oracular (3) Bio::Tools::QRNA.3pm.gz

NAME

       Bio::Tools::QRNA - A Parser for qrna output

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.

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.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       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 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 - Jason Stajich

       Email jason-at-bioperl-dot-org

APPENDIX

       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::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

   next_feature
        Title   : next_feature
        Usage   : my $feature = $parser->next_feature
        Function: Get the next QRNA feature
        Returns :
        Args    :

   PAM_model
        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_model
        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_file
        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_name
        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_version
        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_date
        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)