Michael Bekaert > ora > Bio::ORA

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NAME ^

Bio::ORA - Olfactory Receptor family Assigner (ORA) [bioperl module]

SYNOPSIS ^

Take a sequence object from, say, an inputstream, and find an Olfactory Receptor gene. HMM profiles are used in order to identify location, frame and orientation of such gene.

Creating the ORA object, eg:

  my $inputstream = Bio::SeqIO->new( -file => 'seqfile', -format => 'fasta' );
  my $seqobj = $inputstream->next_seq();
  my $ORA_obj = Bio::ORA->new( $seqobj );

Obtain an array holding the start point, the stop point, the DNA sequence and amino-acid sequence, eg:

  my $array_ref = $ORA_obj->{'_result'} if ( $ORA_obj->find() );

Display result in genbank format, eg:

  $ORA_obj->show( 'genbank' );

DESCRIPTION ^

Bio::ORA is a featherweight object for identifying mammalian olfactory receptor genes. The sequences should not be longer than 40kb. The returned array include location, sequence and statistic for the putative olfactory receptor gene. Fully functional with DNA and EST sequence, no intron supported.

See Synopsis above for the object creation code.

DRIVER SCRIPT ^

  #!/usr/bin/perl
  use strict;
  use warnings;
  use Bio::Seq;
  use Bio::ORA;

  my $inseq = Bio::SeqIO->new( '-file' => q{<} . $ARGV[0], -format => 'fasta' );
  while (my $seq = $inseq->next_seq) {
    my $ORA_obj = Bio::ORA->new( $seq );
    if ( $ORA_obj->find() ) {
      $ORA_obj->show( 'genbank' );
    } else {
      print {*STDOUT} "  no hit!\n";
    }
  }

REQUIREMENTS ^

To use this module you may need: * Bioperl (http://bioperl.org/) modules, * HMMER v3+ distribution (http://hmmer.org/) and * FASTA 36+ distribution (ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/).

LOCAL ADAPTATION ^

This module uses three softwares. If HMMER or FASTA are updated make sure that HMMER's hmmscan and FASTA's tfastx36 and fastx36 still exists under these names. You change the call my editing the "Default softwares" section.

  # Default softwares
  my $hmmscan = 'hmmscan';
  my $tfastx = 'tfastx36';
  my $fastx = 'fastx36';

FEEDBACK ^

If you have any problems with or questions about the scripts, please contact us through a GitHub issue (https://github.com/pseudogene/ora/issues). You are invited to contribute new features, fixes, or updates, large or small; we are always thrilled to receive pull requests, and do our best to process them as fast as we can.

AUTHOR ^

Michael Bekaert (michael.bekaert@stir.ac.uk)

Address: Institute of Aquaculture University of Stirling Stirling Scotland, FK9 4LA UK

SEE ALSO ^

perl(1), bioperl web site

LICENSE ^

Copyright 2007-2016 - Michael Bekaert

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program 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. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

APPENDIX ^

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

_findexec

 Title   : _findexec
 Usage   : my $path = $self->_findexec( $exec );
 Function: Find an executable file in the $PATH.
 Returns : The full path to the executable.
 Args    : $exec (mandatory) executable to be find.

new

 Title   : new
 Usage   : my $nb = Bio::ORA->new( $seqobj, $table, $aug, $hmm );
 Function: Initialize ORA object.
 Returns : An ORA object.
 Args    : $seqobj (mandatory) PrimarySeqI object (dna or rna),
           $table (optional) translation table/genetic code number,
              the default value is 1,
           $aug (optional) use other start codon than AUG (default 0),
           $hmm (optional) path to hmm profiles by default ORA looks at
             ./or.hmm.

find

 Title   : find
 Usage   : my $bool = $ORI_obj->find( $evalue, $strand, $start, $end );
 Function: Identify an olfactory receptor protein.
 Returns : boolean.
 Args    : $evalue (optional) set the E-value (expected) threshold.
             Default is 1e-30,
           $strand(optional) strand where search should be done (1 direct,
             -1 reverse or 0 both). Default is 0,
           $start (optional) coordinate of the first nucleotide. Useful
             for coordinate calculation when first is not 1. Default is 1,
           $end (optional) coordinate of the last nucleotide. Default is
             the sequence length.

_what_or

 Title   : _what_or
 Usage   : my $bool = $self->_what_or( $strand );
 Function: Use HMM profiles to identify an olfactory receptor gene.
 Returns : boolean.
 Args    : $strand (optional) strand where search should be done
           (1 direct, -1 reverse or 0 both). Default is 0.

_find_orf

 Title   : _find_orf
 Usage   : my $bool = $self->_find_or( $strand, $start, $end );
 Function: Retrieve the olfactory receptor ORF.
 Returns : boolean.
 Args    : $strand (mandatory) strand where ORA have been found
           (1 direct or -1 reverse),
           $start (mandatory) coordinate of the first nucleotide,
           $end (mandatory) coordinate of the last nucleotide.

getHits

 Title   : getHits
 Usage   : my @hits = Bio::ORA->getHits( $seq, $evalue, $ref );
 Function: Quick localization of ORs (use FASTA).
 Returns : Array of hits start/stop positions.
 Args    : $seq (mandatory) primarySeqI object (dna or rna),
           $evalue (mandatory) det the E-value threshold,
           $ref (optional) path to fasta reference file, by default ORA
             look at ./or.fasta.

fastScan

 Title   : fastScan
 Usage   : my @hits = Bio::ORA->fastScan( $seq, $ref );
 Function: Quick localization of ORs (use FASTA).
 Returns : Array of hits start/stop positions.
 Args    : $seq (mandatory) primarySeqI object (dna or rna),
           $ref (optional) path to fasta reference file, by default ORA
             look at ./or.fasta.

show

 Title   : show
 Usage   : $ORA_obj->show( $outstyle );
 Function: Print result in various style.
 Returns : none.
 Args    : $outstyle (mandatory) 'fasta', 'genbank', 'cvs', 'xml' or 'tsv' style.

_translation

 Title   : _translation
 Usage   : my ( $start, $end ) = $self->_translation();
 Function: format initiation and stop codons for regex.
 Returns : array with initiation and stop codons.
 Args    : none.
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