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.
FEEDBACK
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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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 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://github.com/bioperl/bioperl-live/issues
AUTHOR - Chris Fields
Email cjfields-at-uiuc-dot-eduAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _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
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)
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)
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)
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)
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)
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)
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
analysis_method
Usage : $obj->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/Infernal/i.
Returns : String
Argument : n/a
next_feature
Title : next_feature
Usage : while($gene = $obj->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the RNAMotif result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Returns : A Bio::Tools::Prediction::Gene object.
Args : None (at present)
next_prediction
Title : next_prediction
Usage : while($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)