Search results for "Bio::Index::Abstract"
Bio::Index::Abstract - Abstract interface for indexing a flat file
This object provides the basic mechanism to associate positions in files with names. The position and filenames are stored in DBM which can then be accessed later on. It is the equivalent of flat file indexing (eg, SRS or efetch). This object is the ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::Index::AbstractSeq - base class for AbstractSeq
- bp_fetch.pl - fetches sequences from bioperl indexed databases
- Bio::DB::Flat - Interface for indexed flat files
- 6 more results from BioPerl »
Perl6::Form - Implements the Perl 6 'form' built-in
Formats are Perl 5's mechanism for creating text templates with fixed-width fields. Those fields are then filled in using values from prespecified package variables. Unlike Perl 5, Perl 6 doesn't have a "format" keyword. Or the associated built-in fo...
DCONWAY/Perl6-Form-0.090 - 09 Jan 2019 00:23:27 UTC - Search in distribution
Bio::DB::GFF - Storage and retrieval of sequence annotation data
Bio::DB::GFF provides fast indexed access to a sequence annotation database. It supports multiple database types (ACeDB, relational), and multiple schemas through a system of adaptors and aggregators. The following operations are supported by this mo...
CJFIELDS/Bio-DB-GFF-1.7.4 - 08 Jan 2020 20:41:58 UTC - Search in distribution- Bio::DB::GFF::Adaptor::dbi::pg - Database adaptor for a specific postgres schema
Bio::ToolBox::Data - Reading, writing, and manipulating data structure
This module works with the primary Bio::ToolBox Data structure. Simply, it is a complex data structure representing a tabbed-delimited table (array of arrays), with plenty of options for metadata. Many common bioinformatic file formats are simply tab...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC - Search in distribution- Bio::ToolBox::db_helper - helper interface to various database formats
Bio::DB::SeqFeature::Store - Storage and retrieval of sequence annotation data
Bio::DB::SeqFeature::Store implements the Bio::SeqFeature::CollectionI interface to allow you to persistently store Bio::SeqFeatureI objects in a database and to later to retrieve them by a variety of searches. This module is similar to the older Bio...
CJFIELDS/Bio-DB-SeqFeature-1.7.4 - 09 Jan 2020 04:03:49 UTC - Search in distribution
Bio::Index::Hmmer - indexes HMMER reports and supports retreival based on query
This object allows one to build an index on a HMMER file (or files) and provide quick access to the HMMER report for that accession. For best results 'use strict'. You can also set or customize the unique key used to retrieve by writing your own func...
CJFIELDS/Bio-SearchIO-hmmer-1.7.3 - 25 Sep 2018 00:26:52 UTC - Search in distribution
Bio::Grep::Backend::BackendI - Superclass for all back-ends
Bio::Grep::Backend::BackendI is the superclass for all back-ends. Don't use this class directly....
LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC - Search in distribution
Bio::Index::Stockholm - Interface for indexing Stockholm files
Indexes Stockholm format alignments such as those from Pfam and Rfam. Returns raw stream data using the ID or a Bio::SimpleAlign object (via Bio::AlignIO). This module also allows for ID parsing using a callback: $inx->id_parser(\&get_id); # make the...
CJFIELDS/Bio-AlignIO-stockholm-1.7.3 - 25 Sep 2018 00:14:27 UTC - Search in distribution
Bio::ASN1::EntrezGene::Indexer - Indexes NCBI Sequence files.
Bio::ASN1::EntrezGene::Indexer is a Perl Indexer for NCBI Entrez Gene genome databases. It processes an ASN.1-formatted Entrez Gene record and stores the file position for each record in a way compliant with Bioperl standard (in fact its a subclass o...
CJFIELDS/Bio-ASN1-EntrezGene-1.73 - 25 Sep 2018 02:32:11 UTC - Search in distribution- Bio::ASN1::Sequence::Indexer - Indexes NCBI Sequence files.
FAST::Bio::SearchIO::Writer::TextResultWriter - Object to implement writing a FAST::Bio::Search::ResultI in Text.
This object implements the SearchWriterI interface which will produce a set of Text for a specific FAST::Bio::Search::Report::ReportI interface. You can also provide the argument -filters => \%hash to filter the at the hsp, hit, or result level. %has...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::SearchIO::Writer::HTMLResultWriter - write a FAST::Bio::Search::ResultI in HTML