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Bio::Tools::QRNA(3)   User Contributed Perl Documentation  Bio::Tools::QRNA(3)

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)

perl v5.32.1			  2019-12-07		   Bio::Tools::QRNA(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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