Bio::ToolBox - get_feature_info

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get_feature_info.pl

A program to collect feature information from a BioPerl SeqFeature::Store db.

SYNOPSIS

get_feature_info.pl <filename>

File options:
-i --in <filename>                        input file of list db features
-o --out <filename>                       optional output file

Database options:
-d --db <name>                            annotation database: mysql sqlite
                                            or annotation file: gtf gff ucsc
-a --attrib <attribute1,attribute2,...>   list of attributes to collect
-t --type <primary_tag>                   specify a feature type as needed

General options:
-z --gz                                   compress output file
-v --version                              print version and exit
-h --help                                 show extended documentation

Attributes include:
 Chromosome
 Start
 Stop
 Strand
 Score
 Name
 Alias
 Note
 Type
 Primary_tag
 Source
 Length
 Midpoint
 Phase
 RNA_count (number of transcript subfeatures)
 Exon_count (number of exon subfeatures)
 Gene_length (sum of all merged, collapsed, transcript exon lengths)
 Transcript_length (sum of exon lengths)
 Parent (name)
 Primary_ID
 <tag>

OPTIONS

The command line flags and descriptions:

File options

• –in <filename>

  Specify an input file containing either a list of database features or genomic coordinates for which to collect data. The file should be a tab-delimited text file, one row per feature, with columns representing feature identifiers, attributes, coordinates, and/or data values. The first row should be column headers. Text files generated by other BioToolBox scripts are acceptable. Files may be gzipped compressed.

• –out <filename>

  Optionally specify an alternate output file name. The default is to overwrite the input file.

Database options

• –db <name>

  Specify the name or SQLite file of a Bio::DB::SeqFeature::Store annotation database from which the information may be derived. This may be stored in the metadata comments of the input file, or an alternative file may be provided.

  Alternatively, specify an annotation file, e.g. GTF, GFF3, or UCSC gene table, that may be parsed into memory.

  The input file should include Name or ID columns that match features in the provided database. If a Type column is not present, then a type should be provided with the --type option. Note that mixing and matching files and
  databases may not always work as well as intended.

• –attrib <attribute>

  Specify the attribute to collect for each feature. Standard GFF attributes may be collected, as well as values from specific group tags. These tags are found in the group (ninth) column of the source GFF file. Standard attributes include the following

  • Chromosome
  • Start
  • Stop
  • Strand
  • Score
  • Name
  • Alias
  • Note
  • Type
  • Primary_tag
  • Source
  • Length
  • Midpoint
  • Phase
  • RNA_count (number of transcript subfeatures)
  • Exon_count (number of exon subfeatures)
  • Gene_length (sum of all merged, collapsed, transcript exon lengths)
  • Transcript_length (sum of exon lengths)
  • Parent (name)
  • Primary_ID
  • <tag>

  If attrib is not specified on the command line, then an interactive list will be presented to the user for selection. Especially useful when you can’t remember the feature’s tag keys in the database.

• –type <primary_tag>

  When the input file does not have a type column, a type or primary_tag may be provided. This is especially useful to restrict the database search when there are multiple features with the same name.

General options

• –gz

  Indicate whether the output file should (not) be compressed by gzip. If compressed, the extension ‘.gz’ is appended to the filename. If a compressed file is opened, the compression status is preserved unless specified otherwise.

• –version

  Print the version number.

• –help

  Display this help.

DESCRIPTION

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 source GFF file.

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.