| Bio::SeqIO::embl(3pm) | User Contributed Perl Documentation | Bio::SeqIO::embl(3pm) |
Bio::SeqIO::embl - EMBL sequence input/output stream
It is probably best not to use this object directly, but rather go through the SeqIO handler system. Go:
$stream = Bio::SeqIO->new(-file => $filename, -format => 'EMBL');
while ( (my $seq = $stream->next_seq()) ) {
# do something with $seq
}
This object can transform Bio::Seq objects to and from EMBL flat file databases.
There is a lot of flexibility here about how to dump things which should be documented more fully.
There should be a common object that this and Genbank share (probably with Swissprot). Too much of the magic is identical.
print "ID ", $func($annseq), "\n";
To generate the ID line. If it is not there, it generates a sensible ID line using a number of tools.
If you want to output annotations in EMBL format they need to be stored in a Bio::Annotation::Collection object which is accessible through the Bio::SeqI interface method annotation().
The following are the names of the keys which are polled from a Bio::Annotation::Collection object.
reference - Should contain Bio::Annotation::Reference objects
comment - Should contain Bio::Annotation::Comment objects
dblink - Should contain Bio::Annotation::DBLink objects
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of 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
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.
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:
https://github.com/bioperl/bioperl-live/issues
Email birney@ebi.ac.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args :
Title : _write_ID_line
Usage : $self->_write_ID_line($seq);
Function: Writes the EMBL Release 87 format ID line to the stream, unless
: there is a user-supplied ID line generation function in which
: case that is used instead.
: ( See Bio::SeqIO::embl::_id_generation_function(). )
Returns : nothing
Args : Bio::Seq object
Title : _is_valid_division Usage : $self->_is_valid_division($div) Function: tests division code for validity Returns : true if $div is a valid EMBL release 87 taxonomic division. Args : taxonomic division code string
Title : _is_valid_molecule_type Usage : $self->_is_valid_molecule_type($mol) Function: tests molecule type for validity Returns : true if $mol is a valid EMBL release 87 molecule type. Args : molecule type string
Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and undef for error Args : array of 1 to n Bio::SeqI objects
Title : _print_EMBL_FTHelper Usage : Function: Internal function Returns : 1 if writing succeeded, otherwise undef Args :
Title : _read_EMBL_Contig Usage : Function: convert CO lines into annotations Returns : Args :
Title : _read_EMBL_References Usage : Function: Reads references from EMBL format. Internal function really Example : Returns : Args :
Title : _read_EMBL_Species
Usage :
Function: Reads the EMBL Organism species and classification
lines.
Example :
Returns : A Bio::Species object
Args : a reference to the current line buffer, accession number
Title : _read_EMBL_DBLink
Usage :
Function: Reads the EMBL database cross reference ("DR") lines
Example :
Returns : A list of Bio::Annotation::DBLink objects
Args :
Title : _read_EMBL_TaxID_DBLink
Usage :
Function: Reads the EMBL database cross reference to NCBI TaxID ("OX") lines
Example :
Returns : A list of Bio::Annotation::DBLink objects
Args :
Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional)
Title : _read_FTHelper_EMBL Usage : _read_FTHelper_EMBL($buffer) Function: reads the next FT key line Example : Returns : Bio::SeqIO::FTHelper object Args : filehandle and reference to a scalar
Title : _write_line_EMBL Usage : Function: internal function Example : Returns : 1 if writing succeeded, else undef Args :
Title : _write_line_EMBL_regex
Usage :
Function: internal function for writing lines of specified
length, with different first and the next line
left hand headers and split at specific points in the
text
Example :
Returns : nothing
Args : file handle, first header, second header, text-line, regex for line breaks, total line length
Title : _post_sort Usage : $obj->_post_sort($newval) Function: Returns : value of _post_sort Args : newvalue (optional)
Title : _show_dna Usage : $obj->_show_dna($newval) Function: Returns : value of _show_dna Args : newvalue (optional)
Title : _id_generation_func Usage : $obj->_id_generation_func($newval) Function: Returns : value of _id_generation_func Args : newvalue (optional)
Title : _ac_generation_func Usage : $obj->_ac_generation_func($newval) Function: Returns : value of _ac_generation_func Args : newvalue (optional)
Title : _sv_generation_func Usage : $obj->_sv_generation_func($newval) Function: Returns : value of _sv_generation_func Args : newvalue (optional)
Title : _kw_generation_func Usage : $obj->_kw_generation_func($newval) Function: Returns : value of _kw_generation_func Args : newvalue (optional)
| 2021-08-15 | perl v5.32.1 |