Bio::ToolBox - data2gff

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data2gff.pl

A program to convert a generic data file to GFF format.

SYNOPSIS

data2gff.pl [–options…] <filename>

File options:
-i --in <filename>                    input file: txt
-o --out <filename>                   output file name
-H --noheader                         input file has no header row
-0 --zero                             file is in 0-based coordinate system

Column indices:
-a --ask                              interactive selection of columns
-c --chr <index>                      chromosome column
-b --begin --start <index>            start coordinate column
-e --end --stop <index>               stop coordinate column
-s --score <index>                    score column
-t --strand <index>                   strand column
-n --name <text | index>              name column or base name text
-d --id <index>                       primary ID column
-g --tags <index,index,...>           zero or more columns for tag attributes
-r --source <text | index>            source column or text
-y --type <text | index>              type column or text

General options:
--unique                              make IDs unique
--sort                                sort output by genomic coordinates
-z --gz                               compress output file
-Z --bgz                              bgzip compress output file
-v --version                          print version and exit
-h --help                             show extended documentation

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 convert to GFF format. The file should be a tab-delimited text file, one row per feature, with columns representing feature identifiers, attributes, coordinates, and/or data values. Files may be gzipped compressed.

• –out <filename>

  Optionally specify the name of of the output file. The default is to use the input file base name. The ‘.gff’ extension is automatically added if required.

• –noheader

  The input file does not have column headers, often found with UCSC derived annotation data tables.

• –zero

  Input file is in interbase or 0-based coordinates. This should be automatically detected for most known file formats, e.g. BED.

Column indices

• –ask

  Indicate that the program should interactively ask for column indices or text strings for the GFF attributes, including coordinates, source, type, etc. It will present a list of the column names to choose from. Enter nothing for non-relevant columns or to accept default values.

• –chr <column_index>

  The index of the dataset in the data table to be used as the chromosome or sequence ID column in the gff data.

• –start <column_index>

• –begin <column_index>

  The index of the dataset in the data table to be used as the start position column in the gff data.

• –stop <column_index>

• –end <column_index>

  The index of the dataset in the data table to be used as the stop or end position column in the gff data.

• –score <column_index>

  The index of the dataset in the data table to be used as the score column in the gff data.

• –strand <column_index>

  The index of the dataset in the data table to be used for strand information. Accepted values might include any of the following “+, -, 1, -1, 0, .”.

• –name <text

  column_index>

  Enter either the text that will be shared name among all the features, or the index of the dataset in the data table to be used as the name of each gff feature. This information will be used in the ‘group’ column.

• –id <column_index>

  The index of the dataset in the data table to be used as the unique ID of each gff feature. This information will be used in the ‘group’ column of GFF v3 files only. The default is to automatically generate a unique identifier.

• –tags <column_indices>

  Provide a comma delimited list of column indices that contain values to be included as group tags in the GFF features. The key will be the column name.

• –source <text

  column_index>

  Enter either a text string or a column index representing the GFF source that should be used for the features. The default is ‘data’.

• –type <text

  column_index>

  Enter either a text string or a column index representing the GFF ‘type’ or ‘method’ that should be used for the features. If not defined, it will use the column name for either the ‘score’ or ‘name’ column, if defined. As a last resort, it will use the most creative method of ‘Experiment’.

General options

• –unique

  Indicate whether the feature names should be made unique. A count number is appended to the name of subsequent features to make them unique. Using a base text string for the name will automatically generate unique names.

• –sort

  Sort the output file by genomic coordinates. Automatically enabled when compressing with bgzip.

• –gz

  Indicate 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 the POD documentation

DESCRIPTION

This program will convert a data file into a GFF version 3 formatted text file. Only simple conversions are performed, where each data line is converted to a single feature. Complex features with parent-child relationships (such as genes) should be converted with something more advanced.

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.