Bio::Tools QRNA
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Summary
Bio::Tools::QRNA - A Parser for qrna output
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Generic
Inherit
Bio::Root::IO Bio::SeqAnalysisParserI
Synopsis
  use Bio::Tools::QRNA;
my $parser = Bio::Tools::QRNA->new(-file => $qrnaoutput);
while( my $feature = $parser->next_feature ) {
# do something here
}
Description
Parses QRNA output (E.Rivas:
http://selab.janelia.org/software.html ftp://selab.janelia.org/pub/software/qrna/).
This module is not complete, but currently it packs information from
each QRNA alignment into a single Bio::SeqFeature::Generic object.
Not all options for QRNA output have been tested or tried. It has
been tested on sliding window output (-w -x) and shuffled output (-b
or -B).
See t/QRNA.t for example usage.
At some point we may have more complicated feature object which will
support this data rather than forcing most of the information into
tag/value pairs in a SeqFeature::Generic.
Running with -verbose => 1 will store extra data in the feature. The
entire unparsed entry for a particular feature will be stored as a
string in the tag 'entry' it is accessible via:
  my ($entry) = $f->each_tag_value('entry');
The winning model for any given alignment test will be the name stored
in the primary_tag field of feature. The bit score will stored in the
score field. The logoddpost is available via the a tag/value pair.
This example code will show how to print out the score and log odds
post for each model.
  # assuming you got a feature already
print "model score logoddspost\n";
foreach my $model ( qw(OTH COD RNA) ) {
my ($score) = $f->get_tag_values("$model\_score");
my ($logoddspost) = $f->get_tag_values("$model\_logoddspost");
print "$model $score $logoddspost\n";
}
The start and end of the alignment for both the query and hit sequence
are available through the Bio::SeqFeature::FeaturePair interface,
specifically Bio::SeqFeature::FeaturePair::feature1 and
Bio::SeqFeature::FeaturePair::feature2. Additionally if you have
run QRNA with an input file which has the location of the alignment
stored in the FASTA filename as in (ID/START-END) which is the default
output format from Bio::AlignIO::fasta produced alignment output,
this module will re-number start/end for the two sequences so they are
in the actual coordinates of the sequence rather than the relative
coordinates of the alignment. You may find the bioperl utillity
script search2alnblocks useful in creating your input files for QRNA.
Some other words of warning, QRNA uses a 0 based numbering system for
sequence locations, Bioperl uses a 1 based system. You'll notice that
locations will be +1 they are reported in the raw QRNA output.
Methods
next_featureDescriptionCode
_parse_pair
No description
Code
PAM_modelDescriptionCode
RNA_modelDescriptionCode
seq_fileDescriptionCode
program_nameDescriptionCode
program_versionDescriptionCode
program_dateDescriptionCode
_make_feature
No description
Code
Methods description
next_featurecode    nextTop
 Title   : next_feature
Usage : my $feature = $parser->next_feature
Function: Get the next QRNA feature
Returns :
Args :
PAM_modelcodeprevnextTop
 Title   : PAM_model
Usage : $obj->PAM_model($newval)
Function:
Example :
Returns : value of PAM_model (a scalar)
Args : on set, new value (a scalar or undef, optional)
RNA_modelcodeprevnextTop
 Title   : RNA_model
Usage : $obj->RNA_model($newval)
Function:
Example :
Returns : value of RNA_model (a scalar)
Args : on set, new value (a scalar or undef, optional)
seq_filecodeprevnextTop
 Title   : seq_file
Usage : $obj->seq_file($newval)
Function:
Example :
Returns : value of seq_file (a scalar)
Args : on set, new value (a scalar or undef, optional)
program_namecodeprevnextTop
 Title   : program_name
Usage : $obj->program_name($newval)
Function:
Example :
Returns : value of program_name (a scalar)
Args : on set, new value (a scalar or undef, optional)
program_versioncodeprevnextTop
 Title   : program_version
Usage : $obj->program_version($newval)
Function:
Example :
Returns : value of program_version (a scalar)
Args : on set, new value (a scalar or undef, optional)
program_datecodeprevnextTop
 Title   : program_date
Usage : $obj->program_date($newval)
Function:
Example :
Returns : value of program_date (a scalar)
Args : on set, new value (a scalar or undef, optional)
Methods code
next_featuredescriptionprevnextTop
sub next_feature {
    my ($self) = @_;
    my $f = shift @{$self->{'_parsed_features'} || []};
    if( ! defined $f && $self->_parse_pair ) {
	$f = shift @{$self->{'_parsed_features'} || []};
    }
    return $f;
}
_parse_pairdescriptionprevnextTop
sub _parse_pair {
   my ($self,@args) = @_;
   my (@features,%data);
   my $seenstart = 0;
   while( defined( $_ = $self->_readline) ) {
       next if( /^\#\-\-/o );
       if( /^\#\s+(qrna)\s+(\S+)\s+\(([^\)]+)\)/o ) {
	   $self->program_name($1);
	   $self->program_version($2);
	   $self->program_date($3);
       } elsif( /^\#\s+(PAM model)\s+\=\s+(.+)\s+$/o ) {
	   $self->PAM_model($2);
       } elsif( /^\#\s+(RNA model)\s+\=\s+(\S+)/o ) {
	   $self->RNA_model($2);
       } elsif( /^\#\s+(seq file)\s+\=\s+(.+)\s+$/o ) {
	   $self->seq_file($2);	   
       } elsif( /^\#\s+(\d+)\s+\[([\-+])\s+strand\]/o ) {
	   if( $seenstart ) { 
	       if( $data{'alignment_len'} ) {
		   push @features, $self->_make_feature(\%data);
	       }
	       $self->_pushback($_);
	       last;
	   }
	   $seenstart = 1;
       } elsif( /^\#/ ) {
	   next;
       } elsif( />(\S+)\s+\((\d+)\)/ ) {
	   if( @{$data{'seqs'} || []} == 2 ) { 
	       $self->warn( "already seen seqs ".join(' ', ,map { $_->[0] } 
						      @{$data{'seqs'}}). "\n");
	   } else { 
	       push @{$data{'seqs'}}, [$1,$2];
	   }
       } elsif( /^length alignment:\s+(\d+)\s+\(id\=(\d+(\.\d+)?)\)/o ) {
	   
	   if( $data{'alignment_len'} ) {
	       push @features, $self->_make_feature(\%data);	
	       # reset all the data but the 'seqs' field
%data = ( 'seqs' => $data{'seqs'} ); } if( /\(((sre_)?shuffled)\)/ ) { $data{'shuffled'} = $1; } $data{'alignment_len'} = $1; $data{'alignment_pid'} = $2; } elsif ( /^pos([XY]):\s+(\d+)\-(\d+)\s+\[(\d+)\-(\d+)\]\((\d+)\)\s+
\-\-\s+\((\S+\s+\S+\s+\S+\s+\S+)\)/ox
) { $data{"seq\_$1"}->{'aln'} = [ $2,$3, $4,$5, $6]; @{$data{"seq\_$1"}->{'base_comp'}} = split(/\s+/,$7); } elsif( /^winner\s+\=\s+(\S{3})/ ) { $data{'winning_model'} = $1; } elsif( /^(\S{3})\s+ends\s+\=\s+(\-?\d+)\s+(\-?\d+)/ ) { # QRNA is 0-based
# Bioperl is 1 based
$data{'model_location'}->{$1} = [ $2,$3 ]; } elsif( /^\s+(logoddspost)?OTH\s+\=\s+/ox ) { while( /(\S+)\s+\=\s+(\-?\d+(\.\d+))/g ) { my ($model,$score)= ($1,$2); if( $model =~ s/^logoddspost// ) { $data{'model_scores'}->{'logoddspost'}->{$model} = $score; } else { $data{'model_scores'}->{'bits'}->{$model} = $score; } } } $data{'entry'} .= $_; } if( @features ) { push @{$self->{'_parsed_features'}}, @features; return scalar @features; } return 0;
}
PAM_modeldescriptionprevnextTop
sub PAM_model {
    my $self = shift;
    return $self->{'PAM_model'} = shift if @_;
    return $self->{'PAM_model'};
}
RNA_modeldescriptionprevnextTop
sub RNA_model {
    my $self = shift;

    return $self->{'RNA_model'} = shift if @_;
    return $self->{'RNA_model'};
}
seq_filedescriptionprevnextTop
sub seq_file {
    my $self = shift;

    return $self->{'seq_file'} = shift if @_;
    return $self->{'seq_file'};
}
program_namedescriptionprevnextTop
sub program_name {
    my $self = shift;

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

    return $self->{'program_version'} = shift if @_;
    return $self->{'program_version'};
}
program_datedescriptionprevnextTop
sub program_date {
    my $self = shift;
    return $self->{'program_date'} = shift if @_;
    return $self->{'program_date'};
}
_make_featuredescriptionprevnextTop
sub _make_feature {
     my ($self,$data) = @_; 
    my ($qoffset,$hoffset) = (1,1);
    # when you run qrna and have produced ID/START-END
# formatted input strings we can remap the location
# to the original
# name is stored as the first entry in the seq array ref
my ($qid,$hid) = ( $data->{'seqs'}->[0]->[0], $data->{'seqs'}->[1]->[0]); if( $qid =~ /(\S+)\/(\d+)\-(\d+)/ ) { ($qid,$qoffset) = ($1,$2); } if( $hid =~ /(\S+)\/(\d+)\-(\d+)/ ) { ($hid,$hoffset) = ($1,$2); } my $f = Bio::SeqFeature::FeaturePair->new(); my ($s,$e) = @{$data->{'model_location'}->{$data->{'winning_model'}}}; my $qf = Bio::SeqFeature::Generic->new ( -primary_tag => $data->{'winning_model'}, -source_tag => $self->program_name, -score => $data->{'model_scores'}->{'bits'}->{$data->{'winning_model'}}, -start => $s+$qoffset, -end => $e+$qoffset, -seq_id => $qid, -strand => ($s < $e ) ? 1 : -1, ); my $hf = Bio::SeqFeature::Generic->new ( -primary_tag => $qf->primary_tag, -source_tag => $qf->source_tag, -score => $qf->score, -seq_id => $hid, -start => $s + $hoffset, -end => $e + $hoffset, -strand => $qf->strand, ); $f->feature1($qf); $f->feature2($hf); $f->add_tag_value('alignment_len', $data->{'alignment_len'}); $f->add_tag_value('alignment_pid', $data->{'alignment_pid'}); # store the other model scores and data
foreach my $model ( @Models ) { $f->add_tag_value("$model\_score", $data->{'model_scores'}->{'bits'}->{$model}); $f->add_tag_value("$model\_logoddspost", $data->{'model_scores'}->{'logoddspost'}->{$model}); if( ! $data->{'model_location'}->{$model} ) { if( $self->verbose > 0 ) { $self->debug( $data->{'entry'} ); } $self->throw("no location parsed for $model in ", (map { @$_ } @{$data->{'seqs'}}), " ", $f->start, " ", $f->end); } else { $f->add_tag_value("$model\_positions", join("..",@{$data->{'model_location'}->{$model} })); } } # probably a better way to store this - as
# a seq object perhaps
$f->add_tag_value('seq1', @{$data->{'seqs'}->[0]}); $f->add_tag_value('seq2', @{$data->{'seqs'}->[1]}); $f->add_tag_value('entry', $data->{'entry'}) if $self->verbose > 0; if( $data->{'shuffled'} ) { $f->add_tag_value('shuffled', $data->{'shuffled'}); } return $f; } 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 - Jason StajichTop
Email jason-at-bioperl-dot-org
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::QRNA->new();
Function: Builds a new Bio::Tools::QRNA object
Returns : an instance of Bio::Tools::QRNA
Args : -fh/-file filehandle/filename standard input for
Bio::Root:IO objects