Bio::DB::Fasta - Fast indexed access to fasta files River stage two • 60 direct dependents • 65 total dependents

Bio::DB::Fasta provides indexed access to a single Fasta file, several files, or a directory of files. It provides persistent random access to each sequence entry (either as a Bio::PrimarySeqI-compliant object or a string), and to subsequences within...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::DB::Flat::BDB::fasta - fasta adaptor for Open-bio standard BDB-indexed flat file River stage two • 60 direct dependents • 65 total dependents

This module allows fasta files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use it via Bio::DB::Flat....

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::DB::SeqFeature::Store::berkeleydb - Storage and retrieval of sequence annotation data in Berkeleydb files River stage zero No dependents

Bio::DB::SeqFeature::Store::berkeleydb is the Berkeleydb adaptor for Bio::DB::SeqFeature::Store. You will not create it directly, but instead use Bio::DB::SeqFeature::Store->new() to do so. See Bio::DB::SeqFeature::Store for complete usage instructio...

CJFIELDS/Bio-DB-SeqFeature-1.7.4 - 09 Jan 2020 04:03:49 UTC

Bio::Index::Qual - Interface for indexing (multiple) fasta qual files River stage two • 60 direct dependents • 65 total dependents

Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionality for indexing qual files, and retrieving the sequence from them. For best results 'use strict'. Bio::Index::Qual supports the Bio::DB::BioSeqI ...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::Seq - Sequence object, with features River stage two • 60 direct dependents • 65 total dependents

A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently Bio::Prim...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::Index::Fasta - Interface for indexing (multiple) fasta files River stage two • 60 direct dependents • 65 total dependents

Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionality for indexing fasta files, and retrieving the sequence from them. For best results 'use strict'. Bio::Index::Fasta supports the Bio::DB::BioSeq...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::ToolBox - Tools for querying and analysis of genomic data River stage zero No dependents

The Bio::ToolBox libraries provide a useful interface for working with bioinformatic data. Many bioinformatic data analysis revolves around working with tables of information, including lists of genomic annotation (genes, promoters, etc.) or defined ...

TJPARNELL/Bio-ToolBox-1.68 - 24 Jan 2021 19:38:27 UTC

Bio::DB::Qual - Fast indexed access to quality files River stage two • 60 direct dependents • 65 total dependents

Bio::DB::Qual provides indexed access to a single Fasta file, several files, or a directory of files. It provides random access to each quality score entry without having to read the file from the beginning. Access to subqualities (portions of a qual...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::DB::Sam - Read SAM/BAM database files River stage one • 1 direct dependent • 1 total dependent

This module provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across...

LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC

Bio::DB::HTS - Read files using HTSlib including BAM/CRAM, Tabix and BCF database files River stage one • 1 direct dependent • 1 total dependent

This module provides a Perl interface to the HTSlib library for indexed and unindexed SAM/BAM/CRAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information a...

AVULLO/Bio-DB-HTS-3.01 - 23 Apr 2019 13:51:11 UTC

Bio::DB::GFF - Storage and retrieval of sequence annotation data River stage one • 2 direct dependents • 2 total dependents

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

Bio::DB::EMBL - Database object interface for EMBL entry retrieval River stage one • 1 direct dependent • 8 total dependents

Allows the dynamic retrieval of sequence objects Bio::Seq from the EMBL 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 (...

CJFIELDS/Bio-DB-EMBL-1.7.4 - 04 Mar 2019 05:02:40 UTC

Bio::DB::USeq - Read USeq archive database files River stage zero No dependents

Bio::DB::USeq is a BioPerl style adaptor for reading USeq files. USeq files are compressed, indexed data files supporting modern bioinformatic datasets, including genomic points, scores, and intervals. More information about the USeq software package...

TJPARNELL/Bio-DB-USeq-0.25 - 02 Jan 2019 19:51:06 UTC

Bio::ViennaNGS - A Perl distribution for Next-Generation Sequencing (NGS) data analysis River stage zero No dependents

Bio::ViennaNGS is a distribution of Perl modules and utilities for building efficient Next-Generation Sequencing (NGS) analysis pipelines. It covers various aspects of NGS data analysis, including (but not limited to) conversion of sequence annotatio...

MTW/Bio-ViennaNGS-v0.19.2 - 11 Dec 2018 13:25:00 UTC

FAST::Bio::Seq - Sequence object, with features River stage zero No dependents

A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently FAST::Bio...

DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC

Bio::DB::RefSeq - Database object interface for RefSeq retrieval River stage one • 1 direct dependent • 8 total dependents

Allows the dynamic retrieval of sequence objects Bio::Seq from the RefSeq nucleotide database using the dbfetch script at EBI: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch At this time the module specifically retrieves nucleotide sequences only. In ord...

CJFIELDS/Bio-DB-RefSeq-1.7.4 - 07 Dec 2019 22:10:26 UTC

Bio::PrimarySeq - Bioperl lightweight sequence object River stage two • 60 direct dependents • 65 total dependents

PrimarySeq is a lightweight sequence object, storing the sequence, its name, a computer-useful unique name, and other fundamental attributes. It does not contain sequence features or other information. To have a sequence with sequence features you sh...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::DB::DBFetch - Database object for retrieving using the dbfetch script River stage two • 60 direct dependents • 65 total dependents

Allows the dynamic retrieval of entries from databases using the dbfetch script at EBI: http://www.ebi.ac.uk/cgi-bin/dbfetch. In order to make changes transparent we have host type (currently only ebi) and location (defaults to ebi) separated out. Th...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::DB::GenBank - Database object interface to GenBank River stage two • 3 direct dependents • 10 total dependents

Allows the dynamic retrieval of Bio::Seq sequence objects from the GenBank database at NCBI, via an Entrez query. WARNING: Please do NOT spam the Entrez web server with multiple requests. NCBI offers Batch Entrez for this purpose. Note that when quer...

CJFIELDS/Bio-DB-NCBIHelper-1.7.7 - 30 Jun 2021 13:56:04 UTC

Bio::Index::Blast - Indexes Blast reports and supports retrieval based on query accession(s) River stage two • 60 direct dependents • 65 total dependents

This object allows one to build an index on a blast file (or files) and provide quick access to the blast report for that accession. This also allows for ID parsing using a callback: $inx->id_parser(\&get_id); # make the index $inx->make_index($file_...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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