Bio::Tools::Run::Phrap man page on Pidora

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Bio::Tools::Run::PhrapUser Contributed Perl DocumentaBio::Tools::Run::Phrap(3)

NAME
       Bio::Tools::Run::Phrap - a wrapper for running Phrap

SYNOPSIS
	 use Bio::Tools::Run::Phrap;
	 use Bio::SeqIO;

	 my $sio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'fasta');
	 my @seq;
	 while(my $seq = $sio->next_seq()){
	   push @seq,$seq;
	 }
	 my $prun =Bio::Tools::Run::Phrap->new(arguments=>'-penalty -3 -minmatch 10');
	 my $assembly = $prun->run(\@seq);
	 foreach my $contig($assembly->all_contigs){
	   my $collection = $contig->get_features_collection;
	   foreach my $sf($collection->get_all_features){
	     print $sf->primary_id."\t".$sf->start."\t".$sf->end."\n";
	   }
	 }

DESCRIPTION
	 Wrapper module for Phrap program
	 Phrap available at: http://www.phrap.org/

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	:

   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	:

   _writeSeqFile
	Title	:   _writeSeqFile
	Usage	:   $factory->_writeSeqFile($seq)
	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			  2011-07-21	     Bio::Tools::Run::Phrap(3)
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