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)