NAME

Bio::ViennaNGS::Fasta - Moose wrapper for Bio::DB::Fasta

SYNOPSIS

  use Bio::ViennaNGS::Fasta;

  my $f = Bio::ViennaNGS::Fasta->new( fa => "data/foo.fa", );

  # get all FASTA IDs
  my @ids = $f->fastaids;

  # get a reference to a hash of Bio::PrimarySeq::Fasta objects whose
  # keys are the Fasta IDs
  my $ps = $f->primaryseq;

  # get the strand-specific genomic sequence for a certain Fasta ID
  my $id = "chr1";
  my $start = 287;
  my $end = 1289;
  my $strand = "+";
  my $seq = $foo->stranded_subsequence($id,$start,$end,$strand);

DESCRIPTION

This module provides a Moose interface to Bio::DB::Fasta.

METHODS

stranded_subsequence

Title : stranded_subsequence

Usage : $obj->stranded_subsequence($id,$start,$end,$strand)

Function : Returns the DNA/RNA sequence for $id from $start to $end.

Args : $id is the Fasta ID (a Bio::PrimarySeq::Fasta object). $start and $end should be self-explnatory, $strand is 1 or -1 for [+] or [-] strand, respectively.

Returns : A string.

DEPENDENCIES

Bio::Perl >= 1.00690001

Bio::DB::Fasta

Moose

Carp

namespace::autoclean

SEE ALSO

Bio::ViennaNGS

Bio::DB::Fasta

AUTHOR

Michael T. Wolfinger, <michael@wolfinger.eu>

COPYRIGHT AND LICENSE

Copyright (C) 2014-2015 by Michael T. Wolfinger

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.0 or, at your option, any later version of Perl 5 you may have available.

This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.