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Full Discussion: Re-ordering data
Top Forums Shell Programming and Scripting Re-ordering data Post 302502119 by quincyjones on Monday 7th of March 2011 12:38:21 AM
Old 03-07-2011
Thanx Chubler. Only problem is that strand column is missing.
Code:
qqq	start	end	strand	zzFactor	ttt	cut-off	seq_position	kmer_location	k-mer	Score
qqq10	100017878		100017978	XXX	crsmsgw	0.6429	26	qqq10:100017953	cgcccgg	0.753
qqq10	100017878		100017978	YYY	crsmsgw	0.6429	26	qqq10:100017953	cgcccgg	0.753

 
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Bio::SeqFeature::SiRNA::Pair(3pm)			User Contributed Perl Documentation			 Bio::SeqFeature::SiRNA::Pair(3pm)

NAME
Bio::SeqFeature::SiRNA::Pair - Perl object for small inhibitory RNA (SiRNA) oligo pairs SYNOPSIS
use Bio::SeqFeature::SiRNA::Pair; my $pair = Bio::SeqFeature::SiRNA::Pair-> new( -sense => $bio_seqfeature_sirna_oligo, # strand=1 -antisense => $bio_seqfeature_sirna_oligo, # strand= -1 -primary => 'SiRNA::Pair', -source_tag => 'Bio::Tools::SiRNA', -start => 8, -end => 31, -rank => 1, -fxgc => 0.5, -tag => { note => 'a note' } ); $target_sequence->add_SeqFeature($pair); DESCRIPTION
Object methods for (complementary) pairs of Bio::SeqFeature::SiRNA::Oligo objects - inherits Bio::SeqFeature::Generic. See that package for information on inherited methods. Does not include methods for designing SiRNAs -- see Bio::Tools::SiRNA SEE ALSO
Bio::SeqFeature::Oligo, Bio::Tools::SiRNA. 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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR
Donald Jackson (donald.jackson@bms.com) APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ METHODS
new Title : new Usage : my $sirna_pair = Bio::SeqFeature::SiRNA::Pair->new(); Purpose : Create a new SiRNA::Pair object Returns : Bio::Tools::SiRNA object Args : -start 10 -end 31 -rank 1 # 'Rank' in Tuschl group's rules -fxgc 0.5 # GC fraction for target sequence -primary 'SiRNA::Pair', # default value -source_tag 'Bio::Tools::SiRNA' -tag { note => 'A note' } -sense a Bio::SeqFeature::SiRNA::Oligo object with strand = 1 -antisense a Bio::SeqFeature::SiRNA::Oligo object with strand = -1 ); Note : SiRNA::Pair objects are typically created by a design algorithm such as Bio::Tools::SiRNA rank Title : rank Usage : my $pair_rank = $sirna_pair->rank() Purpose : Get/set the 'quality rank' for this pair. See Bio::Tools::SiRNA for a description of ranks. Returns : scalar Args : scalar (optional) indicating pair rank fxGC Title : fxGC Usage : my $fxGC = $sirna_pair->fxGC(); Purpose : Get/set the fraction of GC for this pair - based on TARGET sequence, not oligos. Returns : scalar between 0-1 Args : scalar between 0-1 (optional) sense Title : sense Usage : my $sense_oligo = $sirna_pair->sense() Purpose : Get/set the SiRNA::Oligo object corresponding to the sense strand Returns : Bio::SeqFeature::SiRNA::Oligo object Args : Bio::SeqFeature::SiRNA::Oligo object antisense Title : antisense Usage : my $antisense_oligo = $sirna_pair->antisense() Purpose : Get/set the SiRNA::Oligo object corresponding to the antisense strand Returns : Bio::SeqFeature::SiRNA::Oligo object Args : Bio::SeqFeature::SiRNA::Oligo object perl v5.14.2 2012-03-02 Bio::SeqFeature::SiRNA::Pair(3pm)

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