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# -*-CPerl-*- |
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# Last changed Time-stamp: <2014-12-20 00:32:02 mtw> |
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package Bio::ViennaNGS::Fasta; |
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use 5.12.0; |
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use version; our $VERSION = qv('0.12_07'); |
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use Bio::Perl 1.00690001; |
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use Bio::DB::Fasta; |
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use Moose; |
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use Carp; |
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use Data::Dumper; |
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use namespace::autoclean; |
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has 'fa' => ( |
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is => 'rw', |
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isa => 'Str', |
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required => 1, |
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predicate => 'has_fa', |
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); |
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has 'fastadb' => ( |
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is => 'rw', |
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isa => 'Bio::DB::Fasta', |
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builder => '_get_fastadb', |
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predicate => 'has_db', |
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lazy => 1, |
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); |
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has 'fastaids' => ( |
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is => 'ro', |
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isa => 'ArrayRef', |
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builder => '_get_fastaids', |
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predicate => 'has_ids', |
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lazy => 1, |
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); |
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has 'primaryseq' => ( |
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is => 'ro', |
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isa => 'HashRef', |
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builder => '_get_primaryseq', |
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lazy => 1, |
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); |
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before 'primaryseq' => sub{ |
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my $self = shift; |
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$self->fastaids; |
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}; |
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before 'fastaids' => sub{ |
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my $self = shift; |
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$self->fastadb; |
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}; |
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sub _get_fastadb { |
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my $self = shift; |
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my $this_function = (caller(0))[3]; |
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confess "ERROR [$this_function] Fasta input not available" |
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unless (-f $self->fa); |
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my $db = Bio::DB::Fasta->new($self->fa) or croak $!; |
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return $db; |
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} |
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sub _get_fastaids { |
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my $self = shift; |
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my $this_function = (caller(0))[3]; |
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confess "ERROR [$this_function] Attribute 'fastadb' not found $!" |
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unless ($self->has_db); |
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my $db = $self->fastadb or croak $!; |
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my @ids = $db->ids or croak $!; |
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return \@ids; |
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} |
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sub _get_primaryseq { |
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my $self = shift; |
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my $this_function = (caller(0))[3]; |
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confess "ERROR [$this_function] Attribute 'fastaids' not found $!" |
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unless ($self->has_ids); |
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my %fobj = (); |
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my $db = $self->fastadb or croak $!; |
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foreach my $id (@{$self->fastaids}) { |
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$fobj{$id} = $db->get_Seq_by_id($id); # Bio::PrimarySeq::Fasta object |
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} |
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return \%fobj; |
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} |
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# stranded_subsequence ($id,$start,$stop,$strand) |
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# retrieve RNA/DNA sequence from a Bio::PrimarySeqI / |
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# Bio::PrimarySeq::Fasta object |
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sub stranded_subsequence { |
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my ($self,$id,$start,$end,$strand) = @_; |
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my ($this_function,$seq,$rc,$p,$obj); |
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$this_function = (caller(0))[3]; |
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my @dummy = $self->fastaids; |
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confess "ERROR [$this_function] Attribute 'fastaids' not found $!" |
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unless ($self->has_ids); |
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$p = $self->primaryseq; # Hash of Bio::PrimarySeq::Fasta objects |
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confess "ERROR [$this_function] Fasta ID $id not found in hash $!" |
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unless (exists $$p{$id}); |
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$obj = $$p{$id}; |
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$seq = $obj->subseq($start => $end); |
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if ($strand eq '-1' || $strand eq '-') { |
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$rc = revcom($seq); |
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$seq = $rc->seq(); |
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} |
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# print "id:$id\nstart:$start\nend:$end\n"; |
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return $seq; |
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} |
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sub has_sequid { |
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my ($self,$id) = @_; |
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my $ids = $self->fastaids; |
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#$i = grep{$_ eq $id}@{$ids} ? 1 : 0; |
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for my $j (@$ids){ |
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if ($id eq $j){return 1;} |
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else {return 0;} |
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} |
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return -1; |
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} |
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__PACKAGE__->meta->make_immutable; |
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1; |
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__END__ |
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=head1 NAME |
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Bio::ViennaNGS::Fasta - Moose wrapper for Bio::DB::Fasta |
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=head1 SYNOPSIS |
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use Bio::ViennaNGS::Fasta; |
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my $f = Bio::ViennaNGS::Fasta->new( fa => "data/foo.fa", ); |
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# get all FASTA IDs |
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my @ids = $f->fastaids; |
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# get a reference to a hash of Bio::PrimarySeq::Fasta objects whose |
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# keys are the Fasta IDs |
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my $ps = $f->primaryseq; |
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# get the strand-specific genomic sequence for a certain Fasta ID |
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my $id = "chr1"; |
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my $start = 287; |
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my $end = 1289; |
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my $strand = "+"; |
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my $seq = $foo->stranded_subsequence($id,$start,$end,$strand); |
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=head1 DESCRIPTION |
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This module provides a L<Moose> interface to L<Bio::DB::Fasta>. |
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=head1 METHODS |
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=over |
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=item stranded_subsequence |
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Title : stranded_subsequence |
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Usage : $obj->stranded_subsequence($id,$start,$end,$strand) |
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Function: Returns the DNA/RNA sequence for C<$id> from |
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C<$start> to C<$end>. |
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Args : C<$id> is the Fasta ID (a L<Bio::PrimarySeq::Fasta> object). |
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C<$start> and C<$end> should be self-explnatory, C<$strand> |
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is 1 or -1 for [+] or [-] strand, respectively |
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Returns : A string |
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=back |
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=head1 DEPENDENCIES |
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=over 5 |
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=item L<Bio::Perl> >= 1.00690001 |
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=item L<Bio::DB::Fasta> |
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=item L<Moose> |
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=item L<Carp> |
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=item L<namespace::autoclean> |
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=back |
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=head1 SEE ALSO |
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=over 2 |
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=item L<Bio::ViennaNGS> |
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=item L<Bio::DB::Fasta> |
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=back |
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=head1 AUTHOR |
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Michael T. Wolfinger, E<lt>michael@wolfinger.euE<gt> |
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=head1 COPYRIGHT AND LICENSE |
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Copyright (C) 2014 by Michael T. Wolfinger |
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This library is free software; you can redistribute it and/or modify |
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it under the same terms as Perl itself, either Perl version 5.16.3 or, |
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at your option, any later version of Perl 5 you may have available. |
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This software is distributed in the hope that it will be useful, but |
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WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. |
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=cut |