Bio::Tools::Run EMBOSSacd
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Summary
Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Data::Dumper
Inherit
Bio::Root::Root
Synopsis
  use Bio::Factory::EMBOSS;
# get an EMBOSS application object from the EMBOSS factory
$factory = Bio::Factory::EMBOSS->new();
$application = $factory->program('embossversion');
# run the application with an optional hash containing parameters
$result = $application->run(); # returns a string or creates a file
print $result . "\n";
$water = $factory->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 = Bio::AlignIO->new(-format => 'emboss', -file => $wateroutfile); while( my $aln = $alnin->next_aln ) { # process the alignment -- these will be Bio::SimpleAlign objects }
Description
The EMBOSSacd represents all the possible command line arguments that
can be given to an EMBOSS application.
Do not create this object directly. It will be created and attached to
its corresponding Bio::Tools::Run::EMBOSSApplication if you set
  $application->verbose > 0
Call
  $application->acd
to retrive the Bio::Tools::Run::EMBOSSApplication::EMBOSSacd object.
See also Bio::Tools::Run::EMBOSSApplication and Bio::Factory::EMBOSS.
Methods
BEGIN Code
newDescriptionCode
_row
No description
Code
nameDescriptionCode
printDescriptionCode
mandatoryDescriptionCode
qualifierDescriptionCode
categoryDescriptionCode
valuesDescriptionCode
descrDescriptionCode
unnamedDescriptionCode
defaultDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : $emboss_prog->acd($prog_name);
Function: Constructor for the class.
Calls EMBOSS program 'acdc', converts the
HTML output into XML and uses XML::Twig XML
parser to write out a hash of qualifiers which is
then blessed.
Throws : without program name
Returns : new object
Args : EMBOSS program name
namecodeprevnextTop
 Title   : name
Usage : $embossacd->name
Function: sets/gets the name of the EMBOSS program
Setting is done by the EMBOSSApplication object,
you should only get it.
Throws :
Returns : name string
Args : None
printcodeprevnextTop
 Title   : print
Usage : $embossacd->print; $embossacd->print('-word');
Function: Print out the qualifiers.
Uses Data::Dumper to print the qualifiers into STDOUT.
A valid qualifier name given as an argment limits the output.
Throws :
Returns : print string
Args : optional qualifier name
mandatorycodeprevnextTop
 Title   : mandatory
Usage : $acd->mandatory
Function: gets a mandatory subset of qualifiers
Throws :
Returns : Bio::Tools::Run::EMBOSSacd object
Args : none
qualifiercodeprevnextTop
 Title   : qualifier
Usage : $acd->qualifier($string)
Function: tests for the existence of the qualifier
Throws :
Returns : boolean
Args : string, name of the qualifier
categorycodeprevnextTop
 Title   : category
Usage : $acd->category($qual_name)
Function: Return the category of the qualifier
Throws :
Returns : 'mandatory' or 'optional' or 'advanced' or
'associated' or 'general'
Args : string, name of the qualifier
valuescodeprevnextTop
 Title   : values
Usage : $acd->values($qual_name)
Function: Return the possible values for the qualifier
Throws :
Returns : string
Args : string, name of the qualifier
descrcodeprevnextTop
 Title   : descr
Usage : $acd->descr($qual_name)
Function: Return the description of the qualifier
Throws :
Returns : boolean
Args : string, name of the qualifier
unnamedcodeprevnextTop
 Title   : unnamed
Usage : $acd->unnamed($qual_name)
Function: Find if the qualifier can be left unnamed
Throws :
Returns : 0 if needs to be named, order number otherwise
Args : string, name of the qualifier
defaultcodeprevnextTop
 Title   : default
Usage : $acd->default($qual_name)
Function: Return the default value for the qualifier
Throws :
Returns : scalar
Args : string, name of the qualifier
Methods code
BEGINTop
BEGIN {
    %QUALIFIER_CATEGORIES = 
	(
	 'Mandatory qualifiers'            => 'mandatory',
	 'Standard (Mandatory) qualifiers' => 'mandatory',
	 'Optional qualifiers'             => 'optional',
	 'Additional (Optional) qualifiers'=> 'optional',
	 'Advanced qualifiers'             => 'advanced',
	 'Advanced (Unprompted) qualifiers'=> 'advanced',
	 'Associated qualifiers'           => 'associated',
	 'General qualifiers'              => 'general',
	);
    $QUAL;			# qualifier category
}
newdescriptionprevnextTop
sub new {
    my($class, $prog) = @_;

    eval {require XML::Twig;};
    Bio::Root::Root->warn("You need XML::Twig for EMBOSS ACD parsing")
	    and return undef if $@;

    Bio::Root::Root->throw("Need EMBOSSprogram name as an argument")
	     unless $prog;
    # reset global hash
%OPT = (); my $version = `embossversion -auto`; my $file; if ($version lt "2.8.0") { # reading from EMBOSS program acdc stdout (prior to version 2.8.0)
$file = `acdc $prog -help -verbose -acdtable 2>&1`; } else { # reading from EMBOSS program acdtable stdout (version 2.8.0 or greater)
$file = `acdtable $prog -help -verbose 2>&1`; } # converting HTML -> XHTML for XML parsing
$file =~ s/(border)/$1="1"/; $file =~ s/=(\d+)/="$1"/g; $file =~ s/<br>/<br><\/br>/g; $file =~ s/&nbsp;//g; my $t = new XML::Twig( TwigHandlers => { '/table/tr' =>\& _row } ); $t->parse( $file); # results written into global %OPT
my %acd = %OPT; # copy to a private hash
$acd{'_name'} = $prog; bless\% acd, $class;
}
_rowdescriptionprevnextTop
sub _row {
    my ($t, $row)= @_;

    return if $row->text eq "(none)"; #  no qualifiers in this category
my $name = $row->first_child; # qualifier name
my $namet = $name->text; if ($namet =~ /qualifiers$/) { # set category
$QUAL = $QUALIFIER_CATEGORIES{$namet}; if( ! defined $QUAL ) { warn("-- namet is $namet\n"); } return; } my $unnamed = 0; if ($namet =~ /\(Parameter (\d+)\)/) { # unnamed parameter
$unnamed = $1; $namet =~ s/\(Parameter (\d+)\)//; $namet =~ s/[\[\]]//g ; # name is in brackets
} my $desc = $name->next_sibling; my $values = $desc->next_sibling; my $default = $values->next_sibling; $OPT{$namet}{'unnamed'} = $unnamed; $OPT{$namet}{'category'} = $QUAL; $OPT{$namet}{'descr'} = $desc->text; $OPT{$namet}{'values'} = $values->text; $OPT{$namet}{'default'} = $default->text; $t->purge; # to reduce memory requirements
}
namedescriptionprevnextTop
sub name {
    my ($self,$value) = @_;
    if (defined $value) {
	$self->{'_name'} = $value;
    }
    return $self->{'_name'};
}
printdescriptionprevnextTop
sub print {
    my ($self, $value) = @_;
    if ($value and $self->{$value}) {
	print Dumper $self->{$value};
    } else {
	print Dumper $self;
    }
}
mandatorydescriptionprevnextTop
sub mandatory {
    my ($self) = @_;
    my %mand;
    foreach my $key (keys %{$self}) {
	next unless $key =~ /^-/; #ignore other attributes
$mand{$key} = $self->{$key} if $self->{$key}{category} eq 'mandatory'; } bless\% mand;
}
qualifierdescriptionprevnextTop
sub qualifier {
    my ($self, $value) = @_;

    $self->throw("Qualifier has to start with '-'") 
	unless $value =~ /^-/;
    $self->{$value} ? 1 : 0
}
categorydescriptionprevnextTop
sub category {
    my ($self, $value) = @_;

    $self->throw("Not a valid qualifier name [$value]")
	unless $self->qualifier($value);
    $self->{$value}->{'category'};
}
valuesdescriptionprevnextTop
sub values {
    my ($self, $value) = @_;

    $self->throw("Not a valid qualifier name [$value]")
	unless $self->qualifier($value);
    $self->{$value}->{'values'};
}
descrdescriptionprevnextTop
sub descr {
    my ($self, $value) = @_;

    $self->throw("Not a valid qualifier name [$value]")
	unless $self->qualifier($value);
    $self->{$value}->{'descr'};
}
unnameddescriptionprevnextTop
sub unnamed {
    my ($self, $value) = @_;

    $self->throw("Not a valid qualifier name [$value]")
	unless $self->qualifier($value);
    $self->{$value}->{'unnamed'};
}
defaultdescriptionprevnextTop
sub default {
    my ($self, $value) = @_;

    $self->throw("Not a valid qualifier name [$value]")
	unless $self->qualifier($value);
    $self->{$value}->{'default'};
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
 
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 BugsTop
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 - Heikki LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
Address:
     EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Qualifier queriesTop
These methods can be used test qualifier names and read values.