Search results for "dist:BioPerl LOCATION"
Bio::Location::Fuzzy - Implementation of a Location on a Sequence which has unclear start and/or end locations
This module contains the necessary methods for representing a Fuzzy Location, one that does not have clear start and/or end points. This will initially serve to handle features from Genbank/EMBL feature tables that are written as 1^100 meaning betwee...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Location::Split - Implementation of a Location on a Sequence which has multiple locations (start/end points)
This implementation handles locations which span more than one start/end location, or and/or lie on different sequences, and can work with split locations that depend on the specific order of the sublocations ('join') or don't have a specific order b...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence
This is an implementation of Bio::LocationI to manage simple location information on a Sequence....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Location::Simple - Implementation of a Simple Location on a Sequence
This is an implementation of Bio::LocationI to manage exact location information on a Sequence: '22' or '12..15' or '16^17'. You can test the type of the location using length() function () or directly location_type() which can one of two values: 'EX...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence which has unclear start/end location
This interface encapsulates the necessary methods for representing a Fuzzy Location, one that does not have clear start and/or end points. This will initially serve to handle features from Genbank/EMBL feature tables that are written as 1^100 meaning...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
This interface encapsulates the necessary methods for representing the location of a sequence feature that has more that just a single start/end pair. Some examples of this are the annotated exons in a gene or the annotated CDS in a sequence file....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
Objects implementing this interface are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. While this may seem trivial for simple locations, there are different ways to do it for fuzzy or compound (...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Location::WidestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range
CoordinatePolicyI implementing objects are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. This class will compute the coordinates such that always the widest possible range is returned, but by u...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Location::AvWithinCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
CoordinatePolicyI implementing objects are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. This class will compute the coordinates such that for fuzzy locations of type WITHIN and BETWEEN the ave...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Location::NarrowestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
CoordinatePolicyI implementing objects are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. This class will compute the coordinates such that always the narrowest possible range is returned, but b...
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::LocationI - A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects
This is a pure interface class - in other words, all this does is define methods which other (concrete) classes will actually implement. The Bio::DB::LocationI class defines methods used to retrieve location data from a sequence. This is returned in ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Factory::LocationFactoryI - A factory interface for generating locations from a string
An interface for Location Factories which generate Bio::LocationI objects from a string....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Factory::FTLocationFactory - A FeatureTable Location Parser
Implementation of string-encoded location parsing for the Genbank feature table encoding of locations....
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::SeqUtils - Additional methods for PrimarySeq objects
This class is a holder of methods that work on Bio::PrimarySeqI- compliant sequence objects, e.g. Bio::PrimarySeq and Bio::Seq. These methods are not part of the Bio::PrimarySeqI interface and should in general not be essential to the primary functio...
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
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
Bio::Tools::Seg - parse seg output
"seg" identifies low-complexity regions on a protein sequence. It is usually part of the "WU-BLAST" and "InterProScan" packages. The Bio::Tools::Seg module will only parse the "fasta" output modes of "seg", i.e. "seg -l" (low complexity regions only)...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC