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PROGRAM:

NAME

gtf2gff3 - Converts GTF formatted files to valid GFF3 files

VERSION

This document describes version 0.1

SYNOPSIS

gtf2gff3 --cfg gtf2gff3_MY_CONFIG.cfg gtf_file > gff3_file

DESCRIPTION

This script will convert GTF formatted files to valid GFF3 formatted files. It will map
the value in column 3 (\"type\" column) to valid SO, but because many non standard term
may appear in that column in GTF files, you may edit the config file to provide your own
GTF feature to SO mapping. The script will also build gene models from exons, CDSs and
other features given in the GTF file. It is currently tested on Ensemble and Twinscan
GTF, and it should work on any other files that follow the same specification. It does
not work on GTF from the UCSC table browser because those files use the same ID for gene
and transcript, so it is impossible to group multiple transcripts to a gene. See the
README that came with the script for more info.

OPTIONS:

--cfg
Provide the filename for a config file. See the configuration file provided with this
script for format details. Use this configuration file to modify the behavior of the
script. If no config file is given it looks for ./gtf2gff3.cfg, ~/gtf2gff3.cfg or
/etc/gtf2gff3.cfg in that order.

--help
Provide a detailed man page style help message and then exit.

DIAGNOSTICS

"ERROR: Missing or non-standard attributes: parse_attributes"
A line in the GTF file did not have any attributes, or it's attributes column was
unparsable.

"ERROR: Non-transcript gene feature not supported. Please contact the author for support:
build_gene"
This warning indicates that a line was skipped because it contained a non-transcript
gene feature, and the code is not currently equipped to handle this type of feature.
This probably isn't too hard to add, so contact me if you get this error and would
like to have these features supported.

"ERROR: Must have at least exons or CDSs to build a transcript: build_trnsc"
Some feature had a transcript_id and yet there were no exons or CDSs associated with
that transcript_id so the script failed to build a transcript.

"ERROR: seq_id conflict: validate_and_finish_trnsc"
Found two features within the same transcript that didn't share the same seq_id.

"ERROR: source conflict: validate_and_finish_trnsc"
Found two features within the same transcript that didn't share the same source.

"ERROR: type conflict: validate_and_finish_trnsc"
Found two features within the same transcript that were expected to share the same
type and yet they didn't.

"ERROR: strand conflict: validate_and_finish_trnsc"
Found two features within the same transcript that didn't share the same strand.

"ERROR: seq_id conflict: validate_and_build_gene"
Found two features within the same gene that didn't share the same seq_id.

"ERROR: source conflict: validate_and_build_gene"
Found two features within the same gene that didn't share the same source.

"ERROR: strand conflict: validate_and_build_gene"
Found two features within the same gene that didn't share the same strand.

"ERROR: gene_id conflict: validate_and_build_gene"
Found two features within the same gene that didn't share the same gene_id.

"FATAL: Can't open GTF file: file_name for reading."
Unable to open the GTF file for reading.

"FATAL: Need exons or CDSs to build transcripts: process_start"
A start_codon feature was annotated and yet there were no exons or CDSs associated
with that transcript_id so the script failed.

"FATAL: Untested code in process_start. Contact the aurthor for support."
The script is written to infer a start codon based on the presence of a 5' UTR, but we
had no example GTF of this type when we wrote the code, so we killed process rather
than run untested code. Contact the author for support.

"FATAL: Invalid feature set: process_start"
We tried to consider all possible ways of infering a start codon or infering a a non-
coding gene, and yet we've failed. Your combination of gene features doesn't make
sense to us. You should never get this error, and if you do, we'd really like to see
the GTF file that generated it. Please contact the author for support.

"FATAL: Need exons or CDSs to build transcripts: process_stop"
A stop_codon feature was annotated and yet there were no exons or CDSs associated with
that transcript_id so the script failed.

"FATAL: Untested code in process_stop. Contact the aurthor for support."
The script is written to infer a stop codon based on the presence of a 3' UTR, but we
had no example GTF of this type when we wrote the code, so we killed process rather
than run untested code. Contact the author for support.

"FATAL: Invalid feature set: process_stop"
We tried to consider all possible ways of infering a stop codon or infering a a non-
coding gene, and yet we've failed. Your combination of gene features doesn't make
sense to us. You should never get this error, and if you do, we'd really like to see
the GTF file that generated it. Please contact the author for support.

"FATAL: Invalid feature set: process_exon_CDS_UTR"
We tried to consider all possible ways of infering exons, CDSs and UTRs and yet we've
failed. Your combination of gene features doesn't make sense to us. You really
should ever get this error, and if you do, we'd really like to see the GTF file that
generated it. Please contact the author for support.

"FATAL: Array reference required: sort_features."
A user shouldn't be able to trigger this error. It almost certainly indicates a
software bug. Please contact the author.

"FATAL: Can't determine strand in: sort_feature_types."
This may indicate that your GTF file does not indicate the strand for features that
require it. It may also indicate a software bug. Please contact the author.

"FATAL: Hash reference required: sort_feature_types."
A user shouldn't be able to trigger this error. It almost certainly indicates a
software bug. Please contact the author.

"FATAL: Invalid value passed to strand: strand."
This may indicate that your GTF file does not indicate the strand for features that
require it. Consider using the DEFAULT_STRAND parameter in the config file. It may
also indicate a software bug. Please contact the author.

CONFIGURATION AND ENVIRONMENT

A configuration file is provided with this script. The script will look for that
configuration file in ./gtf2gff3.cfg, ~/gtf2gff3.cfg or /etc/gtf2gff3.cfg in that order.
If the configuration file is not found in one of those locations and one is not provided
via the --cfg flag it will try to choose some sane defaults, but you really should provide
the configuration file. See the supplied configuration file itself as well as the README
that came with this package for format and details about the configuration file.

DEPENDENCIES

This script requires the following perl packages that are available from CPAN
(www.cpan.org).

Getopt::Long; use Config::Std;

INCOMPATIBILITIES

None reported.

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