Bio::Tools Infernal
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Tools::Infernal - A parser for Infernal output
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Generic
Data::Dumper
Inherit
Bio::Tools::AnalysisResult
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
}
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.
Methods
_initialize
No description
Code
motif_tagDescriptionCode
source_tagDescriptionCode
desc_tagDescriptionCode
covariance_modelDescriptionCode
rfamDescriptionCode
minscoreDescriptionCode
program_versionDescriptionCode
analysis_methodDescriptionCode
next_featureDescriptionCode
next_predictionDescriptionCode
_current_hit
No description
Code
Methods description
motif_tagcode    nextTop
 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)
source_tagcodeprevnextTop
 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)
desc_tagcodeprevnextTop
 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)
covariance_modelcodeprevnextTop
 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)
rfamcodeprevnextTop
 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)
minscorecodeprevnextTop
 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)
program_versioncodeprevnextTop
 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
analysis_methodcodeprevnextTop
 Usage     : $obj->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/Infernal/i.
Returns : String
Argument : n/a
next_featurecodeprevnextTop
 Title   : next_feature
Usage : while($gene = $obj->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the RNAMotif result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Returns : A Bio::Tools::Prediction::Gene object.
Args : None (at present)
next_predictioncodeprevnextTop
 Title   : next_prediction
Usage : while($gene = $obj->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the RNAMotif result
file. Call this method repeatedly until FALSE is returned.
Returns : A Bio::SeqFeature::Generic object
Args : None (at present)
Methods code
_initializedescriptionprevnextTop
sub _initialize {
  my($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);
}
motif_tagdescriptionprevnextTop
sub motif_tag {
    my $self = shift;

    return $self->{'motif_tag'} = shift if @_;
    return $self->{'motif_tag'};
}
source_tagdescriptionprevnextTop
sub source_tag {
    my $self = shift;

    return $self->{'source_tag'} = shift if @_;
    return $self->{'source_tag'};
}
desc_tagdescriptionprevnextTop
sub desc_tag {
    my $self = shift;

    return $self->{'desc_tag'} = shift if @_;
    return $self->{'desc_tag'};
}
covariance_modeldescriptionprevnextTop
sub covariance_model {
    my $self = shift;

    return $self->{'_cmodel'} = shift if @_;
    return $self->{'_cmodel'};
}
rfamdescriptionprevnextTop
sub rfam {
    my $self = shift;

    return $self->{'_rfam'} = shift if @_;
    return $self->{'_rfam'};
}
minscoredescriptionprevnextTop
sub minscore {
    my $self = shift;

    return $self->{'_minscore'} = shift if @_;
    return $self->{'_minscore'};
}
program_versiondescriptionprevnextTop
sub program_version {
    my $self = shift;

    return $self->{'_program_version'} = shift if @_;
    return $self->{'_program_version'};
}
analysis_methoddescriptionprevnextTop
sub analysis_method {
     my ($self, $method) = @_;  
    if($method && ($method !~ /Infernal/i)) {
    $self->throw("method $method not supported in " . ref($self));
    }
    return $self->SUPER::analysis_method($method);
}
next_featuredescriptionprevnextTop
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 $self->next_prediction(@args);
}
next_predictiondescriptionprevnextTop
sub next_prediction {
    my ($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;
}
_current_hitdescriptionprevnextTop
sub _current_hit {
    my $self = shift;
    return $self->{'_currhit'} = shift if @_;
    return $self->{'_currhit'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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/
AUTHOR - Chris FieldsTop
Email cjfields-at-uiuc-dot-edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 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