| Bio::SeqIO::swiss(3pm) | User Contributed Perl Documentation | Bio::SeqIO::swiss(3pm) |
Bio::SeqIO::swiss - Swissprot sequence input/output stream
It is probably best not to use this object directly, but rather go through the SeqIO handler system:
use Bio::SeqIO;
$stream = Bio::SeqIO->new(-file => $filename,
-format => 'swiss');
while ( my $seq = $stream->next_seq() ) {
# do something with $seq
}
This object can transform Bio::Seq objects to and from Swiss-Pprot flat file databases.
There is a lot of flexibility here about how to dump things which needs to be documented.
A Uniprot/Swiss-Prot entry holds information on one protein sequence. If that sequence is identical across genes and species, they are all merged into one entry. This creates complex needs for several annotation fields in swiss-prot format.
The latest syntax for GN line is described in the user manual:
http://www.expasy.ch/sprot/userman.html#GN_line
Each of the possibly multiple genes in an entry can have Name, Synonyms (only if there is a name), OrderedLocusNames (names from genomic sequences) and ORFNames (temporary or cosmid names). "Name" here really means "symbol". This complexity is now dealt with the following way:
A new Bio::AnnotationI class was created in order to store the data in tag-value pairs. This class (Bio::Annotation::TagTree) is stored in the Bio::Annotation::Collection object and is accessed like all other annotations. The tag name is 'gene_name'.
There is a single Bio::Annotation::TagTree per sequence record, which corresponds to the original class that stored this data (Bio::Annotation::StructuredValue). Depending on how we progress this may change to represent each group of gene names.
For now, to access the gene name tree annotation, one uses the below method:
my ($gene) = $seq->annotation->get_Annotations('gene_name');
If you are only interested in displaying the values, value() returns a string with similar formatting.
There are several ways to get directly at the information you want if you know the element (tag) for the data. For gene names all data is stored with the element-tag pairs:
"element1=tag1, tag2, tag3; element2=tag4, tag5;"
This normally means the element will be 'Name', 'Synonyms', etc. and the gene names the values. Using findval(), you can do the following:
# grab a flattened list of all gene names
my @names = $ann->findval('Name');
# or iterated through the nodes and grab the name for each group
for my $node ($ann->findnode('gene_name')) {
my @names = $node->findval('Name');
}
The current method for parsing gene name data (and reconstructing gene name output) is very generic. This is somewhat preemptive if, for instance, UniProt decides to update and add another element name to the current ones using the same formatting layout. Under those circumstances, one can iterate through the tag tree in a safe way and retrieve all node data like so.
# retrieve the gene name nodes (groups like names, synonyms, etc).
for my $ann ($seq->annotation->get_Annotations('gene_name')) {
# each gene name group
for my $node ($ann->findnode('gene_name')) {
print "Gene name:\n";
# each gene name node (tag => value pair)
for my $n ($node->children) {
print "\t".$n->element.": ".$n->children."\n";
}
}
}
For more uses see Bio::Annotation::TagTree.
Since Uniprot/Swiss-Prot format have been around for quite some time, the parser is also able to read in the older GN line syntax where genes are separated by AND and various symbols by OR. The first symbol is taken to be the 'Name' and the remaining ones are stored as 'Synonyms'.
Also, for UniProt output we support using other Bio::AnnotationI, but in this case we only use the stringified version of the annotation. This is to allow for backwards compatibility with code that previously used Bio::Annotation::SimpleValue or other Bio::AnnotationI classes.
print "ID ", $func($seq), "\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 Swissprot 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
gene_name - Should contain Bio::Annotation::SimpleValue object
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 elia@tll.org.sg
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_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : array of 1 to n Bio::SeqI objects
Title : _generateCRCTable Usage : Function: Example : Returns : Args :
Title : _crc32 Usage : Function: Example : Returns : Args :
Title : _crc64 Usage : Function: Example : Returns : Args :
Title : _print_swissprot_FTHelper Usage : Function: Example : Returns : Args :
Title : _read_swissprot_References Usage : Function: Reads references from swissprot format. Internal function really Example : Returns : Args :
Title : _read_swissprot_Species
Usage :
Function: Reads the swissprot Organism species and classification
lines.
Able to deal with unconventional species names.
Example : OS Unknown prokaryotic organism
$genus = undef ; $species = Unknown prokaryotic organism
Returns : A Bio::Species object
Args :
Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional)
Title : _read_FTHelper_swissprot Usage : _read_FTHelper_swissprot(\$buffer) Function: reads the next FT key line Example : Returns : Bio::SeqIO::FTHelper object Args :
Title : _write_line_swissprot Usage : Function: internal function Example : Returns : Args :
Title : _write_line_swissprot_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 |