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Bio::Tools::Run::Phrap.3pm
Langue: en
Version: 2009-11-04 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::Phrap - a wrapper for running PhrapSYNOPSIS
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 :
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre