Bio::Tools::Run::Alignment::Exonerate man page on Fedora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Fedora logo
[printable version]

Bio::Tools::Run::AlignUser:ContributedBio::Tools::Run::Alignment::Exonerate(3)

NAME
       Bio::Tools::Run::Alignment::Exonerate

SYNOPSIS
	 use Bio::Tools::Run::Alignment::Exonerate;
	 use Bio::SeqIO;

	 my $qio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'fasta');
	 my $query = $qio->next_seq();
	 my $tio = Bio::SeqIO->new(-file=>$ARGV[1],-format=>'fasta');
	 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=>'--model est2genome --bestn 10');
	 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 $hsp->start."\t".$hsp->end."\n";
	     }
	   }
	 }

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.

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 one
	of the Bioperl mailing lists.  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
	the bugs and their resolution.	Bug reports can be submitted via the
	web:

	 http://bugzilla.open-bio.org/

AUTHOR - Shawn Hoon
	 Email shawnh-at-stanford.edu

APPENDIX
	The rest of the documentation details each of the object
	methods. Internal methods are usually preceded with a _

   program_name
	Title	: program_name
	Usage	: $factory>program_name()
	Function: holds the program name
	Returns:  string
	Args	: None

   program_dir
	Title	: program_dir
	Usage	: $factory->program_dir(@params)
	Function: returns the program directory, obtained from ENV variable.
	Returns:  string
	Args	:

   new
	Title	: new
	Usage	: my $factory= Bio::Tools::Run::Phrap->new();
	Function: creates a new Phrap factory
	Returns:  Bio::Tools::Run::Phrap
	Args	:

   version
	Title	: version
	Usage	: exit if $prog->version() < 1.8
	Function: Determine the version number of the program
	Example :
	Returns : float or undef
	Args	: none

   run
	Title	:   run()
	Usage	:   my $feats = $factory->run($seq)
	Function:   Runs Phrap
	Returns :   An array of Bio::SeqFeature::Generic objects
	Args	:   A Bio::PrimarySeqI

   _input
	Title	:   _input
	Usage	:   $factory->_input($seqFile)
	Function:   get/set for input file
	Returns :
	Args	:

   _run
	Title	:   _run
	Usage	:   $factory->_run()
	Function:   Makes a system call and runs Phrap
	Returns :   An array of Bio::SeqFeature::Generic objects
	Args	:

   _writeInput
	Title	:   _writeInput
	Usage	:   $factory->_writeInput($query,$target)
	Function:   Creates a file from the given seq object
	Returns :   A string(filename)
	Args	:   Bio::PrimarySeqI

   _setparams
	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	:

perl v5.14.1			  2011Bio::Tools::Run::Alignment::Exonerate(3)
[top]

List of man pages available for Fedora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net