/ 
bioperl-run-1.5.2_005-RC
/ Bio::Tools::Run::Phrap

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

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, obtiained 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    :