convert GFF3 to refFlat.txt (genePred)

Discussion:

John Malone

2009-11-06 23:43:21 UTC

Hi,

I'd like to convert a GFF3 file into a refFlat (genePred) file. Do
you have a script that will do this?

Thanks,

John

Jennifer Jackson

2009-11-07 05:31:25 UTC

Permalink

Hello,

We do not have a utility to do that particular conversion, but we do have the reverse for an earlier version of the GTF format. Perhaps it would be a place to start when creating your own? It is is the kent source tree:

gpToGtf
http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities

One option may be to try to load the data as a custom track, then output the data in genePred format using the Table browser. There are a few versions of GFF/GTF format and not all sources are consistent with the formatting rules. These are the description we use:
http://genome.ucsc.edu/FAQ/FAQformat#format3
http://genome.ucsc.edu/FAQ/FAQformat#format4

Also, these prior mailing list answers may be helpful:
Open google and paste in "gtf site:lists.soe.ucsc.edu/pipermail/genome"

We hope this is helpful. I am not sure how familiar you are with the browser, but just in case, more details for the Table browser, Custom Tracks, etc. can be found by using the top blue navigation bar links Help & FAQ, but if you would like specific pointers or have a question, please ask.
Jennifer

------------------------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group

Sent: Friday, November 6, 2009 3:43:21 PM GMT -08:00 US/Canada Pacific
Subject: [Genome] convert GFF3 to refFlat.txt (genePred)
Hi,
I'd like to convert a GFF3 file into a refFlat (genePred) file. Do
you have a script that will do this?
Thanks,
John
_______________________________________________
https://lists.soe.ucsc.edu/mailman/listinfo/genome

Jennifer Jackson

2009-11-09 17:09:18 UTC

Permalink

Hello,

Good news - there is a new conversion program that does just what you want to do. It is not documented on the link I gave you, but it is in the kent source tree, same location as the other utilities. Once compiled, type the program name to see the usage:

gff3ToGenePred - convert a GFF3 file to a genePred file
usage:
gff3ToGenePred inGff3 outGp
options:
-honorStartStopCodons - only set CDS start/stop status to complete if there are
corresponding start_stop codon records
This converts:
- top-level gene records with mRNA records
- top-level mRNA records
- mRNA records can contain exon and CDS, or only CDS, or only
exon for non--coding.

Very glad that we could help,
Jennifer

------------------------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group

Sent: Friday, November 6, 2009 9:31:25 PM GMT -08:00 US/Canada Pacific
Subject: Re: [Genome] convert GFF3 to refFlat.txt (genePred)
Hello,
We do not have a utility to do that particular conversion, but we do
have the reverse for an earlier version of the GTF format. Perhaps it
would be a place to start when creating your own? It is is the kent
gpToGtf
http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities
One option may be to try to load the data as a custom track, then
output the data in genePred format using the Table browser. There are
a few versions of GFF/GTF format and not all sources are consistent
http://genome.ucsc.edu/FAQ/FAQformat#format3
http://genome.ucsc.edu/FAQ/FAQformat#format4
Open google and paste in "gtf
site:lists.soe.ucsc.edu/pipermail/genome"
We hope this is helpful. I am not sure how familiar you are with the
browser, but just in case, more details for the Table browser, Custom
Tracks, etc. can be found by using the top blue navigation bar links
Help & FAQ, but if you would like specific pointers or have a
question, please ask.
Jennifer
------------------------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group

Sent: Friday, November 6, 2009 3:43:21 PM GMT -08:00 US/Canada

Pacific

Subject: [Genome] convert GFF3 to refFlat.txt (genePred)
Hi,
I'd like to convert a GFF3 file into a refFlat (genePred) file. Do
you have a script that will do this?
Thanks,
John
_______________________________________________
https://lists.soe.ucsc.edu/mailman/listinfo/genome

_______________________________________________
https://lists.soe.ucsc.edu/mailman/listinfo/genome

Angie Hinrichs

2009-11-09 19:35:56 UTC

Permalink

Hi John,

Another Kent source utility to try is ldHgGene, which translates GFF version 1 or GTF into the genePred format. That is the program that we use to load GFF/GTF files into our database. When we get a GFF3 file, we write a little sed or perl script to translate it into one of our recognized flavors of GFF/GTF, and then use ldHgGene. You will want to use the -out=file.gp option so that it creates a file instead of trying to load a mysql database table.

Hope that helps,
Angie

Sent: Friday, November 6, 2009 3:43:21 PM GMT -08:00 US/Canada

Pacific

_______________________________________________
https://lists.soe.ucsc.edu/mailman/listinfo/genome

John Malone

2009-11-10 00:49:02 UTC

Permalink

Thanks for that! Will check it out.

I'm looking for the gff3ToGenePred in the src/utils path but don't
see it.....is this script something that hasn't made it in yet? Or
maybe I have the wrong path for the Kent source utilities (I see most
of them there though)

Thanks again,

John

Jennifer Jackson

2009-11-10 02:29:41 UTC

Permalink

Hello,

Look in:
~/kent/src/hg/utils

I will try to see if we can have this added to the set of compiles utilities on the ftp Downloads server as well.

Jennifer

------------------------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group

Sent: Monday, November 9, 2009 4:49:02 PM GMT -08:00 US/Canada Pacific
Subject: Re: [Genome] convert GFF3 to refFlat.txt (genePred)
Thanks for that! Will check it out.
I'm looking for the gff3ToGenePred in the src/utils path but don't
see it.....is this script something that hasn't made it in yet? Or
maybe I have the wrong path for the Kent source utilities (I see most
of them there though)
Thanks again,
John