Search results for "dist:BioPerl genbank"
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::SeqIO::genbank - GenBank sequence input/output stream
This object can transform Bio::Seq objects to and from GenBank flat file databases. There is some flexibility here about how to write GenBank output that is not fully documented. Optional functions _show_dna() (output only) shows the dna or not _post...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::Flat::BDB::genbank - genbank adaptor for Open-bio standard BDB-indexed flat file
This module allows genbank 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
bp_genbank2gff3.pl - Genbank-gtgbrowse-friendly GFF3
This script uses Bio::SeqFeature::Tools::Unflattener and Bio::Tools::GFF to convert GenBank flatfiles to GFF3 with gene containment hierarchies mapped for optimal display in gbrowse. The input files are assumed to be gzipped GenBank flatfiles for ref...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::gbxml - GenBank sequence input/output stream using SAX
This object can transform Bio::Seq objects to and from GenBank XML flatfiles....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::gbdriver - GenBank handler-based push parser
This object can transform Bio::Seq objects to and from GenBank flat file databases. The key difference between this parser and the tried-and-true Bio::SeqIO::genbank parser is this version separates the parsing and data manipulation into a 'driver' m...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::FTHelper - Helper class for EMBL/Genbank feature tables
Represents one particular Feature with the following fields key - the key of the feature loc - the location string of the feature <other fields> - other fields...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq - Sequence object, with features
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::SeqIO - Handler for SeqIO Formats
Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use. The Bio::SeqIO system can be thought of like biological file ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Taxon - A node in a represented taxonomy
This is the next generation (for Bioperl) of representing Taxonomy information. Previously all information was managed by a single object called Bio::Species. This new implementation allows representation of the intermediate nodes not just the specie...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Species - Generic species object.
NOTE: This class is planned for deprecation in favor of the simpler Bio::Taxon. Please use that class instead. Provides a very simple object for storing phylogenetic information. The classification is stored in an array, which is a list of nodes in a...
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
bp_dbsplit - script to split an input set of database(s) into smaller pieces
This script will take as input a list of filenames or a single file or from STDIN a sequence database and split the database into separate files of X numbers of sequences. You specify X with the "--size/-s" parameter. The input and output sequence fo...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Root::IO - BioPerl base IO handling class
This module provides methods that will usually be needed for any sort of file- or stream-related input/output, e.g., keeping track of a file handle, transient printing and reading from the file handle, a close method, automatically closing the handle...
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::LocationI - Abstract interface of a Location on a Sequence
This Interface defines the methods for a Bio::LocationI, an object which encapsulates a location on a biological sequence. Locations need not be attached to actual sequences as they are stand alone objects. LocationI objects are used by Bio::SeqFeatu...
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
Bio::DB::QueryI - Object Interface to queryable sequence databases
This interface provides facilities for managing sequence queries such as those offered by Entrez. A query object is created by calling new() with a database-specific argument list. From the query object you can either obtain the list of IDs returned ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_search2gff - turn a SearchIO report into GFF
This script will turn a SearchIO report (BLAST, FASTP, SSEARCH, AXT, WABA) into GFF. The options are: -i infilename - (optional) inputfilename, will read either ARGV files or from STDIN -o filename - the output filename [default STDOUT] -f format - s...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC