Search results for "distribution:Bio-ToolBox Bio::Annotation::Reference"
Bio::ToolBox::Data - Reading, writing, and manipulating data structure
This module works with the primary Bio::ToolBox Data structure. Simply, it is a complex data structure representing a tabbed-delimited table (array of arrays), with plenty of options for metadata. Many common bioinformatic file formats are simply tab...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
Bio::ToolBox::db_helper - helper interface to various database formats
In most cases, this module does not need to be used directly. The methods available to Bio::ToolBox::Data and Bio::ToolBox::Data::Feature provide convenient access to the methods described here. These are helper subroutines to work with relevant data...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
Bio::ToolBox::GeneTools - SeqFeature agnostic methods for working with gene models
This module provides numerous exportable functions for working with gene SeqFeature models. This assumes that the gene models follow the BioPerl Bio::SeqFeatureI convention with nested SeqFeature objects representing the gene, transcript, and exons. ...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
Bio::ToolBox::parser::gff - parse GFF3, GTF, and GFF files
This module parses a GFF file into SeqFeature objects. It natively handles GFF3, GTF, and general GFF files. For both GFF3 and GTF files, fully nested gene models, typically gene => transcript => (exon, CDS, etc), may be built using the appropriate a...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
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
Bio::ToolBox::Data::Stream - Read, Write, and Manipulate Data File Line by Line
This module works similarly to the Bio::ToolBox::Data object, except that rows are read from a file handle rather than a memory structure. This allows very large files to be read, manipulated, and even written without slurping the entire contents int...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
Bio::ToolBox::Data::Feature - Objects representing rows in a data table
A Bio::ToolBox::Data::Feature is an object representing a row in the data table. Usually, this in turn represents an annotated feature or segment in the genome. As such, this object provides convenient methods for accessing and manipulating the value...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
get_relative_data.pl - A program to collect data in bins around a relative position.
This program will collect data around a relative coordinate of a genomic feature or region. The data is collected in a series of windows flanking the feature start (5' position for stranded features), end (3' position), or the midpoint position. The ...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
correlate_position_data.pl - A script to calculate correlations between two datasets along the length of a feature.
This program will calculate statistics between the positioned scores of two different datasets over a window from an annotated feature or chromosomal segment. These statistics will help determine whether the positions or distribution of scores across...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
get_intersecting_features.pl - A program to pull out overlapping features from the database.
This program will take a list of reference features and identify target features which intersect them. The reference features may be either named features (name and type) or genomic regions (chromosome, start, stop). By default, the search region for...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC