Bio::Tools::Run::Phrap - a wrapper for running Phrap 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"; } } Wrapper module for Phrap program Phrap available at: http://www.phrap.org/

Mailing Lists
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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.bioperl.org/ Email shawnh-at-stanford.edu 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 :