diff variant_effect_predictor/Bio/Factory/EMBOSS.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Factory/EMBOSS.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,284 @@
+# $Id: EMBOSS.pm,v 1.10 2002/10/22 07:38:32 lapp Exp $
+#
+# BioPerl module for Bio::Factory::EMBOSS
+#
+#
+# Cared for by Heikki Lehvaslaiho <[e-mail]>
+#
+# Copyright Heikki Lehvaslaiho
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Factory::EMBOSS - EMBOSS appliaction factory class
+
+=head1 SYNOPSIS
+
+  # get an EMBOSS factory
+  use Bio::Factory::EMBOSS;
+  $f = Bio::Factory::EMBOSS -> new();
+  # get an EMBOSS application  object from the factory
+  $water = $f->program('water');
+
+  # here is an example of running the application
+  # water can compare 1 seq against 1->many sequences
+  # in a database using Smith-Waterman
+  my $seq_to_test; # this would have a seq here
+  my @seqs_to_check; # this would be a list of seqs to compare 
+                     # (could be just 1)
+  my $wateroutfile = 'out.water';
+  $water->run({ '-sequencea' => $seq_to_test,
+              '-seqall'    => \@seqs_to_check,
+              '-gapopen'   => '10.0',
+              '-gapextend' => '0.5',
+              '-outfile'   => $wateroutfile});
+  # now you might want to get the alignment
+  use Bio::AlignIO;
+  my $alnin = new Bio::AlignIO(-format => 'emboss',
+			       -file   => $wateroutfile);
+
+  while( my $aln = $alnin->next_aln ) {
+      # process the alignment -- these will be Bio::SimpleAlign objects
+  }
+
+=head1 DESCRIPTION
+
+The EMBOSS factory class encapsulates access to EMBOSS programs.  A
+factory object allows creation of only known applications.
+
+If you want to check command line options before sending them to the
+program set $factory-E<gt>verbose to positive integer. The value is
+passed on to programs objects and the ADC description of the available
+command line options is parsed and compared to input.
+
+See also L<Bio::Tools::Run::EMBOSSApplication> and
+L<Bio::Tools::Run::EMBOSSacd>.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to the
+Bioperl mailing lists  Your participation is much appreciated.
+
+  [e-mail]                         - General discussion
+  http://bio.perl.org/MailList.html             - About the mailing lists
+
+=head2 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
+ email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Heikki Lehvaslaiho
+
+Email:  [e-mail]
+Address:
+
+     EMBL Outstation, European Bioinformatics Institute
+     Wellcome Trust Genome Campus, Hinxton
+     Cambs. CB10 1SD, United Kingdom
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin...
+
+package Bio::Factory::EMBOSS;
+use vars qw(@ISA $EMBOSSVERSION);
+use strict;
+
+use Bio::Root::Root;
+use Bio::Tools::Run::EMBOSSApplication;
+use Bio::Factory::ApplicationFactoryI;
+@ISA = qw(Bio::Root::Root Bio::Factory::ApplicationFactoryI );
+
+$EMBOSSVERSION = "2.0.0";
+
+sub new {
+  my($class,@args) = @_;
+  my $self = $class->SUPER::new(@args);
+  # set up defaults
+
+  my($location) =
+      $self->_rearrange([qw(LOCATION )],
+			@args);
+
+  $self->{ '_programs' } = {};
+  $self->{ '_programgroup' } = {};
+  $self->{ '_groups' } = {};
+
+  $self->location($location) if $location;
+
+  $self->_program_list; # retrieve info about available programs
+
+  return $self;
+
+}
+
+=head2 location
+
+ Title   : location
+ Usage   : $embossfactory->location
+ Function: get/set the location of EMBOSS programs.
+           Valid values are 'local' and 'novella'.
+ Returns : string, defaults to 'local'
+ Args    : string 
+
+=cut
+
+sub location {
+    my ($self, $value) = @_;
+    my %location = ('local' => '1',
+		    'novella' => '1'
+		    );
+    if (defined $value) {
+	$value = lc $value;
+	if ($location{$value}) {
+	    $self->{'_location'} = $value;
+	} else {
+	    $self->warn("Value [$value] not a valid value for ".
+			"location(). Defaulting to [local]");
+	    $self->{'_location'} = 'local';
+	}
+    }
+    $self->{'_location'} ||= 'local';
+    return $self->{'_location'};
+}
+
+
+=head2 program
+
+ Title   : program
+ Usage   : $embossfactory->program('program_name')
+ Function: Creates a representation of a single EMBOSS program
+ Returns : Bio::Tools::Run::EMBOSSApplication object
+ Args    : string, program name
+
+=cut
+
+sub program {
+    my ($self, $value) = @_;
+
+    unless( $self->{'_programs'}->{$value} ) {
+	$self->warn("Application [$value] is not available!");
+	return undef;
+    }
+    my $attr = {};
+    $attr->{name} = $value;
+    $attr->{verbose} = $self->verbose;
+
+    my $appl = Bio::Tools::Run::EMBOSSApplication ->new($attr);
+    return $appl;
+}
+
+=head2 version
+
+ Title   : $self->version
+ Usage   : $embossfactory->version()
+ Function: gets the version of EMBOSS programs
+ Throws  : if EMBOSS suite is not accessible
+ Returns : version value
+ Args    : None
+
+=cut
+
+sub version {
+    my ($self) = @_;
+    my ($version);
+    eval {
+	$version = `embossversion -auto`;
+    };
+    $self->throw("EMBOSS suite of programs is not available \n\n$@")
+	if $@;
+    chop $version;
+
+    # compare versions
+    my ($thisv, $embossv);
+    $version =~ /(\d+)\.(\d+)\.(\d+)/;
+    $thisv = "$1.$2$3";
+    $EMBOSSVERSION =~ /(\d+)\.(\d+)\.(\d+)/;
+    $embossv = "$1.$2$3";
+    $self->throw("EMBOSS has to be at least version $EMBOSSVERSION\n")
+	if $thisv < $embossv;
+
+    return $version;
+}
+
+
+=head2 Programs
+
+These methods allow the programmer to query the EMBOSS suite and find
+out which program names can be used and what arguments can be used.
+
+=head2 program_info
+
+ Title   : program_info
+ Usage   : $embossfactory->program_info('emma')
+ Function: Finds out if the program is available.
+ Returns : definition string of the program, undef if program name not known
+ Args    : string, prgramname
+
+=cut
+
+sub program_info {
+    my ($self, $value) = @_;
+    return $self->{'_programs'}->{$value};
+}
+
+
+=head2 Internal methods
+
+Do not call these methods directly
+
+=head2 _program_list
+
+ Title   : _program_list
+ Usage   : $embossfactory->_program_list()
+ Function: Finds out what programs are available.
+           Writes the names into an internal hash.
+ Returns : true if successful
+ Args    : None
+
+=cut
+
+sub _program_list {
+    my ($self) = @_;
+    if( $^O =~ /MSWIN/i ||
+	$^O =~ /Mac/i ) { return; }
+    {
+	local * SAVERR;
+	open SAVERR, ">&STDERR";
+	open STDERR, ">/dev/null";
+	open(WOSSOUT, "wossname -auto |") || return;
+	open STDERR, ">&SAVERR";
+
+    }
+    local $/ = "\n\n";
+    while(<WOSSOUT> ) {	
+	my ($groupname) = (/^([A-Z][A-Z0-9 ]+)$/m);
+	#print $groupname, "\n" if $groupname;
+	$self->{'_groups'}->{$groupname} = [] if $groupname;
+	while ( /^([a-z]\w+) +(.+)$/mg ) {
+	    #print "$1\t$2 \n" if $1;
+	    $self->{'_programs'}->{$1} = $2 if $1; 
+	    $self->{'_programgroup'}->{$1} = $groupname if $1;
+	    push @{$self->{'_groups'}->{$groupname}}, $1 if $1;
+	}
+    }
+    close(WOSSOUT);
+
+}
+
+1;