From: Mason Meyer <mmeyer20@uncc.edu>
To: Valdir Barth <valdirbarth@gmail.com>
CC: Ann Loraine <Ann.Loraine@uncc.edu>
Date: Mon, Oct 30, 2017 at 6:58 PM
Subject: Re: Windows version does not read gff file properly

Hello Valdir,

My name is Mason Meyer, IGB Support Specialist. Thanks for contacting our team for assistance with your issue.

I spent some time trying to reproduce the issue of the gene label not displaying on Windows, but I was not yet able to. When trying to reproduce the issue on my Windows machine, I was able to label by the gene field so that the text "lysT" was displayed (see screenshot). When I copied the data from your e-mail, I did have to convert the spaces into tabs so IGB would open the file, but I imagine you didn't experience this problem since you have the actual file.

I have been trying to figure out what might be causing this label option issue for you and not me. Is your file labeled with the extension ".gff3"?

I feel confident that we can resolve the issue quickly if we figure out why it is happening. Are you able to send me the GFF3 file to use for testing? If not, please let me know and we can look into other ways of resolving the issue.

Thanks again,

Mason Meyer
IGB Support Specialist

From: Valdir Barth <valdirbarth@gmail.com>
To: Mason Meyer <mmeyer20@uncc.edu>
Date: Sun, Nov 26, 2017 at 9:21 PM
Subject: Re: Windows version does not read gff file properly

Hello,
Thanks for the reply. I actually found out what was causing it. It has nothing to do with the OS.

When I download the GFF3 file from NCBI`s nucleotide page (Accession AL123456.3), the first line after comments is:
AL123456 EMBL region 1 4411532 . + . ID=id0;Dbxref=taxon:83332;gbkey=Src;mol_type=genomic DNA;strain=H37Rv

And only THEN it starts with the genome annotation:
AL123456 EMBL gene 1 1524 . + . ID=gene0;Name=dnaA;gbkey=Gene;gene=dnaA;gene_biotype=protein_coding;locus_tag=Rv0001

With that first line, IGB does not read the label fields properly, that is why I could not get it to show the gene name. It actually reads it as a gene that is mapped throughout the whole genome of the bacteria (from position 1 to 4411532).
After I deleted that first line, I can select "gene" in the label field dropdown.

Sorry for the miscommunication. Maybe this could still be addressed somehow if this is not supposed to happen?

Thank you,

Valdir

From: Mason Meyer <mmeyer20@uncc.edu>
To: Valdir Barth <valdirbarth@gmail.com>
Date: Thu, Nov 30, 2017 at 5:12 PM
Subject: Re: Windows version does not read gff file properly

Hello again Valdir,

I am glad you were able to find out what was causing the issue. I looked into this to see if other GFF3 files also seemed to have this issue and it seems to me that this issue may not be the norm. This must be something NCBI is doing to their GFF3 files, but IGB is actually reading the files as expected. Our team may be able to add some error-handling to files containing this additional line at the beginning, though. I will discuss this issue with the rest of the team and will track this in our issue-tracking system so we can plan work on this task.

Thank you for continuing to look into this issue. If you have any other questions or feedback for us, please be sure to let me know.

Thanks again,

Mason Meyer
IGB Support Specialist