06-17-2010
pseudocoder
Would it be a way to do the same with bash? It will be easier for me to understand.
I was wondering if there is any way to calculate the frequency of each sequence? In other words, let assume that after 'trimming' the sequences there are several that are identical, would it be possible to determine the frequency and include it as part of the ID line? Something like this:
Quote:
> Seq A Freq 50
AGAGATAGATAGAGCTGAT
> Seq B Freq 25
AGAGATAGATAGAGCTGAT
> Seq C Freq 25
AGAGATAGATAGAGCTGAT
Thanks
Last edited by Xterra; 06-17-2010 at 05:00 AM..
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LEARN ABOUT DEBIAN
bio::assembly::singlet
Bio::Assembly::Singlet(3pm) User Contributed Perl Documentation Bio::Assembly::Singlet(3pm)
NAME
Bio::Assembly::Singlet - Perl module to hold and manipulate
singlets from sequence assembly contigs.
SYNOPSIS
# Module loading
use Bio::Assembly::IO;
# Assembly loading methods
$aio = Bio::Assembly::IO->new( -file => 'test.ace.1',
-format => 'phrap' );
$assembly = $aio->next_assembly;
foreach $singlet ($assembly->all_singlets) {
# do something
}
# OR, if you want to build the singlet yourself,
use Bio::Assembly::Singlet;
$singlet = Bio::Assembly::Singlet->new(
-id => 'Singlet1',
-seqref => $seq
);
DESCRIPTION
A singlet is a sequence that phrap was unable to align to any other sequences.
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 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 - Chad S. Matsalla
bioinformatics1 at dieselwurks.com
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : $singlet = $io->new( -seqref => $seq )
Function: Create a new singlet object
Returns : A Bio::Assembly::Singlet object
Args : -seqref => Bio::Seq-compliant sequence object for the singlet
seqref
Title : seqref
Usage : $seqref = $singlet->seqref($seq);
Function: Get/set the sequence to which this singlet refers
Returns : A Bio::Seq-compliant object
Args : A Bio::Seq-compliant or Bio::Seq::Quality object
_seq_to_singlet
Title : _seq_to_singlet
Usage : $singlet->seqref($seq)
Function: Transform a sequence into a singlet
Returns : 1 for sucess
Args : A Bio::Seq-compliant object
perl v5.14.2 2012-03-02 Bio::Assembly::Singlet(3pm)