Bio::Assembly::IO - Handler for Assembly::IO Formats
use Bio::Assembly::IO; $in = Bio::Assembly::IO->new(-file=>"<inputfilename", -format=>'phrap'); $out = Bio::Assembly::IO->new(-file=>">outputfilename", -format=>'phrap'); while ( my $seq = $in->next_seq() ) { $out->write_seq($seq); }
Bio::Assembly::IO is a handler module for formats in the Assembly::IO set (e.g. Bio::Assembly::IO::phrap).
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Robson Francisco de Souza
E-mail: rfsouza@citri.iq.usp.br
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : Bio::Assembly::IO->new(-file =>$filename,-format=>'format') Function: Returns a new assembly stream Returns : A Bio::Assembly::IO::Handler initialised with the appropriate format Args : -file => $filename -format => format
Title : next_assembly Usage : $cluster = $stream->next_assembly() Function: Reads the next assembly object from the stream and returns it. Returns : a Bio::Assembly::ScaffoldI compliant object Args : none
Title : _load_format_module Usage : *INTERNAL Assembly::IO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
Title : _guess_format Usage : $obj->_guess_format($filename) Function: guess format based on file suffix Example : Returns : guessed format of filename (lower case) Args : Notes : formats that _filehandle() will guess includes only phrap, by now.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.