[Gmod-help] convert GFF files

[Scott Cain]

Hello Raul,

The sample you posted already looks very much like GFF3; is that the
sample you really meant to post?

The only thing I can see that makes this not GFF3 is that the item in
the third column  (data_Day1_532:BLOCK1) is not a valid Sequence
Ontology type--and additionally, there is other data encoded in the
type which ought to go elsewhere (assuming it's important enough to
save).  For example, I would dump the NimbleScan from the source
column and instead put what is in column 3 in column 2.  Then for
column 3, I don't know exactly what you should put since I don't know
enough about your data, but I would guess "probe" would probably be
suitable, and if not probe, probably some other child of "reagent".
See

  http://www.sequenceontology.org/miso/current_cvs/term/SO:0000051

for the Sequence Ontology term browser.

As for tools, there is no tool for converting between GFF and near-GFF
flavors: it is just too complicated a task for writing a generic tool.
 However, given that the suggestions I just made are relatively
simple, you could probably do it in Excel or other spreadsheet
software and export as tab delimited text.

Scott


On Mon, Apr 20, 2009 at 10:48 AM, Petrin, Raul <raul-petrin at uiowa.edu> wrote:
> Hi
>
> I know that you got a lot of email regarding Convert GFF to GFF3, but I was
> reading but I didn’t found this full information.
>
> I have one file that I would like to convert to GFF3. Example.
>
>
>
> ##gff-version 3
>
> SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
> 11                 61                 1406.89          .
> .
> seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000011;count=1
>
> SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
> 29                 87                 1286.67          .
> .
> seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000029;count=1
>
> SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
> 62                 118               1244.11          .
> .
> seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000062;count=1
>
> SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
> 87                 142               1321.22          .
> .
> seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000087;count=1
>
> SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
> 114               168               1431.89          .
> .
> seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000114;count=1
>
> SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
> 151               207               1098.56          .
> .
> seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000151;count=1
>
> SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
> 179               241               1658.33          .
> .
> seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000179;count=1
>
> SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
> 197               255               1747.22          .
> .
> seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000197;count=1
>
> SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
> 225               282               1359.78          .
> .
> seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000225;count=1
>
> SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
> 253               310               2027.00          .
> .
> seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000253;count=1
>
> SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
> 291               350               1631.78          .
> .
> seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000291;count=1
>
>
>
> Which tools can I use to convert?
>
> Thank you so much.
>
>
>
> Raul Petrin
>
> 2121 ML - 384-1015
>
> University of Iowa
>
>
>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research