bp_genbank2gff31p
Usage
bp_genbank2gff3.pl [options]
filename(s)
perl bp_genbank2gff3.pl
--dir
path_to_files
--zip
perl bp_genbank2gff3.pl
--filter
exon
--filter
intron
file.gbk.gz
perl bp_genbank2gff3.pl
*gbk.gz
curl ftp://ftp.ncbi.nih.gov/genomes/Saccharomyces_cerevisiae/CHR_X/NC_001142.gbk
\
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)
create the
file
if
any
manual
input
is
saved)
--sofile
-l
path
to
to
the
so.obo
file
to
use
for
feature
type
mapping
wait for
user
input
to
choose
the
correct
one
each genbank
record
--nolump
-n
separate
file
for
each
reference
sequence
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
use --noCDS
to
convert
to
g-r-p-e.
--format
-f
Input
format
(SeqIO
types):
GenBank,
Swiss
or
Uniprot,
EMBL
work
Overview
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 > exonmeans 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, andCDS 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 additionsand 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 changethose 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 RefSeqDate: 2006-03-13 21:22:26 GMT-- unspecified errors (sample data works now).From: Eric Just <e-just <at> northwestern.edu>Subject: genbank2gff3.plDate: 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
Releases
9 releases since Debian 5.0 (Lenny); the text changed 7 times.