mid Title : mid Usage : my $mid=$instance->mid; Function: Get/Set the motif id Throws : Example : Returns : scalar Args : scalar score Title : score Usage : my $score=$instance->score; Function: Get/Set the score (mismatches) between the instance and the attached (or initial) PSM Throws : Example : Returns : real number Args : real number anchor Title : anchor Usage : my $anchor=$instance->anchor; Function: Get/Set the anchor which shows what coordinate system start/end use Throws : Example : Returns : string Args : string start Title : start Usage : my $start=$instance->start; Function: Get/Set the position of the instance on the sequence used Throws : Example : Returns : integer Args : integer minstance Title : minstance Usage : my $minstance=$misntance->score; Function: Get/Set the unique identifier- sequence id/motif id, for example PRM1_TATAbox. Not necessarily human readable. Throws : Example : Returns : string Args : string relpos Title : relpos Usage : my $seqpos=$instance->relpos; Function: Get/Set the relative position of the instance with respect to the transcription start site (if known). Can and usually is negative. Throws : Example : Returns : integer Args : integer annotation Title : annotation Usage : $ann = $seq->annotation or $seq->annotation($annotation) Function: Gets or sets the annotation Returns : L<Bio::AnnotationCollectionI> object Args : None or L<Bio::AnnotationCollectionI> object See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information species Title : species Usage : $species = $seq->species() or $seq->species($species) Function: Gets or sets the species Returns : L<Bio::Species> object Args : None or L<Bio::Species> object See Bio::Species for more information frame Title : frame Usage : my $frane=$instance->frame; Function: Get/Set the frame of a DNA instance with respect to a protein motif used. Returns undef if the motif was not protein or the DB is protein. Throws : Example : Returns : integer Args : integer (0, 1, 2) perl v5.14.2 2012-03-02 Bio::Matrix::PSM::InstanceSite(3pm)

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