Bio::ClusterIO(3pm)

💖 Bio::ClusterIO 💖

okay bestie, so this is a page from the User Contributed Perl Documentation and it's all about Bio::ClusterIO — your girl for cluster formats 🧬✨

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✨ NAME ✨

Bio::ClusterIO — Handler for Cluster Formats 🎀

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🌸 SYNOPSIS 🌸

#NB: This example is unigene specific

use Bio::ClusterIO;

$stream  = Bio::ClusterIO->new('-file' => "Hs.data",
                               '-format' => "unigene");
# note: we quote -format to keep older perl's from complaining.

while ( my $in = $stream->next_cluster() ) {
    print $in->unigene_id() . "\n";
    while ( my $sequence = $in->next_seq() ) {
        print $sequence->accession_number() . "\n";
    }
}
# Parsing errors are printed to STDERR.

no cap, that comment is telling you the truth: parsing errors get printed to STDERR 👀

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🦋 DESCRIPTION 🦋

So ClusterIO links up with the ClusterIO format module and they read all kinds of cluster formats together — like NCBI UniGene and friends. it's giving dynamic duo energy fr fr 💅

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👑 CONSTRUCTORS 👑

💜 Bio::ClusterIO->new()

$str = Bio::ClusterIO->new(-file => 'filename',
                           -format=>$format);

The new() class method is the one that makes you a brand new Bio::ClusterIO object ✨ and once you've got it, you can use it to pull out cluster objects or print them. new() is taking these parameters, bestie:

• -file — a file path that's gonna be opened for reading 📂
• -format — you tell it the format of the file here. supported formats include:

unigene              *.data  UniGene build files.
dbsnp                *.xml   dbSNP XML files

If you don't specify a format but you do give a filename, the module will try to deduce it from the filename 🔍 and if that doesn't work out? it just assumes the main UniGene build format. lowkey forgiving, we love that 🙈

The format name is case insensitive. 'UNIGENE', 'UniGene' and 'unigene' all work, and so do dbSNP, dbsnp, and DBSNP — yes bestie, all of them, periodt 💅

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🌈 OBJECT METHODS 🌈

Detailed summaries are down below, but here's the main character lineup:

⭐ $cluster = $str->next_cluster()

Grabs the next cluster from the stream. that's it, that's the job 🫶

⭐ TIEHANDLE(), READLINE(), PRINT()

okay so these ones are still hanging around in here because they were in the SeqIO module — feedback appreciated, fr fr. Over there they provide the tie interface. peep perltie if you want the whole lore 👀

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💌 FEEDBACK 💌

🎀 Mailing Lists

User feedback is, like, integral to how this and every other Bioperl module grows and evolves 🌱 so send your comments and suggestions, preferably to one of the Bioperl mailing lists. your participation is much appreciated bestie!!

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🩷 Support

Please send usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

— rather than sliding into the module maintainer's DMs directly 🙈 so many experienced and responsive experts will be able to look at your problem and fix it fast. and please include a thorough description of the problem with code and data examples if at all possible 💯

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolutions. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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💫 AUTHOR - Andrew Macgregor 💫

Email andrew@anatomy.otago.ac.nz 📧

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📖 APPENDIX 📖

the rest of this doc spills the details on each object method. heads up: internal methods usually start with a _ 👑

🔥 new

Title   : new
Usage   : Bio::ClusterIO->new(-file => $filename, -format => 'format')
Function: Returns a new cluster stream
Returns : A Bio::ClusterIO::Handler initialised with the appropriate format
Args    : -file => $filename
          -format => format

🔥 format

Title   : format
Usage   : $format = $stream->format()
Function: Get the cluster format
Returns : cluster format
Args    : none

🔥 next_cluster

Title   : next_cluster
Usage   : $cluster = $stream->next_cluster()
Function: Reads the next cluster object from the stream and returns it.
Returns : a L<Bio::ClusterI> compliant object
Args    : none

🔥 cluster_factory

Title   : cluster_factory
Usage   : $obj->cluster_factory($newval)
Function: Get/set the object factory to use for creating the cluster
          objects.
Example :
Returns : a L<Bio::Factory::ObjectFactoryI> compliant object
Args    : on set, new value (a L<Bio::Factory::ObjectFactoryI>
          compliant object or undef, optional)

🔥 object_factory

Title   : object_factory
Usage   : $obj->object_factory($newval)
Function: This is an alias to cluster_factory with a more generic name.
Example :
Returns : a L<Bio::Factory::ObjectFactoryI> compliant object
Args    : on set, new value (a L<Bio::Factory::ObjectFactoryI>
          compliant object or undef, optional)

🔥 _load_format_module

Title   : _load_format_module
Usage   : *INTERNAL ClusterIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args    :

🔥 _guess_format

Title   : _guess_format
Usage   : $obj->_guess_format($filename)
Function: guess format based on file suffix
Example :
Returns : guessed format of filename (lower case)
Args    :
Notes   : formats that _filehandle() will guess include unigene and dbsnp

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and that's a wrap, bestie!! 🎀 this whole page is running on perl v5.34.0 and it was dated 2022-03-27, so go forth and parse those clusters, you absolute icon 👑💖