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# $Id: Infernal.pm 15231 2008-12-22 21:51:02Z cjfields $
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# BioPerl module for Bio::Tools::Infernal
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# Cared for by Chris Fields <cjfields-at-uiuc-dot-edu>
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# Copyright Chris Fields
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# You may distribute this module under the same terms as perl itself
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# POD documentation - main docs before the code
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Bio::Tools::Infernal - A parser for Infernal output
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use Bio::Tools::Infernal;
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my $parser = Bio::Tools::Infernal->new(-file => $rna_output,
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-motiftag => 'misc_binding'
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-desctag => 'Lysine riboswitch',
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#parse the results, get a Bio::SeqFeature::FeaturePair
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while( my $motif = $parser->next_prediction) {
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This is a highly experimental parser for Infernal output from the cmsearch
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program. At some point it is anticipated that this will morph into a proper
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SearchIO parser, along with the related RNAMotif and ERPIN tools.
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The Infernal suite of programs are used for generating RNA CM (covariance
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models) and searching sequences using CMs to locate potentially similar
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structures. The program is under active development; it is anticiapted that
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this will support the latest version available.
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This parser has been tested and is capable of parsing Infernal 0.7 and 0.71
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output. However, future Infernal versions may break parsing as the output is
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constantly evolving, so keep an eye on this space for additional notes.
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Currently data is parsed into a Bio::SeqFeature::FeaturePair object, consisting
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of a query (the covariance model) and the hit (sequence searched).
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Model data is accessible via the following:
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Data SeqFeature::FeaturePair Note
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--------------------------------------------------------------------------
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primary tag $sf->primary_tag Rfam ID (if passed to new())
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start $sf->start Based on CM length
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end $sf->end Based on CM length
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score $sf->score Bit score
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strand $sf->strand 0 (CM does not have a strand)
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seqid $sf->seq_id Rfam ID (if passed to new())
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display name $sf->feature1->display_name CM name (if passed to new())
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source $sf->feature1->source tag 'Infernal' followed by version
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Hit data is accessible via the following:
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Data SeqFeature::FeaturePair Note
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------------------------------------------------------------------
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score(bits) $sf->hscore
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Primary Tag $sf->hprimary_tag
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Source Tag $sf->hsource_tag
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Added FeaturePair tags are :
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secstructure - entire description line (in case the regex used for
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sequence ID doesn't adequately catch the name
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model - name of the descriptor file (may include path to file)
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midline - contains structural information from the descriptor
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hit - sequence of motif, separated by spaces according to
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matches to the structure in the descriptor (in
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seqname - raw sequence name (for downstream parsing if needed)
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An additional parameter ('minscore') is added due to the huge number
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of spurious hits generated by cmsearch. This screens data, only building
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and returning objects when a minimal bitscore is present.
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See t/rnamotif.t for example usage.
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User feedback is an integral part of the evolution of this and other
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Bioperl modules. Send your comments and suggestions preferably to
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the Bioperl mailing list. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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=head2 Reporting Bugs
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Report bugs to the Bioperl bug tracking system to help us keep track
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of the bugs and their resolution. Bug reports can be submitted via the
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http://bugzilla.open-bio.org/
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=head1 AUTHOR - Chris Fields
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Email cjfields-at-uiuc-dot-edu
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The rest of the documentation details each of the object methods.
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Internal methods are usually preceded with a _
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# Let the code begin...
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package Bio::Tools::Infernal;
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use Bio::SeqFeature::Generic;
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use Bio::SeqFeature::FeaturePair;
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use base qw(Bio::Tools::AnalysisResult);
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our($MotifTag,$SrcTag,$DescTag) = qw(misc_binding Infernal infernal);
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our $DEFAULT_VERSION = '0.71';
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Usage : my $obj = Bio::Tools::Infernal->new();
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Function: Builds a new Bio::Tools::Infernal object
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Returns : an instance of Bio::Tools::Infernal
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Args : -fh/-file - for input filehandle/filename
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-motiftag - primary tag used in gene features (default 'misc_binding')
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-desctag - tag used for display_name name (default 'infernal')
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-srctag - source tag used in all features (default 'Infernal')
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-rfam - Rfam id number
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-cm - covariance model used in analysis (may be same as rfam #)
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-minscore - minimum score (simple screener, since Infernal generates
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a ton of spurious hits)
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-version - Infernal program version
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# yes, this is actually _initialize, but the args are passed to
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# see Bio::Tools::AnalysisResult for further details
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my($self,@args) = @_;
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$self->warn('Use of this module is deprecated. Use Bio::SearchIO::infernal instead');
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$self->SUPER::_initialize(@args);
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my ($motiftag,$desctag,$srctag,$rfam,$cm,$ms,$ver) =
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$self->SUPER::_rearrange([qw(MOTIFTAG
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$self->motif_tag(defined $motiftag ? $motiftag : $MotifTag);
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$self->source_tag(defined $srctag ? $srctag : $SrcTag);
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$self->desc_tag(defined $desctag ? $desctag : $DescTag);
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$cm && $self->covariance_model($cm);
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$rfam && $self->rfam($rfam);
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$self->program_version(defined $ver ? $ver : $DEFAULT_VERSION);
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$self->minscore(defined $ms ? $ms : $MINSCORE);
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Usage : $obj->motif_tag($newval)
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Function: Get/Set the value used for 'motif_tag', which is used for setting the
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Default is 'misc_binding' as set by the global $MotifTag.
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'misc_binding' is used here because a conserved RNA motif is capable
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of binding proteins (regulatory proteins), antisense RNA (siRNA),
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small molecules (riboswitches), or nothing at all (tRNA,
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terminators, etc.). It is recommended that this be changed to other
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tags ('misc_RNA', 'protein_binding', 'tRNA', etc.) where appropriate.
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For more information, see:
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http://www.ncbi.nlm.nih.gov/collab/FT/index.html
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Returns : value of motif_tag (a scalar)
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Args : on set, new value (a scalar or undef, optional)
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return $self->{'motif_tag'} = shift if @_;
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return $self->{'motif_tag'};
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Usage : $obj->source_tag($newval)
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Function: Get/Set the value used for the 'source_tag'.
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Default is 'Infernal' as set by the global $SrcTag
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Returns : value of source_tag (a scalar)
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Args : on set, new value (a scalar or undef, optional)
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return $self->{'source_tag'} = shift if @_;
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return $self->{'source_tag'};
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Usage : $obj->desc_tag($newval)
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Function: Get/Set the value used for the query motif. This will be placed in
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the tag '-display_name'. Default is 'infernal' as set by the global
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$DescTag. Use this to manually set the descriptor (motif searched for).
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Since there is no way for this module to tell what the motif is from the
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name of the descriptor file or the Infernal output, this should
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be set every time an Infernal object is instantiated for clarity
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Returns : value of exon_tag (a scalar)
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Args : on set, new value (a scalar or undef, optional)
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return $self->{'desc_tag'} = shift if @_;
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return $self->{'desc_tag'};
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=head2 covariance_model
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Title : covariance_model
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Usage : $obj->covariance_model($newval)
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Function: Get/Set the value used for the covariance model used in the analysis.
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Returns : value of exon_tag (a scalar)
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Args : on set, new value (a scalar or undef, optional)
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sub covariance_model{
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return $self->{'_cmodel'} = shift if @_;
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return $self->{'_cmodel'};
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Usage : $obj->rfam($newval)
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Function: Get/Set the Rfam accession number
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Returns : value of exon_tag (a scalar)
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Args : on set, new value (a scalar or undef, optional)
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return $self->{'_rfam'} = shift if @_;
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return $self->{'_rfam'};
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Usage : $obj->minscore($newval)
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Function: Get/Set the minimum score threshold for generating SeqFeatures
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Returns : value of exon_tag (a scalar)
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Args : on set, new value (a scalar or undef, optional)
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return $self->{'_minscore'} = shift if @_;
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return $self->{'_minscore'};
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=head2 program_version
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Title : program_version
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Usage : $obj->program_version($newval)
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Function: Get/Set the Infernal program version
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Returns : value of exon_tag (a scalar)
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Args : on set, new value (a scalar or undef, optional)
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Note: this is set to $DEFAULT_VERSION by, um, default
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sub program_version {
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return $self->{'_program_version'} = shift if @_;
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return $self->{'_program_version'};
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=head2 analysis_method
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Usage : $obj->analysis_method();
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Purpose : Inherited method. Overridden to ensure that the name matches
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sub analysis_method {
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my ($self, $method) = @_;
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if($method && ($method !~ /Infernal/i)) {
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$self->throw("method $method not supported in " . ref($self));
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return $self->SUPER::analysis_method($method);
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Usage : while($gene = $obj->next_feature()) {
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Function: Returns the next gene structure prediction of the RNAMotif result
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file. Call this method repeatedly until FALSE is returned.
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The returned object is actually a SeqFeatureI implementing object.
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This method is required for classes implementing the
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SeqAnalysisParserI interface, and is merely an alias for
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next_prediction() at present.
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Returns : A Bio::Tools::Prediction::Gene object.
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Args : None (at present)
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my ($self,@args) = @_;
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# even though next_prediction doesn't expect any args (and this method
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# does neither), we pass on args in order to be prepared if this changes
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return $self->next_prediction(@args);
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=head2 next_prediction
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Title : next_prediction
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Usage : while($gene = $obj->next_prediction()) {
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Function: Returns the next gene structure prediction of the RNAMotif result
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file. Call this method repeatedly until FALSE is returned.
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Returns : A Bio::SeqFeature::Generic object
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Args : None (at present)
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sub next_prediction {
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my ($start, $end, $strand, $score);
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my %hsp_key = ('0' => 'structure',
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while($line = $self->_readline) {
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next if $line =~ m{^\s+$};
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if ($line =~ m{^sequence:\s+(\S+)} ){
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$self->_current_hit($1);
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} elsif ($line =~ m{^hit\s+\d+\s+:\s+(\d+)\s+(\d+)\s+(\d+\.\d+)\s+bits}xms) {
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($start, $end, $score) = ($1, $2, $3);
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($start, $end) = ($end, $start);
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#$self->debug(sprintf("Hit: %-30s\n\tStrand:%-4d Start:%-6d End:%-6d Score:%-10s\n",
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# $self->_current_hit, $strand, $start, $end, $score));
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} elsif ($line =~ m{^(\s+)[<>\{\}\(\)\[\]:_,-\.]+}xms) { # start of HSP
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$self->_pushback($line); # set up for loop
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# what is length of the gap to the structure data?
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my $offset = length($1);
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my ($ct, $strln) = 0;
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while ($line = $self->_readline) {
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next if $line =~ m{^\s*$}; # toss empty lines
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# exit loop if at end of file or upon next hit/HSP
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if (!defined($line) || $line =~ m{^(sequence|hit)}) {
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$self->_pushback($line);
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# iterate to keep track of each line (4 lines per hsp block)
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my $iterator = $ct%4;
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# strlen set only with structure lines (proper length)
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$strln = length($line) if $iterator == 0;
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# only grab the data needed (hit start and stop in hit line above;
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# query start, end are from the actual query length (entire hit is
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# mapped to CM data, so all CM data is represented
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# yes this is kinda clumsy, but I'll probably morph this into
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# a proper SearchIO module soon. For now this works...
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my $data = substr($line, $offset, $strln-$offset);
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$hsp->{ $hsp_key{$iterator} } .= $data;
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if ($self->minscore < $score) {
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my ($name, $program, $rfam, $cm, $dt, $st, $mt) =
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($self->_current_hit, $self->analysis_method, $self->rfam,
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$self->covariance_model, $self->desc_tag, $self->source_tag,
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my $ver = $self->program_version || '';
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if ($name =~ m{(?:gb|gi|emb|dbj|sp|pdb|bbs|ref|lcl)\|(\d+)((?:\:|\|)\w+\|(\S*.\d+)\|)?}xms) {
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my $fp = Bio::SeqFeature::FeaturePair->new();
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my $strlen = $hsp->{'model'} =~ tr{A-Za-z}{A-Za-z}; # gaps don't count
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my $qf = Bio::SeqFeature::Generic->new( -primary_tag => $mt,
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-source_tag => "$st $ver",
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-display_name => $cm || '',
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-seq_id => $rfam || '',
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-strand => 0, # covariance model does not have a strand
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my $hf = Bio::SeqFeature::Generic->new( -primary_tag => $mt,
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-source_tag => "$st $ver",
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-display_name => $dt || '',
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$fp->feature2($hf); # should emphasis be on the hit?
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$fp->add_tag_value('secstructure', $hsp->{'structure'});
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$fp->add_tag_value('model', $hsp->{'model'});
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$fp->add_tag_value('midline', $hsp->{'midline'});
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$fp->add_tag_value('hit', $hsp->{'hit'});
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$fp->add_tag_value('seq_name', $name);
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$fp->display_name($dt);
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return (defined($line)) ? 1 : 0;
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return $self->{'_currhit'} = shift if @_;
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return $self->{'_currhit'};
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Bio/Tools/Infernal.pm
