#
# BioPerl module for Bio::Tools::Infernal
#
# 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::Infernal - A parser for Infernal output
=head1 SYNOPSIS
use Bio::Tools::Infernal;
my $parser = Bio::Tools::Infernal->new(-file => $rna_output,
-motiftag => 'misc_binding'
-desctag => 'Lysine riboswitch',
-cm => 'RF00168',
-rfam => 'RF00168',
-minscore => 20);
#parse the results, get a Bio::SeqFeature::FeaturePair
while( my $motif = $parser->next_prediction) {
# do something here
}
=head1 DESCRIPTION
This is a highly experimental parser for Infernal output from the cmsearch
program. At some point it is anticipated that this will morph into a proper
SearchIO parser, along with the related RNAMotif and ERPIN tools.
The Infernal suite of programs are used for generating RNA CM (covariance
models) and searching sequences using CMs to locate potentially similar
structures. The program is under active development; it is anticiapted that
this will support the latest version available.
This parser has been tested and is capable of parsing Infernal 0.7 and 0.71
output. However, future Infernal versions may break parsing as the output is
constantly evolving, so keep an eye on this space for additional notes.
Currently data is parsed into a Bio::SeqFeature::FeaturePair object, consisting
of a query (the covariance model) and the hit (sequence searched).
Model data is accessible via the following:
Data SeqFeature::FeaturePair Note
--------------------------------------------------------------------------
primary tag $sf->primary_tag Rfam ID (if passed to new())
start $sf->start Based on CM length
end $sf->end Based on CM length
score $sf->score Bit score
strand $sf->strand 0 (CM does not have a strand)
seqid $sf->seq_id Rfam ID (if passed to new())
display name $sf->feature1->display_name CM name (if passed to new())
source $sf->feature1->source tag 'Infernal' followed by version
Hit data is accessible via the following:
Data SeqFeature::FeaturePair Note
------------------------------------------------------------------
start $sf->hstart
end $sf->hend
score(bits) $sf->hscore
strand $sf->hstrand
seqid $sf->hseqid
Primary Tag $sf->hprimary_tag
Source Tag $sf->hsource_tag
Added FeaturePair tags are :
secstructure - entire description line (in case the regex used for
sequence ID doesn't adequately catch the name
model - name of the descriptor file (may include path to file)
midline - contains structural information from the descriptor
used as a query
hit - sequence of motif, separated by spaces according to
matches to the structure in the descriptor (in
SecStructure).
seqname - raw sequence name (for downstream parsing if needed)
An additional parameter ('minscore') is added due to the huge number
of spurious hits generated by cmsearch. This screens data, only building
and returning objects when a minimal bitscore is present.
See t/rnamotif.t for example usage.
=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::Infernal;
use strict;
use Bio::SeqFeature::Generic;
use Bio::SeqFeature::FeaturePair;
use Data::Dumper;
use base qw(Bio::Tools::AnalysisResult);
our($MotifTag,$SrcTag,$DescTag) = qw(misc_binding Infernal infernal);
our $MINSCORE = 0;
our $DEFAULT_VERSION = '0.71';
=head2 new
Title : new
Usage : my $obj = Bio::Tools::Infernal->new();
Function: Builds a new Bio::Tools::Infernal object
Returns : an instance of Bio::Tools::Infernal
Args : -fh/-file - for input filehandle/filename
-motiftag - primary tag used in gene features (default 'misc_binding')
-desctag - tag used for display_name name (default 'infernal')
-srctag - source tag used in all features (default 'Infernal')
-rfam - Rfam id number
-cm - covariance model used in analysis (may be same as rfam #)
-minscore - minimum score (simple screener, since Infernal generates
a ton of spurious hits)
-version - Infernal program version
=cut
# yes, this is actually _initialize, but the args are passed to
# the constructor.
# see Bio::Tools::AnalysisResult for further details
sub _initialize {
my($self,@args) = @_;
$self->warn('Use of this module is deprecated. Use Bio::SearchIO::infernal instead');
$self->SUPER::_initialize(@args);
my ($motiftag,$desctag,$srctag,$rfam,$cm,$ms,$ver) =
$self->SUPER::_rearrange([qw(MOTIFTAG
DESCTAG
SRCTAG
RFAM
CM
MINSCORE
VERSION
)],@args);
$self->motif_tag(defined $motiftag ? $motiftag : $MotifTag);
$self->source_tag(defined $srctag ? $srctag : $SrcTag);
$self->desc_tag(defined $desctag ? $desctag : $DescTag);
$cm && $self->covariance_model($cm);
$rfam && $self->rfam($rfam);
$self->program_version(defined $ver ? $ver : $DEFAULT_VERSION);
$self->minscore(defined $ms ? $ms : $MINSCORE);
}
=head2 motif_tag
Title : motif_tag
Usage : $obj->motif_tag($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 'Infernal' 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 'infernal' 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 Infernal output, this should
be set every time an Infernal 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 covariance_model
Title : covariance_model
Usage : $obj->covariance_model($newval)
Function: Get/Set the value used for the covariance model used in the analysis.
Returns : value of exon_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub covariance_model{
my $self = shift;
return $self->{'_cmodel'} = shift if @_;
return $self->{'_cmodel'};
}
=head2 rfam
Title : rfam
Usage : $obj->rfam($newval)
Function: Get/Set the Rfam accession number
Returns : value of exon_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub rfam {
my $self = shift;
return $self->{'_rfam'} = shift if @_;
return $self->{'_rfam'};
}
=head2 minscore
Title : minscore
Usage : $obj->minscore($newval)
Function: Get/Set the minimum score threshold for generating SeqFeatures
Returns : value of exon_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub minscore {
my $self = shift;
return $self->{'_minscore'} = shift if @_;
return $self->{'_minscore'};
}
=head2 program_version
Title : program_version
Usage : $obj->program_version($newval)
Function: Get/Set the Infernal program version
Returns : value of exon_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
Note: this is set to $DEFAULT_VERSION by, um, default
=cut
sub program_version {
my $self = shift;
return $self->{'_program_version'} = shift if @_;
return $self->{'_program_version'};
}
=head2 analysis_method
Usage : $obj->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/Infernal/i.
Returns : String
Argument : n/a
=cut
sub analysis_method {
my ($self, $method) = @_;
if($method && ($method !~ /Infernal/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 = $obj->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the RNAMotif result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Returns : A Bio::Tools::Prediction::Gene object.
Args : None (at present)
=cut
sub next_feature {
my ($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 = $obj->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the RNAMotif result
file. Call this method repeatedly until FALSE is returned.
Returns : A Bio::SeqFeature::Generic object
Args : None (at present)
=cut
sub next_prediction {
my ($self) = @_;
my ($start, $end, $strand, $score);
my %hsp_key = ('0' => 'structure',
'1' => 'model',
'2' => 'midline',
'3' => 'hit');
my $line;
PARSER:
while($line = $self->_readline) {
next if $line =~ m{^\s+$};
if ($line =~ m{^sequence:\s+(\S+)} ){
$self->_current_hit($1);
next PARSER;
} elsif ($line =~ m{^hit\s+\d+\s+:\s+(\d+)\s+(\d+)\s+(\d+\.\d+)\s+bits}xms) {
$strand = 1;
($start, $end, $score) = ($1, $2, $3);
if ($start > $end) {
($start, $end) = ($end, $start);
$strand = -1;
}
#$self->debug(sprintf("Hit: %-30s\n\tStrand:%-4d Start:%-6d End:%-6d Score:%-10s\n",
# $self->_current_hit, $strand, $start, $end, $score));
} elsif ($line =~ m{^(\s+)[<>\{\}\(\)\[\]:_,-\.]+}xms) { # start of HSP
$self->_pushback($line); # set up for loop
# what is length of the gap to the structure data?
my $offset = length($1);
my ($ct, $strln) = 0;
my $hsp;
HSP:
while ($line = $self->_readline) {
next if $line =~ m{^\s*$}; # toss empty lines
chomp $line;
# exit loop if at end of file or upon next hit/HSP
if (!defined($line) || $line =~ m{^(sequence|hit)}) {
$self->_pushback($line);
last HSP;
}
# iterate to keep track of each line (4 lines per hsp block)
my $iterator = $ct%4;
# strlen set only with structure lines (proper length)
$strln = length($line) if $iterator == 0;
# only grab the data needed (hit start and stop in hit line above;
# query start, end are from the actual query length (entire hit is
# mapped to CM data, so all CM data is represented
# yes this is kinda clumsy, but I'll probably morph this into
# a proper SearchIO module soon. For now this works...
my $data = substr($line, $offset, $strln-$offset);
$hsp->{ $hsp_key{$iterator} } .= $data;
$ct++;
}
if ($self->minscore < $score) {
my ($name, $program, $rfam, $cm, $dt, $st, $mt) =
($self->_current_hit, $self->analysis_method, $self->rfam,
$self->covariance_model, $self->desc_tag, $self->source_tag,
$self->motif_tag);
my $ver = $self->program_version || '';
my $qid = $name;
if ($name =~ m{(?:gb|gi|emb|dbj|sp|pdb|bbs|ref|lcl)\|(\d+)((?:\:|\|)\w+\|(\S*.\d+)\|)?}xms) {
$qid = $1;
}
my $fp = Bio::SeqFeature::FeaturePair->new();
my $strlen = $hsp->{'model'} =~ tr{A-Za-z}{A-Za-z}; # gaps don't count
my $qf = Bio::SeqFeature::Generic->new( -primary_tag => $mt,
-source_tag => "$st $ver",
-display_name => $cm || '',
-score => $score,
-start => 1,
-end => $strlen,
-seq_id => $rfam || '',
-strand => 0, # covariance model does not have a strand
);
my $hf = Bio::SeqFeature::Generic->new( -primary_tag => $mt,
-source_tag => "$st $ver",
-display_name => $dt || '',
-score => $score,
-start => $start,
-end => $end,
-seq_id => $qid,
-strand => $strand
);
$fp->feature1($qf);
$fp->feature2($hf); # should emphasis be on the hit?
$fp->add_tag_value('secstructure', $hsp->{'structure'});
$fp->add_tag_value('model', $hsp->{'model'});
$fp->add_tag_value('midline', $hsp->{'midline'});
$fp->add_tag_value('hit', $hsp->{'hit'});
$fp->add_tag_value('seq_name', $name);
$fp->display_name($dt);
return $fp;
} else {
next PARSER;
}
}
}
return (defined($line)) ? 1 : 0;
}
sub _current_hit {
my $self = shift;
return $self->{'_currhit'} = shift if @_;
return $self->{'_currhit'};
}
1;