How convert .gff to .gff3??

[mruizm]

Hi there! I'm trying to convert a simple .gff file to a .gff3 to extract the intergenic sequences of a genome, i was searching for a tool or script to do that but i can find anything :/ little help!
Regards!

[WhatsOEver]

1) Are you sure that you have gff (which is a quite old format) and not gff2/gtf?
2) Both formats contain start/stop coordinates of genes/exons/transcripts. Why would you want to have gff3 for determining intergenic regions?

[mruizm]

Answering your questions, here is an example of my gff file:

scaffold_1 JGI exon 2253 4325 . - . name "estExt_Genemark.C_10001"; transcriptId 143574
scaffold_1 JGI CDS 2418 4325 . - 0 name "estExt_Genemark.C_10001"; proteinId 143574; exonNumber 1
scaffold_1 JGI start_codon 4323 4325 . - 0 name "estExt_Genemark.C_10001"
scaffold_1 JGI stop_codon 2418 2420 . - 0 name "estExt_Genemark.C_10001"
scaffold_1 JGI exon 5719 7023 . - . name "fgenesh1_pm.1_#_2"; transcriptId 97261
scaffold_1 JGI CDS 5719 7023 . - 0 name "fgenesh1_pm.1_#_2"; proteinId 97261; exonNumber 2

There is a program called GFFEX that extract intergenic regions with the fasta and the gff3 faster than other programs.

[WhatsOEver]

As expected, you're file is in gtf/gff2 format.
I had a brief look at the program (version 2.2 from http://bioinfo.icgeb.res.in/gff/gffdownloads/) and it is able to handle that format without re-formating anything. Also from looking at the perl scripts, it should be able to handle it - although I'm not sure how it handles "start_codon" / "stop_codon" entries, but "exon", "CDS", "mRNA", etc... are covered.
What was the (error) message you got when you tried to run the program?

[mruizm]

The error message looks like this:

cat: final1: No such file or directory
C
O
M
P
L
E
T
E

adding description to UPSTREAM/PROMOTER_sequences
C
O
M
P
L
E
cat: local: No such file or directory
T
E


Processing the Output Files

1/7 Processes Completed

2/7 Processes Completed

3/7 Processes Completed

4/7 Processes Completed

5/7 Processes Completed

6/7 Processes Completed

All Processes are Completed successfully

ERROR with the run, no output files generated
ERROR: bad input files

######################################################################
Thanks for using GFF-Extractor !!!!
######################################################################

i tried to transform the file with gffreader from cufflinks but i obtain the same error message...