NAME

get_gene_regions.pl

A script to collect specific, often un-annotated regions from genes.

SYNOPSIS

get_gene_regions.pl [--options...] --db <text> --out <filename>

get_gene_regions.pl [--options...] --in <filename> --out <filename>

Options:
--db <text>
--in <filename>  (gff,gtf,gff3,refFlat,genePred,knownGene)
--out <filename> 
--feature <type | type:source>
--transcript [all|mRNA|ncRNA|snRNA|snoRNA|tRNA|rRNA|miRNA|lincRNA|misc_RNA]
--region [tss|tts|exon|altExon|commonExon|firstExon|lastExon|
          intron|firstIntron|lastIntron|splice]
--start=<integer>
--stop=<integer>
--unique
--slop <integer>
--mix
--bed
--gz
--version
--help

OPTIONS

The command line flags and descriptions:

--db <text>

Specify the name of a Bio::DB::SeqFeature::Store annotation database from which gene or feature annotation may be derived. A database is required for generating new data files with features. For more information about using annotation databases, see https://code.google.com/p/biotoolbox/wiki/WorkingWithDatabases. Also see --in as an alternative.

--in <filename>

Alternative to a database, a gene table or annotation file may be provided. A GTF, GFF, GFF3, or UCSC gene table, including refFlat, genePred (gene prediction), or known gene table may be provided. Files may be gzipped.

--out <filename>

Specify the output filename.

--feature <type | type:source>

Specify the parental gene feature type (primary_tag) or type:source when using a database. If not specified, a list of available types will be presented interactively to the user for selection. This is not relevant for GFF3 source files (all gene or transcript features are considered). This is helpful when gene annotation from multiple sources are present in the same database, e.g. refSeq and ensembl sources. More than one feature may be included, either as a comma-delimited list or multiple options.

--transcript [all|mRNA|ncRNA|snRNA|snoRNA|tRNA|rRNA|miRNA|lincRNA|misc_RNA]

Specify the transcript type (usually a gene subfeature) from which to collect the regions. Multiple types may be specified as a comma-delimited list, or 'all' may be specified. If not specified, an interactive list will be presented from which the user may select.

--region <region>

Specify the type of region to retrieve. If not specified on the command line, the list is presented interactively to the user for selection. Ten possibilities are possible.

tss         The first base of transcription
tts         The last base of transcription
exon        The exons of each transcript
firstExon   The first exon of each transcript
lastExon    The last exon of each transcript
altExon     All alternate exons from multiple transcripts for each gene
commonExon  All common exons between multiple transcripts for each gene
intron      Each intron (usually not defined in the GFF3)
firstIntron The first intron of each transcript
lastIntron  The last intron of each transcript
splice      The first and last base of each intron

--start=<integer>

--stop=<integer>

Optionally specify adjustment values to adjust the reported start and end coordinates of the collected regions. A negative value is shifted upstream (5' direction), and a positive value is shifted downstream. Adjustments are made relative to the feature's strand, such that a start adjustment will always modify the feature's 5'end, either the feature startpoint or endpoint, depending on its orientation.

--unique

For gene features only, take only the unique regions. Useful when multiple alternative transcripts are defined for a single gene.

--slop <integer>

When identifying unique regions, specify the number of bp to add and subtract to the start position (the slop or fudge factor) of the regions when considering duplicates. Any other region within this window will be considered a duplicate. Useful, for example, when start sites of transcription are not precisely mapped, but not useful with defined introns and exons. This does not take into consideration transcripts from other genes, only the current gene. The default is 0 (no sloppiness).

--mix

Allow two or more different transcript types from genes to be used. Some genes may generate more than one transcript type, for example mRNA and certain non-coding RNAs. By default, only one type of RNA transcript type is accepted. This is usually mRNA, if requested.

--bed

Automatically convert the output file to a BED file.

--gz

Specify whether (or not) the output file should be compressed with gzip.

--version

Print the version number.

--help

Display this POD documentation.

DESCRIPTION

This program will collect specific regions from annotated genes and/or transcripts. Often these regions are not explicitly defined in the source GFF3 annotation, necessitating a script to pull them out. These regions include the start and stop sites of transcription, introns, the splice sites (both 5' and 3'), exons, the first (5') or last (3') exons, or all alternate or common exons of genes with multiple transcripts. Importantly, unique regions may only be reported, especially important when a single gene may have multiple alternative transcripts. A slop factor is included for imprecise annotation.

The program will report the chromosome, start and stop coordinates, strand, name, and parent and transcript names for each region identified. The reported start and stop sites may be adjusted with modifiers. A standard biotoolbox data formatted text file is generated. This may be converted into a standard BED or GFF file using the appropriate biotoolbox scripts. The file may also be used directly in data collection.

AUTHOR

Timothy J. Parnell, PhD
Howard Hughes Medical Institute
Dept of Oncological Sciences
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.