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.IX Title "Bio::Tools::Run::Alignment::Exonerate 3pm"
.TH Bio::Tools::Run::Alignment::Exonerate 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH NAME
Bio::Tools::Run::Alignment::Exonerate \- wrapper for the exonerate alignment program
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 2
\&  use Bio::Tools::Run::Alignment::Exonerate;
\&  use Bio::SeqIO;
\&
\&  my $qio = Bio::SeqIO\->new(\-file=>$ARGV[0],\-format=>\*(Aqfasta\*(Aq);
\&  my $query = $qio\->next_seq();
\&  my $tio = Bio::SeqIO\->new(\-file=>$ARGV[1],\-format=>\*(Aqfasta\*(Aq);
\&  my $target = $sio\->next_seq();
\&
\&  #exonerate parameters can all be passed via arguments parameter.
\&  #parameters passed are not checked for validity
\&
\&  my $run = Bio::Tools::Run::Alignment::Exonerate\->
\&      new(arguments=>\*(Aq\-\-model est2genome \-\-bestn 10\*(Aq);
\&  my $searchio_obj = $run\->run($query,$target);
\&
\&  while(my $result = $searchio\->next_result){
\&    while( my $hit = $result\->next_hit ) {
\&      while( my $hsp = $hit\->next_hsp ) {
\&        print $hsp\->start."\et".$hsp\->end."\en";
\&      }
\&    }
\&  }
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
Wrapper for Exonerate alignment program. You can get exonerate at
http://www.ebi.ac.uk/~guy/exonerate/.  This wrapper is written without
parameter checking. All parameters are passed via the arugment
parameter that is passed in the constructor. See SYNOPSIS.  For
exonerate parameters, run exonerate \-\-help for more details.
.SH "PROGRAM VERSIONS"
.IX Header "PROGRAM VERSIONS"
The tests have been shown to pass with exonorate versions 2.0 \- 2.2.
.SH FEEDBACK
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS Support
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Shawn Hoon"
.IX Header "AUTHOR - Shawn Hoon"
.Vb 1
\&  Email shawnh\-at\-stanford.edu
.Ve
.SH APPENDIX
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS program_name
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS program_dir
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns:  string
\& Args    :
.Ve
.SS new
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : my $factory= Bio::Tools::Run::Phrap\->new();
\& Function: creates a new Phrap factory
\& Returns:  Bio::Tools::Run::Phrap
\& Args    :
.Ve
.SS version
.IX Subsection "version"
.Vb 6
\& Title   : version
\& Usage   : exit if $prog\->version() < 1.8
\& Function: Determine the version number of the program
\& Example :
\& Returns : float or undef
\& Args    : none
.Ve
.SS run
.IX Subsection "run"
.Vb 5
\& Title   :   run()
\& Usage   :   my $feats = $factory\->run($seq)
\& Function:   Runs Phrap 
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :   A Bio::PrimarySeqI
.Ve
.SS _input
.IX Subsection "_input"
.Vb 5
\& Title   :   _input
\& Usage   :   $factory\->_input($seqFile)
\& Function:   get/set for input file
\& Returns :
\& Args    :
.Ve
.SS _run
.IX Subsection "_run"
.Vb 5
\& Title   :   _run
\& Usage   :   $factory\->_run()
\& Function:   Makes a system call and runs Phrap
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :
.Ve
.SS _writeInput
.IX Subsection "_writeInput"
.Vb 5
\& Title   :   _writeInput
\& Usage   :   $factory\->_writeInput($query,$target)
\& Function:   Creates a file from the given seq object
\& Returns :   A string(filename)
\& Args    :   Bio::PrimarySeqI
.Ve
.SS _setparams
.IX Subsection "_setparams"
.Vb 6
\& Title   :  _setparams
\& Usage   :  Internal function, not to be called directly
\& Function:  creates a string of params to be used in the command string
\& Example :
\& Returns :  string of params
\& Args    :
.Ve