Search results for "dist:Bio-ToolBox Bio::SeqFeature"
Bio::ToolBox::SeqFeature - Fast, simple SeqFeature implementation
SeqFeature objects represent functional elements on a genomic or chromosomal sequence, such as genes, transcripts, exons, etc. In many cases, especially genes, they have a hierarchical structure, typically in this order gene mRNA or transcript exon C...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
Bio::ToolBox - Tools for querying and analysis of genomic data
The Bio::ToolBox libraries provide a useful interface for working with bioinformatic data. Many bioinformatic data analysis revolves around working with tables of information, including lists of genomic annotation (genes, promoters, etc.) or defined ...
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::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
db_setup.pl - A program to setup a SeqFeature::Store SQLite database from UCSC data
This program will simplify the task of generating an annotation database. You provide the short name of the UCSC database for the species and genome version you are interested in, and the script will automatically download gene annotation and build a...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
Bio::ToolBox::parser::bed - Parser for BED-style formats
This is a parser for converting BED-style and related formats into SeqFeature objects. File formats include the following. Bed Bed <http://genome.ucsc.edu/FAQ/FAQformat.html#format1> files may have 3-12 columns, where the first 3-6 columns are basic ...
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
Bio::ToolBox::Data::core - Common functions to Bio:ToolBox::Data family
Common methods for metadata and manipulation in a Bio::ToolBox::Data data table and Bio::ToolBox::Data::Stream file stream. This module should not be used directly. See the respective modules for more information....
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
db_types.pl - A program to print out the available feature types in a database.
This program will print a list of all of the known feature types present in a Bio::DB::SeqFeature::Store database. The types are organized into groups by their source tag. BigWigSet databases, comprised of a directory of BigWig files and a metadata f...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
data2bed.pl - A program to convert a data file to a bed file.
This program will convert a tab-delimited data file into a BED file, according to the specifications here <http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED>. A minimum of three and a maximum of six columns may be generated. Thin and thick ...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
data2wig.pl - A program to convert a generic data file into a wig file.
This program will convert any tab-delimited data text file into a wiggle formatted text file. This requires that the file contains not only the scores bu also chromosomal coordinates, i.e. chromosome, start, and (optionally) stop. The program should ...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
data2fasta.pl - A program to retrieve sequences from a list of features
This program will take a tab-delimited text file (BED file, for example) and generate either a multi-sequence fasta file containing the sequences of each feature defined in the input file, or optionally a single concatenated fasta file. If concatenat...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
Bio::ToolBox::parser::ucsc - Parser for UCSC genePred, refFlat, etc formats
This is a parser for converting UCSC-style gene prediction flat file formats into BioPerl-style Bio::SeqFeatureI compliant objects, complete with nested objects representing transcripts, exons, CDS, UTRs, start- and stop-codons. Full control is avail...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
get_datasets.pl - A program to collect data for a list of features
This program will collect dataset values from a variety of sources, including features in a BioPerl Bio::DB::SeqFeature::Store database, binary wig files .wib loaded in a database using Bio::Graphics::Wiggle, bigWig files, bigBed files, Bam alignment...
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_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
get_feature_info.pl - A program to collect feature information from a BioPerl SeqFeature::Store db.
This program will collect attributes for a list of features from the database. The attributes may be general attributes, such as chromsome, start, stop, strand, etc., or feature specific attributes stored in the original group field of the original s...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
Bio::ToolBox::db_helper::big
This module provides support for binary BigWig and BigBed files to the Bio::ToolBox package. It also provides minimal support for a directory of one or more bigWig files as a combined database, known as a BigWigSet....
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
get_binned_data.pl - A program to collect data in bins across a list of features.
This program will collect data across a gene or feature body into numerous percentile bins. It is used to determine if there is a spatial distribution preference for the dataset over gene bodies. The number of bins may be specified as a command argum...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC