SYNOPSIS

gff2das --man | --help | --verbose | --version

gff2das --preferred_group g1,g2...gn --gffversion N features.gff > features.das

gff2das --groupclass MyGroup --gffversion 1 v1features.gff > v1features.das

Translate GFF lines to 'DAS [annotations]' format such as are used by DAS/Genboree. Adheres to required interpretation of GFF per documentation in Bio::DB::GFF.

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OPTIONS

Options are specified on the command line. Their case is ignored, and they may be abbreviated to uniqueness (i.e. --h instead of --help).

--gffversion N: Is only used to indicate how to parse attribute value pairs in column 9.; Version 3 expects an '=' between attribute and value.; It is overridden by any '##gff-version' line appearing in the input as allowed by GFF spec.
--preferred_group: controls which attribute in column 9 to promote to the DAS group name and class in column 1 and 2. It is overridden by any '##group-tags' line in the GFF input (c.f. GFF spec). They default to 'Sequence' and 'Transcript' since, per Bio::DB::GFF: 'For backward compatibility, the tags Sequence and Transcript are always treated as grouping tags unless preferred_tags are specified.'; Also, pre Bio::DB::GFF spec: '``Target'' tag is always used for grouping regardless of the preferred_groups() setting'... and it is expected to be followed by either a target name (placed in output column 2 as group name if present) and 2 match location values, or just the match location values, which in either case are placed in DAS tstart and tend columns.
--groupclass: only valid with gffversion = 1 where column 9 holds a single value, namely, a 'group'. This option specifies the common group class, which defaults to '.'.
--help: Display command line usage with options.
--man: Display complete manual page and exit.
--verbose: Provides a trace of processing on STDERR.
--version: Display the scripts version number and exit.

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DESCRIPTION

translate GFF lines to 'DAS [annotation]' format such as are used by DAS/Genboree. Handle group semantics in accordance with GFF documentation in Bio::DB::GFF

GFF validation is very loose - if it has 9 columns it is treated as GFF and parsed.

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EXAMPLES

gff2das --man: print a manpage
gff2das --preferred_group 'TFBS,TF' --gffversion 3 gff2das.test.gff: when TFBS or TF appear as attribute name in column 9 of the GFF, promote it to the GFF class (favoring TFBS if both are present).

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VERSION

$Revision: 0.01$

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AUTHOR

Malcolm Cook (mec@stowers-institute.org)

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DEPENDENCIES

perl

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AVAILABILITY

http://research.stowers-institute.org/mec/software/scripts/gff2das

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TO DO

handle escaping and quoting in column 9.

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gff2das