NAME

get_features.pl

A program to collect and filter annotated features from source files.

SYNOPSIS

get_features.pl --in <filename> --out <filename>

get_features.pl --db <name> --out <filename>

  Source data:
  -d --db <name | filename>     database: name, file.db, or file.sqlite
  -i --in <filename>            input annotation: GFF3, GTF, genePred, etc
  
  Selection:
  -f --feature <type>           feature: gene, mRNA, transcript, etc
  -u --sub                      include subfeatures (true if gff, gtf, refFlat)
  
  Filter features:
  -l --list <filename>          file of feature IDs to keep
  -K --chrskip <regex>          skip features from certain chromosomes
  -x --exclude <tag=value>      exclude features with specific attribute value
  --biotype <regex>             include only specific biotype
  --tsl [best|best1|best2|      specify minimum transcript support level 
         best3|best4|best5|       primarily Ensembl annotation 
         1|2|3|4|5|NA]  
  --gencode                     include only GENCODE tagged genes
  
  Adjustments:
  -b --start=<integer>          modify start positions
  -e --stop=<integer>           modify stop positions
  -p --pos [ 5 | m | 3 | 53 ]   relative position from which to modify
  --collapse                    collapse subfeatures from alt transcripts
  
  Report format options:
  -B --bed                      write BED6 (no --sub) or BED12 (--sub) format
  -G --gff                      write GFF3 format
  -g --gtf                      write GTF format
  -r --refflat                  write UCSC refFlat format
  -t --tag <text>               include specific GFF attributes in text output
  --coord                       include coordinates in text output
  
  General options:
  -o --out <filename>           output file name
  --sort                        sort output by genomic coordinates
  -z --gz                       compress output
  -Z --bgz                      bgzip compress output
  -v --version                  print version and exit
  -h --help                     show full documentation

OPTIONS

The command line flags and descriptions:

Source data

--db <text>

Specify the name of a Bio::DB::SeqFeature::Store annotation database from which gene or feature annotation may be derived. A SQLite file or a named relational database may be provided. Used as an alternate to an input file.

--in <filename>

Specify the filename of a gene annotation file, including GTF, GFF3, or a UCSC-formatted file including, refFlat, genePred, or knownGene. The file may be gzip compressed. Used as an alternate to a database.

Selection

--feature <type>

Provide a feature type to collect. Typically, this corresponds to the GFF type, or 3rd column in a GFF3 or GTF file. Examples include gene, mRNA, or transcript. The default value for input files is 'gene'. For databases, an interactive list will be presented from which one or more may be chosen.

--sub

Optionally include all child subfeatures in the output. For example, transcript, CDS, and/or exon subfeatures of a gene. This option is automatically enabled with GFF, GTF, or refFlat output; it may be turned off with --nosub. With BED output, it will force a BED12 file to be written. It has no effect with standard text.

Filter features

--list <file>

Provide a file containing a list of the feature IDs to keep from the input annotation file. The file must have an ID or Primary_ID column, otherwise an index will be requested interactively from the user. Only those top features whose ID, gene_id, transcript_id, or otherwise SeqFeature primary_id exactly matches one from the list will be retained; names are not checked. Useful if you need to filter based on external criteria.

--chrskip <regex>

Exclude features from the output whose sequence ID or chromosome matches the provided regex-compatible string. Expressions should be quoted or properly escaped on the command line. Examples might be

    'chrM'
    'scaffold.+'
    'chr.+alt|chrUn.+|chr.+_random'
--exclude <tag=value>

Provide a GFF/GTF attribute tag on which to filter out the features matching the indicated value. For example, to filter on protein coding genes using gene_biotype, specify "gene_biotype=protein_coding". This filter does not descend into subfeatures. More than one exclusion tag may be specified with multiple options or a comma-delimited list.

--biotype <regex<gt>

Filter transcripts using the transcript_biotype or biotype GTF/GFF3 attribute, typically found in Ensembl annotation files. Provide a regex compatible string which must match the biotype value to keep the transcripts. For example, to keep specify "miRNA" to keep all micro-RNA transcripts. This works on a subfeature level as well, so that gene may be specified as the feature to collect, and only the gene transcripts belonging to the indicating biotype are retained.

--tsl <level>

Filter transcripts on the Ensembl GTF/GFF3 attribute transcript_support_level, which is described at Ensembl TSL glossary entry. Provide a level of support to filter. Values include:

    1       All splice junctions supported by evidence
    2       Transcript flagged as suspect or only support from multiple ESTs
    3       Only support from single EST
    4       Best supporting EST is suspect
    5       No support
    best    Transcripts at the best (lowest) available level are taken
    best1   The word followed by a digit 1-5, indicating any transcript 
            at or better (lower) than the indicated level
    NA      Only transcripts without a level (NA) are retained.
--gencode

Boolean option to filter transcripts as part of the GENCODE specification. These are marked in Ensembl GTF/GFF3 annotation files as the tag attribute with value "basic". Typically, at least one transcript for every gene is marked as part of the GENCODE set. Transcripts not marked as such usually lack sufficient experimental evidence.

Adjustments

--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 (towards the 5 prime end), and a positive value is shifted downstream (towards the 3 prime end). Adjustments are made relative to the indicated position (--pos option, below) based on the feature strand. Adjustments are only allowed when writing standard BED6 or standard text files.

--pos [ 5 | m | 3 | 53 ]

Indicate the relative position from which both coordinate adjustments are made. Both start and stop adjustments may be made from the respective 5 prime, 3 prime, or middle position as dictated by the feature's strand value. Alternatively, specify '53' to indicate that the start adjustment adjusts the 5 prime end and the stop adjustment adjusts the 3 prime end. The default is '53'.

--collapse

Boolean option to collapse multiple alternate transcripts of a gene into a single artificial transcript, merging overlapping exons and minimizing introns, where appropriate. Genes without alternate transcripts are not collapsed.

Report format options

--bed

With subfeatures enabled, write a BED12 (12-column BED) file. Otherwise, write a standard 6-column BED format file.

--gff

Write a GFF version 3 (GFF3) format output file. Subfeatures are automatically included and coordinate adjustments ignored.

--gtf

Write a GTF format (GFF version 2.2 or 2.5) output file. Subfeatures are automatically included and coordinate adjustments ignored.

--refflat
--ucsc

Write a UCSC-style refFlat format (10 columns) gene annotation table. Subfeatures are automatically included and coordinate adjustments ignored.

--tag <text>

When writing a standard text file, optionally include additional GFF/GTF attribute tags. Specify as a comma-delimited list or as separate options.

--coord

When writing a standard text file, optionally include the chromosome, start, stop, and strand coordinates. These are automatically included in other formats. This is automatically included when adjusting coordinate positions.

General options

--out <filename>

Specify the output file name. Default is the joined list of features.

--sort

Sort the output file by genomic coordinates. Automatically enabled when compressing with bgzip. This may require more memory.

--gz

Specify whether the output file should be compressed with gzip.

--bgz

Specify whether the output file should be compressed with block gzip (bgzip) for tabix compatibility.

--version

Print the version number.

--help

Display this POD documentation.

DESCRIPTION

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, types may be selected interactively from a presented list. Features may be filtered based on various GFF attributes typically found in Ensembl annotation, including transcript_biotype, transcript_support_level, and GENCODE basic tags. Features may also be filtered by chromosome.

Collected features may be written to a variety of formats, including GFF3, GTF, refFlat, simple 6-column BED, or a simple text format. With GFF, GTF, and refFlat formats, subfeatures such as exons are automatically included (which may also be turned off). With a simple text format, the source database or parsed input file are recorded in the header metadata for use in subsequent programs. Coordinates may be optionally included in the text file, which preempts using parsed features in other tools.

Coordinate adjustments

Coordinates of the features may be adjusted as desired when writing to text or BED file formats. Adjustments may be made relative to either the 5 prime, 3 prime, both ends, or the feature midpoint. Positions are based on the feature strand. Use the following examples as a guide.

upstream 500 bp only
  get_features.pl --start=-500 --stop=-1 --pos 5
1 kb total around 5 prime end
  get_features.pl --start=-500 --stop=500 --pos 5
last 500 bp of feature
  get_features.pl --start=-500 --pos 3
middle 500 bp of feature
  get_features.pl --start=-250 --stop=250 --pos m
entire feature plus 1 kb of flanking
  get_features.pl --start=-1000 --stop=1000 --pos 53

Note that positions are always in base coordinates, and the resulting regions may be 1 bp longer depending on whether the reference base was included or not.

AUTHOR

 Timothy J. Parnell, PhD
 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.