Bio::Tools::QRNA(3) User Contributed Perl Documentation Bio::Tools::QRNA(3)NAMEBio::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 availble 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:
http://bugzilla.open-bio.org/
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)
perl v5.14.1 2011-07-22 Bio::Tools::QRNA(3)
