Search results for "dist:BioPerl Bio::SeqIO::embl"
Bio::SeqIO::embl - EMBL sequence input/output stream
This object can transform Bio::Seq objects to and from EMBL flat file databases. There is a lot of flexibility here about how to dump things which should be documented more fully. There should be a common object that this and Genbank share (probably ...
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::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::SeqIO::embldriver - EMBL sequence input/output stream
This object can transform Bio::Seq objects to and from EMBL flat file databases. There is a lot of flexibility here about how to dump things which should be documented more fully. There should be a common object that this and Genbank share (probably ...
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::Tools::EPCR - Parse ePCR output and make features
This object serves as a parser for ePCR data, creating a Bio::SeqFeatureI for each ePCR hit. These can be processed or added as annotation to an existing Bio::SeqI object for the purposes of automated annotation....
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::PrimarySeq - Bioperl lightweight sequence object
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::Tools::isPcr - Parse isPcr output and make features
This object serves as a parser for isPcr data (in the default fasta format), creating a Bio::SeqFeatureI for each isPcr hit. These can be processed or added as annotation to an existing Bio::SeqI object for the purposes of automated annotation. This ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::bsml - BSML sequence input/output stream
This object can transform Bio::Seq objects to and from BSML (XML) flatfiles....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::HandlerBaseI - Interface class for handler methods which interact with any event-driven parsers (drivers).
This interface describes simple class methods used for processing data from an event-based parser (a driver). This is similar in theme to an XML SAX-based driver but differs in that one can optionally pass related data semi-intelligently as chunks (d...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::ipcress - Parse ipcress output and make features
This object serves as a parser for ipcress data, creating a Bio::SeqFeatureI for each ipcress hit. These can be processed or added as annotation to an existing Bio::SeqI object for the purposes of automated annotation. This module is adapted from the...
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::Seq::SequenceTrace - Bioperl object packaging a sequence with its trace
This object stores a sequence with its trace....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::Generic - Generic SeqFeature
Bio::SeqFeature::Generic is a generic implementation for the Bio::SeqFeatureI interface, providing a simple object to provide all the information for a feature on a sequence. For many Features, this is all you will need to use (for example, this is f...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AnnotationCollectionI - Interface for annotation collections
Annotation Collections are a way of storing a series of "interesting facts" about something. We call an "interesting fact" in Bioperl an Annotation (this differs from a Sequence Feature, which is called a Sequence Feature and may or may not have an A...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::GuessSeqFormat - Module for determining the sequence format of the contents of a file, a string, or through a filehandle.
Bio::Tools::GuessSeqFormat tries to guess the format ("swiss", "pir", "fasta" etc.) of the sequence or MSA in a file, in a scalar, or through a filehandle. The guess() method of a Bio::Tools::GuessSeqFormat object will examine the data, line by line,...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::Flat::BinarySearch - BinarySearch search indexing system for sequence files
This module can be used both to index sequence files and also to retrieve sequences from existing sequence files. This object allows indexing of sequence files both by a primary key (say accession) and multiple secondary keys (say ids). This is diffe...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Factory::SequenceProcessorI - Interface for chained sequence processing algorithms
This defines an interface that allows seamless chaining of sequence processing algorithms encapsulated in modules while retaining the overall Bio::SeqIO interface at the end of the pipeline. This is especially useful if you want an easily configurabl...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC