Search results for "Bio::Index"
Bio::SFF::Index - SFF index object
This class represents the index of an SFF file....
LEONT/Bio-SFF-0.007 - 25 Jul 2013 14:00:38 UTC - Search in distribution- Bio::SFF::Entry - An SFF entry
- Bio::SFF::Header - An SFF header
Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).
Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionality for indexing EMBL files, and retrieving the sequence from them. Heavily snaffled from James Gilbert and his Fasta system. Note: for best resul...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::Index::Qual - Interface for indexing (multiple) fasta qual files
- Bio::Index::Fasta - Interface for indexing (multiple) fasta files
- Bio::Index::Fastq - Interface for indexing (multiple) fastq files
- 35 more results from BioPerl »
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::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: $inx->id_parser(\&get_id); # make the...
CJFIELDS/Bio-AlignIO-stockholm-1.7.3 - 25 Sep 2018 00:14:27 UTC - Search in distribution
Bio::Grid::Run::SGE::Index - Provides an interface to load index classes.
JWB/Bio-Grid-Run-SGE-0.066
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20 Nov 2018 22:38:51 UTC
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- Bio::Grid::Run::SGE::Index::Dummy - dummy index for testing purposes
- Bio::Grid::Run::SGE::Index::FileList - Creates an index from a list of files
- lib/Bio/Grid/Run/SGE/Index/ListFromFile.pm
- 15 more results from Bio-Grid-Run-SGE »
perlop - Perl operators and precedence
In Perl, the operator determines what operation is performed, independent of the type of the operands. For example "$x + $y" is always a numeric addition, and if $x or $y do not contain numbers, an attempt is made to convert them to numbers first. Th...
RJBS/perl-5.36.0 - 28 May 2022 00:26:10 UTC - Search in distribution- perlop - Perl operators and precedence
bioaln - Alignment manipulations based on BioPerl
bioaln performs common, routine manipulations of sequence alignments based on BioPerl modules including Bio::AlignIO, Bio::SimpleAlign and Bio::Align::Utilities. By default, bioaln assumes that both the input and the output files are in CLUSTALW form...
YZHERNAND/Bio-BPWrapper-1.15 - 27 Feb 2024 16:55:31 UTC - Search in distribution- biotree - Tree manipulations based on BioPerl
Data::Edit::Xml - Edit data held in the XML format.
Edit data held in the XML format. Version 20201031. The following sections describe the methods in each functional area of this module. For an alphabetic listing of all methods by name see Index....
PRBRENAN/Data-Edit-Xml-20201031 - 31 Oct 2020 23:42:40 UTC - Search in distribution
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
get_features.pl - A program to collect and filter annotated features from source files.
This program will extract a list of features from a database or input annotation file and write them out to a file. Features may be selected using their feature type (the 3rd column in a GFF or GTF file). When selecting features from a database, type...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC - Search in distribution- data2wig.pl - A program to convert a generic data file into a wig file.
- get_binned_data.pl - A program to collect data in bins across a list of features.
- data2bed.pl - A program to convert a data file to a bed file.
- 11 more results from Bio-ToolBox »
GD::SVG - Seamlessly enable SVG output from scripts written using GD
GD::SVG painlessly enables scripts that utilize GD to export scalable vector graphics (SVG). It accomplishes this task by wrapping SVG.pm with GD-styled method calls. To enable this functionality, one need only change the "use GD" call to "use GD::SV...
TWH/GD-SVG-0.33 - 10 May 2009 14:39:31 UTC - Search in distributionMCE::Shared - MCE extension for sharing data supporting threads and processes
This module provides data sharing capabilities for MCE supporting threads and processes. MCE::Hobo provides threads-like parallelization for running code asynchronously....
MARIOROY/MCE-Shared-1.886 - 13 Sep 2023 23:57:14 UTC - Search in distribution
Net::SSLeay - Perl bindings for OpenSSL and LibreSSL
This module provides Perl bindings for libssl (an SSL/TLS API) and libcrypto (a cryptography API)....
CHRISN/Net-SSLeay-1.94 - 08 Jan 2024 01:22:27 UTC - Search in distribution
Data::SeaBASS - Object-oriented interface for reading/writing SeaBASS files
"Data::SeaBASS" provides an easy to use, object-oriented interface for reading, writing, and modifying SeaBASS data files. What is SeaBASS? SeaWiFS <http://oceancolor.gsfc.nasa.gov> Bio-optical Archive and Storage System housed at Goddard Space Fligh...
JLEFLER/Data-SeaBASS-0.192600 - 17 Sep 2019 16:38:49 UTC - Search in distribution
tai_codon.pl - a program to calculate tAI of each codon
FORTUNE/Bio-CUA-1.04
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12 Jul 2015 19:52:07 UTC
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- Bio::CUA - Codon Usage Analyzer.
- Bio::CUA::CUB::Builder - A module to calculate codon usage bias (CUB) metrics at codon level and other parameters
- Bio::CUA::CUB::Calculator - A module to calculate codon usage bias (CUB) indice for protein-coding sequences
- 1 more result from Bio-CUA »
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::DB::GFF::Adaptor::memory - Bio::DB::GFF database adaptor for in-memory databases
- Bio::DB::GFF::Adaptor::berkeleydb - Bio::DB::GFF database adaptor for in-memory databases