Search results for "distribution:BioPerl Bio::Index"
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
Bio::Index::Qual - Interface for indexing (multiple) fasta qual files
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::Index::Fasta - Interface for indexing (multiple) fasta files
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::Index::Fastq - Interface for indexing (multiple) fastq files
Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionality for indexing fastq files, and retrieving the sequence from them. Note: for best results 'use strict'. Bio::Index::Fastq supports the Bio::DB::...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Index::Blast - Indexes Blast reports and supports retrieval based on query accession(s)
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
Bio::Index::GenBank - Interface for indexing one or more GenBank files (i.e. flat file GenBank format).
By default the index that is created uses the LOCUS, ACCESSION, and VERSION identifiers as keys. Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic functionality for indexing GenBank files, and retrieving t...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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
Bio::Index::Swissprot - Interface for indexing one or more Swissprot files.
By default the index that is created uses the AC and ID identifiers as keys. This module inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic functionality for indexing Swissprot files and retrieving Sequence...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Index::SwissPfam - Interface for indexing swisspfam files
SwissPfam is one of the flat files released with Pfam. This modules provides a way of indexing this module. Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionality for indexing SwissPfam files. Only...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Index::BlastTable - Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)
This object allows one to build an index on a tabular 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_inde...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Index::AbstractSeq - base class for AbstractSeq
Provides a common base class for multiple sequence files built using the Bio::Index::Abstract system, and provides a Bio::DB::SeqI interface....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_index.pl - indexes files for use by bp_fetch.pl
bp_index.pl builds a bioperl index for the sequence files given in the argument list, under the index name. For example bp_index.pl nrdb /data/nrdb/nrdb.fasta would build an index called 'nrdb' as the index name for the file nrdb.fasta, and bp_index....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_bioflat_index.pl - index sequence files using Bio::DB::Flat
Create or update a biological sequence database indexed with the Bio::DB::Flat indexing scheme. The arguments are a list of flat files containing the sequence information to be indexed....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::Flat - Interface for indexed flat files
This object provides the basic mechanism to associate positions in files with primary and secondary name spaces. Unlike Bio::Index::Abstract (see Bio::Index::Abstract), this is specialized to work with the "flat index" and BerkeleyDB indexed flat fil...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::Qual - Fast indexed access to quality files
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::Fasta - Fast indexed access to fasta files
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
bp_fetch.pl - fetches sequences from bioperl indexed databases
Fetches sequences using the DB access systems in Bioperl. The most common use of this is to bp_fetch sequences from bioperl indices built using bpindex.pl, or to fetch sequences from the NCBI website The format for retrieving sequences is delibrately...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::GFF::Util::Binning - binning utility for Bio::DB::GFF index
This is a utility module that exports the functions bin(), bin_bot() and bin_top(). These functions translate a range on the genome into a named bin that is used as an index in the Bio::DB::GFF schema. The index makes certain range retrieval queries ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_taxonomy2tree - Building a taxonomic tree based on the full lineages of a set of species names
This scripts looks up the provided species names in the NCBI Taxonomy database, retrieves their full lineage and puts them in a Newick taxonomic tree displayed on screen. bp_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s Human bp_taxonomy2...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::table - sequence input/output stream from a delimited table
This class transforms records in a table-formatted text file into Bio::Seq objects. A table-formatted text file of sequence records for the purposes of this module is defined as a text file with each row corresponding to a sequence, and the attribute...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC