BioPerl

 view release on metacpan or  search on metacpan

Bio/DB/DBFetch.pm  view on Meta::CPAN

=head1 SYNOPSIS

  #do not use this module directly

=head1 DESCRIPTION

Allows the dynamic retrieval of entries from databases using the
dbfetch script at EBI:
L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>cgi-binE<sol>dbfetch>.

In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out.  This allows later
additions of more servers in different geographical locations.

This is a superclass which is called by instantiable subclasses with
correct parameters.

=head1 FEEDBACK

=head2 Mailing Lists

Bio/DB/EMBL.pm  view on Meta::CPAN

  while( my $clone =  $seqio->next_seq ) {
 	print "cloneid is ", $clone->id, "\n";
  }

=head1 DESCRIPTION

Allows the dynamic retrieval of sequence objects L<Bio::Seq> from the
EMBL database using the dbfetch script at EBI:
L<http://www.ebi.ac.uk/Tools/dbfetch/dbfetch>.

In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out.  This allows later
additions of more servers in different geographical locations.

The functionality of this module is inherited from L<Bio::DB::DBFetch>
which implements L<Bio::DB::WebDBSeqI>.

=head1 FEEDBACK

=head2 Mailing Lists

Bio/DB/GFF.pm  view on Meta::CPAN

This method takes a single overloaded argument, which can be any of:

=over 4

=item *

a scalar corresponding to a GFF file on the system

A pathname to a local GFF file.  Any files ending with the .gz, .Z, or
.bz2 suffixes will be transparently decompressed with the appropriate
command-line utility.

=item *

an array reference containing a list of GFF files on the system

For example ['/home/gff/gff1.gz','/home/gff/gff2.gz']

=item *

Bio/DB/GFF.pm  view on Meta::CPAN

This method takes a single overloaded argument, which can be any of:

=over 4

=item *

scalar corresponding to a FASTA file on the system

A pathname to a local FASTA file.  Any files ending with the .gz, .Z, or
.bz2 suffixes will be transparently decompressed with the appropriate
command-line utility.

=item *

array reference containing a list of FASTA files on the
system

For example ['/home/fasta/genomic.fa.gz','/home/fasta/genomic.fa.gz']

=item *

Bio/DB/RefSeq.pm  view on Meta::CPAN

 	print "seqid is ", $seq->id, "\n";
  }

=head1 DESCRIPTION

Allows the dynamic retrieval of sequence objects L<Bio::Seq> from the
RefSeq database using the dbfetch script at EBI:

http://www.ebi.ac.uk/Tools/dbfetch/dbfetch

In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out.  This allows later
additions of more servers in different geographical locations.

The functionality of this module is inherited from L<Bio::DB::DBFetch>
which implements L<Bio::DB::WebDBSeqI>.

This module retrieves entries from EBI although it
retrieves database entries produced at NCBI. When read into bioperl
objects, the parser for GenBank format it used. RefSeq is a
NONSTANDARD GenBank file so be ready for surprises.

Bio/DB/SwissProt.pm  view on Meta::CPAN

=head1 DESCRIPTION

SwissProt is a curated database of proteins managed by the Swiss
Bioinformatics Institute. Additional tools for
parsing and manipulating swissprot files can be found at
ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/.

Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the
SwissProt database via an Expasy retrieval.

In order to make changes transparent we have host type (currently only
expasy) and location (default to Switzerland) separated out.  This
allows the user to pick the closest Expasy mirror for running their
queries.


=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other

Bio/DB/TFBS/transfac_pro.pm  view on Meta::CPAN

}

=head2 Helper methods 

=cut

# internal method which does the indexing
sub _build_index {
    my ($self, $dat_dir, $force) = @_;
    
    # MLDBM would give us transparent complex data structures with DB_File,
    # allowing just one index file, but its yet another requirement and we
    # don't strictly need it
    
    my $index_dir = $self->index_directory;
    my $gene_index      = "$index_dir/gene.dat.index";
    my $reference_index = "$index_dir/reference.dat.index";
    my $matrix_index    = "$index_dir/matrix.dat.index";
    my $factor_index    = "$index_dir/factor.dat.index";
    my $fragment_index  = "$index_dir/fragment.dat.index";
    my $site_index      = "$index_dir/site.dat.index";

Bio/SeqFeature/AnnotationAdaptor.pm  view on Meta::CPAN

   # annotation, use this adaptor, which also implements
   # Bio::AnnotationCollectionI
   my $anncoll = Bio::SeqFeature::AnnotationAdaptor->new(-feature => $feat);

   # this will now return tag/value pairs as
   # Bio::Annotation::SimpleValue objects
   my @anns = $anncoll->get_Annotations("mytag");
   # other added before annotation is available too
   my @dblinks = $anncoll->get_Annotations("dbxref");

   # also supports transparent adding of tag/value pairs in
   # Bio::AnnotationI flavor
   my $tagval = Bio::Annotation::SimpleValue->new(-value => "some value",
                                                  -tagname => "some tag");
   $anncoll->add_Annotation($tagval);
   # this is now also available from the feature's tag/value system
   my @vals = $feat->get_tag_values("some tag");

=head1 DESCRIPTION

L<Bio::SeqFeatureI> defines light-weight annotation of features

Bio/SeqFeature/AnnotationAdaptor.pm  view on Meta::CPAN

that retrieving and adding annotation will always use objects instead
of light-weight tag/value pairs.

In other words, this adaptor allows us to keep the best of both
worlds. If you create tens of thousands of feature objects, and your
only annotation is tag/value pairs, you are best off using the
features' native tag/value system. If you create a smaller number of
features, but with rich and typed annotation mixed with tag/value
pairs, this adaptor may be for you. Since its implementation is by
double-composition, you only need to create one instance of the
adaptor. In order to transparently annotate a feature object, set the
feature using the feature() method. Every annotation you add will be
added to the feature object, and hence will not be lost when you set
feature() to the next object.

=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

t/data/tol-2010-02-18.nhx  view on Meta::CPAN

(((aquifex[&&NHX:TOL=59615],calderobacterium[&&NHX:TOL=59616],hydrogenobacter[&&NHX:TOL=59617],thermocrinis[&&NHX:TOL=59618],hydrogenothermus[&&NHX:TOL=59619],persephonella[&&NHX:TOL=59620],sulfurihydrogenibium[&&NHX:TOL=59621],balnearium[&&NHX:TOL=5...