[AlexReynolds]

That appears to be a different error from what is described in a previous comment. Thanks for the error report and sample GFF file. I'll take a look when I can.

[niti217]

Visit GFF-Ex: http://bioinfo.icgeb.res.in/gff/

GFF-Ex, a Genome Feature extraction package extracts Gene, Exon, Intron, Upstream Region of Gene (Promoters), Intergenic and CDS/cDNA sequences by just tweeting in the Genome Feature File (gff) along with the corresponding genome/chromosome sequence. GFF-Ex. is a fusion of shell and Perl, developed for platforms supporting UNIX based file system.

Installation is easy and very user friendly tool. Works well with files in GFF-2 format and will be upgrading to GFF-3 format as well.

I was wondering if I could use GFF-Ex to seek information on the reverse strand - especially the non coding regions on the opposite strand. Please let me know. Thanks

[albireo]

Hi, I'm getting the same error. Has anybody found out the reason of this exception? Thanks!

Hello Alex!

I've downloaded the precompiled binaries for Linux (64bit) and I still get this "index out range" error. In my case, however, the problem appears to be in the "source" field (the second one), not in the "attributes"...

Traceback (most recent call last):
  File "/home/panos/Programs/temp/bedops-read-only/bin/gff2bed", line 212, in <module>
    sys.exit(main(*sys.argv))
  File "/home/panos/Programs/temp/bedops-read-only/bin/gff2bed", line 162, in main
    cols['source'] = elems[1]
IndexError: list index out of range

You can get one of the gff files I'm using from here.

Any ideas?

[AlexReynolds]

There has been a change to the GTF standard, such that gtf2bed fails to parse newer GTF files (such as the example input that you link to, thanks).

This conversion script will be fixed in BEDOPS 2.3, which will be released later this week.

[albireo]

Thanks a lot Alex

[AlexReynolds]

We have posted BEDOPS v2.3, which includes a fixed gff2bed script:

https://github.com/bedops/bedops/releases/tag/v2.3.0

A more complete revision history is available here:

https://bedops.readthedocs.org/en/latest/content/revision-history.html#v2-3-0

Feel free to send us feedback at: [email protected]

[fireLog2]

We have posted BEDOPS v2.3, which includes a fixed gff2bed script:

https://github.com/bedops/bedops/releases/tag/v2.3.0

A more complete revision history is available here:

https://bedops.readthedocs.org/en/latest/content/revision-history.html#v2-3-0

Feel free to send us feedback at: [email protected]

Thank you! I will give it a try...

[ahmadsam]

I think you people are mistaken. Though the accuracy of the tool has been tested earlier, still because of the query, I re-verified the results of GFF-Ex. The results are satisfactory.
I ran the GFF-Ex with the example files given in the installation directory. After getting the sequence information of the introns, I took a random sequence from the output intron file and aligned it to the corresponding genome file, using BLAST. The results were same as it is specified in the used gff file. What I can visualize or infer from here is, you people might be aligning the different genome reference against the intron sequences, fetched from annotation file (gff) of other version or source.
Anyway, there are few things which have to be taken care of when running GFF-Ex.
1. The gff file should be in gff2 format. (GFF-Ex version for gff3 format file is in progress, which is to be released soon, Keep visiting GFF-Ex)
2. The genome file should be in fasta format.
3. Both the input files (gff & genome fasta files) should be of same version and from same source. You cannot use the gff and genome information from either different version or source.
GFF-Ex is a user-friendly tool that comes with a jargon of accuracy, speed and sensitivity. GFF-Ex is suitable for extracting sequence information of multiple features either specified (gene, exon, CDS) or un-specified (introns, intergenic and region upstream to genes) within gff file. I would like you all to explore it more and take care of the input files.
Personal annotation queries, related to GFF-Ex can also be posted at [email protected]

i have same error for extracting my sequence from wheat genome maybe it because of genome size (mine is 4.1 GB) ..

[achal13r]

@niti217

The output file of GFF-Ex have sequences from both the strands, forward and reverse.

PS: Use the latest release of GFF-Ex_v2.3

[achal13r]

@ahmadsam

Can you try installing a program in a machine with bigger memory like >8GB.

Personal Recommendation: Use the latest version GFF-Ex_v2.3.

[achal13r]

New version of GFF-Ex

New version of GFF-Ex is released. Use the current version "GFF-Ex_v2.3" for best results. See http://bioinfo.icgeb.res.in/gff/