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PROGRAM:

NAME


bp_genbank2gff3.pl -- Genbank->gbrowse-friendly GFF3

SYNOPSIS


bp_genbank2gff3.pl [options] filename(s)

# process a directory containing GenBank flatfiles
perl bp_genbank2gff3.pl --dir path_to_files --zip

# process a single file, ignore explicit exons and introns
perl bp_genbank2gff3.pl --filter exon --filter intron file.gbk.gz

# process a list of files
perl bp_genbank2gff3.pl *gbk.gz

# process data from URL, with Chado GFF model (-noCDS), and pipe to database loader
curl ftp://ftp.ncbi.nih.gov/genomes/Saccharomyces_cerevisiae/CHR_X/NC_001142.gbk \
| perl bp_genbank2gff3.pl -noCDS -in stdin -out stdout \
| perl gmod_bulk_load_gff3.pl -dbname mychado -organism fromdata

Options:
--noinfer -r don't infer exon/mRNA subfeatures
--conf -i path to the curation configuration file that contains user preferences
for Genbank entries (must be YAML format)
(if --manual is passed without --ini, user will be prompted to
create the file if any manual input is saved)
--sofile -l path to to the so.obo file to use for feature type mapping
(--sofile live will download the latest online revision)
--manual -m when trying to guess the proper SO term, if more than
one option matches the primary tag, the converter will
wait for user input to choose the correct one
(only works with --sofile)
--dir -d path to a list of genbank flatfiles
--outdir -o location to write GFF files (can be 'stdout' or '-' for pipe)
--zip -z compress GFF3 output files with gzip
--summary -s print a summary of the features in each contig
--filter -x genbank feature type(s) to ignore
--split -y split output to separate GFF and fasta files for
each genbank record
--nolump -n separate file for each reference sequence
(default is to lump all records together into one
output file for each input file)
--ethresh -e error threshold for unflattener
set this high (>2) to ignore all unflattener errors
--[no]CDS -c Keep CDS-exons, or convert to alternate gene-RNA-protein-exon
model. --CDS is default. Use --CDS to keep default GFF gene model,
use --noCDS to convert to g-r-p-e.
--format -f Input format (SeqIO types): GenBank, Swiss or Uniprot, EMBL work
(GenBank is default)
--GFF_VERSION 3 is default, 2 and 2.5 and other Bio::Tools::GFF versions available
--quiet don't talk about what is being processed
--typesource SO sequence type for source (e.g. chromosome; region; contig)
--help -h display this message

DESCRIPTION


This script uses Bio::SeqFeature::Tools::Unflattener and Bio::Tools::GFF to convert
GenBank flatfiles to GFF3 with gene containment hierarchies mapped for optimal display in
gbrowse.

The input files are assumed to be gzipped GenBank flatfiles for refseq contigs. The files
may contain multiple GenBank records. Either a single file or an entire directory can be
processed. By default, the DNA sequence is embedded in the GFF but it can be saved into
separate fasta file with the --split(-y) option.

If an input file contains multiple records, the default behaviour is to dump all GFF and
sequence to a file of the same name (with .gff appended). Using the 'nolump' option will
create a separate file for each genbank record. Using the 'split' option will create
separate GFF and Fasta files for each genbank record.

Notes
'split' and 'nolump' produce many files

In cases where the input files contain many GenBank records (for example, the chromosome
files for the mouse genome build), a very large number of output files will be produced if
the 'split' or 'nolump' options are selected. If you do have lists of files > 6000, use
the --long_list option in bp_bulk_load_gff.pl or bp_fast_load_gff.pl to load the gff and/
or fasta files.

Designed for RefSeq

This script is designed for RefSeq genomic sequence entries. It may work for third party
annotations but this has not been tested. But see below, Uniprot/Swissprot works, EMBL
and possibly EMBL/Ensembl if you don't mind some gene model unflattener errors (dgg).

G-R-P-E Gene Model

Don Gilbert worked this over with needs to produce GFF3 suited to loading to GMOD Chado
databases. Most of the changes I believe are suited for general use. One main chado-
specific addition is the
--[no]cds2protein flag

My favorite GFF is to set the above as ON by default (disable with --nocds2prot) For
general use it probably should be OFF, enabled with --cds2prot.

This writes GFF with an alternate, but useful Gene model, instead of the consensus model
for GFF3

[ gene > mRNA> (exon,CDS,UTR) ]

This alternate is

gene > mRNA > polypeptide > exon

means the only feature with dna bases is the exon. The others specify only location
ranges on a genome. Exon of course is a child of mRNA and protein/peptide.

The protein/polypeptide feature is an important one, having all the annotations of the
GenBank CDS feature, protein ID, translation, GO terms, Dbxrefs to other proteins.

UTRs, introns, CDS-exons are all inferred from the primary exon bases inside/outside
appropriate higher feature ranges. Other special gene model features remain the same.

Several other improvements and bugfixes, minor but useful are included

* IO pipes now work:
curl ftp://ncbigenomes/... | bp_genbank2gff3 --in stdin --out stdout | gff2chado ...

* GenBank main record fields are added to source feature, e.g. organism, date,
and the sourcetype, commonly chromosome for genomes, is used.

* Gene Model handling for ncRNA, pseudogenes are added.

* GFF header is cleaner, more informative.
--GFF_VERSION flag allows choice of v2 as well as default v3

* GFF ##FASTA inclusion is improved, and
CDS translation sequence is moved to FASTA records.

* FT -> GFF attribute mapping is improved.

* --format choice of SeqIO input formats (GenBank default).
Uniprot/Swissprot and EMBL work and produce useful GFF.

* SeqFeature::Tools::TypeMapper has a few FT -> SOFA additions
and more flexible usage.

TODO


Are these additions desired?
* filter input records by taxon (e.g. keep only organism=xxx or taxa level = classYYY
* handle Entrezgene, other non-sequence SeqIO structures (really should change
those parsers to produce consistent annotation tags).

Related bugfixes/tests
These items from Bioperl mail were tested (sample data generating errors), and found
corrected:

From: Ed Green <green <at> eva.mpg.de>
Subject: genbank2gff3.pl on new human RefSeq
Date: 2006-03-13 21:22:26 GMT
-- unspecified errors (sample data works now).

From: Eric Just <e-just <at> northwestern.edu>
Subject: genbank2gff3.pl
Date: 2007-01-26 17:08:49 GMT
-- bug fixed in genbank2gff3 for multi-record handling

This error is for a /trans_splice gene that is hard to handle, and unflattner/genbank2
doesn't

From: Chad Matsalla <chad <at> dieselwurks.com>
Subject: genbank2gff3.PLS and the unflatenner - Inconsistent order?
Date: 2005-07-15 19:51:48 GMT

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