#
# BioPerl module for Bio::Tools::ERPIN
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Fields <cjfields-at-uiuc-dot-edu>
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::ERPIN - a parser for ERPIN output
=head1 SYNOPSIS
use Bio::Tools::ERPIN;
my $parser = Bio::Tools::ERPIN->new( -file => $rna_output,
-motiftag => 'protein_bind'
-desctag => 'TRAP_binding');
#parse the results
while( my $motif = $parser->next_prediction) {
# do something here
}
=head1 DESCRIPTION
Parses raw ERPIN output.
This module is not currently complete. As is, it will parse raw
ERPIN long format output and pack information into
Bio::SeqFeature::Generic objects.
Several values have also been added in the 'tag' hash. These can be
accessed using the following syntax:
my ($entry) = $feature->get_Annotations('SecStructure');
Added tags are :
tset - training set used for the sequence
tsetdesc - training set description line
cutoff - cutoff value used
database - name of database
dbdesc - description of database
dbratios - nucleotide ratios of database (used to calculate evalue)
descline - entire description line (in case the regex used for
sequence ID doesn't adequately catch the name
accession - accession number of sequence (if present)
logodds - logodds score value
sequence - sequence from hit, separated based on training set
See t/ERPIN.t for example usage.
At some point a more complicated feature object may be used to support
this data rather than forcing most of the information into tag/value
pairs in a SeqFeature::Generic. This will hopefully allow for more
flexible analysis of data (specifically RNA secondary structural
data).
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 AUTHOR - Chris Fields
Email cjfields-at-uiuc-dot-edu
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::ERPIN;
use strict;
use Bio::SeqFeature::Generic;
use base qw(Bio::Tools::AnalysisResult);
our($MotifTag,$SrcTag,$DescTag) = qw(misc_binding ERPIN erpin);
=head2 new
Title : new
Usage : my $obj = Bio::Tools::ERPIN->new();
Function: Builds a new Bio::Tools::ERPIN object
Returns : an instance of Bio::Tools::ERPIN
Args : -fh/-file for input filename
-motiftag => primary tag used in gene features (default 'misc_binding')
-desctag => tag used for display_name name (default 'erpin')
-srctag => source tag used in all features (default 'ERPIN')
=cut
sub _initialize {
my($self,@args) = @_;
$self->warn('Use of this module is deprecated. Use Bio::SearchIO::erpin instead');
$self->SUPER::_initialize(@args);
my ($motiftag,$desctag,$srctag) = $self->SUPER::_rearrange([qw(MOTIFTAG
DESCTAG
SRCTAG
)],
@args);
$self->motif_tag(defined $motiftag ? $motiftag : $MotifTag);
$self->source_tag(defined $srctag ? $srctag : $SrcTag);
$self->desc_tag(defined $desctag ? $desctag : $DescTag);
foreach (qw(_tset _tset_desc _cutoff _db _db_desc
_db_ratios _eval_cutoff _seqid _secacc _seqdesc )) {
$self->{$_}='';
}
}
=head2 motif_tag
Title : motiftag
Usage : $obj->motiftag($newval)
Function: Get/Set the value used for 'motif_tag', which is used for setting the
primary_tag.
Default is 'misc_binding' as set by the global $MotifTag.
'misc_binding' is used here because a conserved RNA motif is capable
of binding proteins (regulatory proteins), antisense RNA (siRNA),
small molecules (riboswitches), or nothing at all (tRNA,
terminators, etc.). It is recommended that this be changed to other
tags ('misc_RNA', 'protein_binding', 'tRNA', etc.) where appropriate.
For more information, see:
http://www.ncbi.nlm.nih.gov/collab/FT/index.html
Returns : value of motif_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub motif_tag{
my $self = shift;
return $self->{'motif_tag'} = shift if @_;
return $self->{'motif_tag'};
}
=head2 source_tag
Title : source_tag
Usage : $obj->source_tag($newval)
Function: Get/Set the value used for the 'source_tag'.
Default is 'ERPIN' as set by the global $SrcTag
Returns : value of source_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub source_tag{
my $self = shift;
return $self->{'source_tag'} = shift if @_;
return $self->{'source_tag'};
}
=head2 desc_tag
Title : desc_tag
Usage : $obj->desc_tag($newval)
Function: Get/Set the value used for the query motif. This will be placed in
the tag '-display_name'. Default is 'erpin' as set by the global
$DescTag. Use this to manually set the descriptor (motif searched for).
Since there is no way for this module to tell what the motif is from the
name of the descriptor file or the ERPIN output, this should
be set every time an ERPIN object is instantiated for clarity
Returns : value of exon_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub desc_tag{
my $self = shift;
return $self->{'desc_tag'} = shift if @_;
return $self->{'desc_tag'};
}
=head2 analysis_method
Usage : $obj->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/ERPIN/i.
Returns : String
Argument : n/a
=cut
#-------------
sub analysis_method {
#-------------
my ($self, $method) = @_;
if($method && ($method !~ /ERPIN/i)) {
$self->throw("method $method not supported in " . ref($self));
}
return $self->SUPER::analysis_method($method);
}
=head2 next_feature
Title : next_feature
Usage : while($gene = $obj->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the ERPIN result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Returns : A Bio::Tools::Prediction::Gene object.
Args : None (at present)
=cut
sub next_feature {
my ($self,@args) = @_;
# even though next_prediction doesn't expect any args (and this method
# does neither), we pass on args in order to be prepared if this changes
# ever
return $self->next_prediction(@args);
}
=head2 next_prediction
Title : next_prediction
Usage : while($gene = $obj->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the ERPIN result
file. Call this method repeatedly until FALSE is returned.
Returns : A Bio::Tools::Prediction::Gene object.
Args : None (at present)
=cut
sub next_prediction {
my ($self) = @_;
my ($motiftag,$srctag,$desctag) = ( $self->motif_tag,
$self->source_tag,
$self->desc_tag);
# hit vars
my ($strand, $start, $end, $sequence, $logodds, $score)=0;
while($_ = $self->_readline) {
#skip blank lines
next if /^\s+$/;
# parse header; there's probably a better way to do this, perhaps by
# mapping, but this works for now...
if(/^Training set:\s+\"(.*)\":$/) {
$self->{'_tset'}=$1;
}
elsif(/\s+(\d+ sequences of length \d+)/){
$self->{'_tset_descr'}=$1;
}
elsif(/^Cutoff:\s+(\S+)\s+$/) {
$self->{'_cutoff'}=$1;
}
elsif(/^Database:\s+\"(.*)\"$/) {
$self->{'_db'}=$1;
}
elsif(/^\s+(\d+ nucleotides to be processed in \d+ sequence)$/) {
$self->{'_db_desc'}=$1;
}
elsif(/^\s+ATGC ratios:\s(\d.\d+)\s+(\d.\d+)\s+(\d.\d+)\s+(\d.\d+)$/) {
my $atgc=sprintf("A=%0.3f T=%0.3f G=%0.3f C=%0.3f", $1, $2, $3, $4);
$self->{'_db_ratios'}=$atgc;
}
elsif(/^E-value at cutoff \S+ for \S+(?:G|M|k)?b double strand data: (\S+)/) {
$self->{'_eval_cutoff'}=$1;
}
# catch hit, store in private hash keys
elsif (/^>(.*)/) {
$self->{_seq_desc} = $1;
if($self->{_seq_desc} =~
/(?:P<db>gb|gi|emb|dbj|sp|pdb|bbs|ref|lcl)\|(\d+)((?:\:|\|)\w+\|(\S*.\d+)\|)?/) {
$self->{_seqid} = $1; # pulls out gid
$self->{_seq_acc} = $3;
} else {
$self->{_seqid} = $self->{_seq_desc};
$self->{_seq_acc} = '';
}
}
# parse next hit
elsif (/^(FW|RC)\s+\d+\s+(\d+)..(\d+)\s+(\d+.\d+)\s+(.*)/) {
($strand, $start, $end, $logodds, $score)=($1, $2, $3, $4, $5);
$score =~ s/^e/1e/i;
chomp ($sequence = $self->_readline); # grab next line, which is the sequence hit
my $gene = Bio::SeqFeature::Generic->new(-seq_id => $self->{_seqid},
-start => $start,
-end => $end,
-strand => $strand eq 'FW' ? 1 : -1,
-score => $score,
-primary_tag => $motiftag,
-source_tag => $srctag,
-display_name => $desctag,
-tag => {
'tset' => $self->{_tset},
'tsetdesc' => $self->{_tset_descr},
'cutoff' => $self->{_cutoff},
'database' => $self->{_db},
'dbdesc' => $self->{_db_desc},
'dbratios' => $self->{_db_ratios},
'descline' => $self->{_seq_desc},
'accession' => $self->{_seq_acc},
'logodds' => $logodds,
'sequence' => $sequence}
);
return $gene;
}
#else {
# $self->debug("unrecognized line: $_");
#}
}
}
1;