Bio::Prospect::File -- interface to Prospect Files
$Id: File.pm,v 1.15 2003/11/18 19:45:45 rkh Exp $
use Bio::Prospect::File; my $pf = new Bio::Prospect::File( $fn ); while( my $t = $pf->next_thread() ) { printf("%s->%s raw=%d mut=%d pair=%d\n", $t->qname(), $t->tname(), $t->raw_score(), $t->mutation_score(), $t->pair_score() ); print $t->alignment(); }
Bio::Prospect::File is a subclass of IO::File and is intended for use for parsing Prospect XML files. It is used by Bio::Prospect::LocalClient to return Thread objects from Prospect output.
Name: new() Purpose: constructor Arguments: Returns: Bio::Prospect::File
Name: fdopen() Purpose: overrides fdopen in IO::File Arguments: same as IO::File::fdopen Returns: nothing
Name: open() Purpose: overrides open in IO::File Arguments: same as IO::File::open Returns: nothing
Name: next_thread() Purpose: return next Thread object Arguments: none Returns: Bio::Prospect::Thread
Name: next_thread_as_xml() Purpose: return next threading xml tag Arguments: none Returns: xml string
Name: _advance() Purpose: INTERNAL METHOD: check if proper Prospect xml Arguments: none Returns: 1 - okay, 0 - bad xml
To install Bio::Prospect::File, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Prospect::File
CPAN shell
perl -MCPAN -e shell install Bio::Prospect::File
For more information on module installation, please visit the detailed CPAN module installation guide.