And thanks to Jason and Don for pointing out the GFF2 to GFF3 translators. They may not help Manny here, but they will help others.<br><br>Dave C.<br><br><div class="gmail_quote">On Fri, Aug 14, 2009 at 1:52 PM, Dave Clements <span dir="ltr"><<a href="mailto:clements@nescent.org">clements@nescent.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Scott,<br><br>That was my guess on the file Manny is using. He's actually using <a href="ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v4.0/Sbicolor/annotation/Sbi1.4/Sbi1.4.gff3.gz" target="_blank">ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v4.0/Sbicolor/annotation/Sbi1.4/Sbi1.4.gff3.gz</a><br>
<br>Manny explicitly said that and Shu picked up on that (Thanks for reading Manny's response carefully!). I'm looking at the file now. It does not have full-length entries, but I can's see why it complains about super_10 in particular.<br>
<br>Dave C.<div><div></div><div class="h5"><br><br><div class="gmail_quote">On Fri, Aug 14, 2009 at 1:47 PM, Scott Cain <span dir="ltr"><<a href="mailto:scott@scottcain.net" target="_blank">scott@scottcain.net</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Shu,<br>
<br>
The file in question:<br>
<div><br>
<a href="ftp://ftp.jgi-psf.org/pub/JGI_data/Sorghum_bicolor/v1.0/Sorbi1_GeneModels_Sbi1_4_Sbi1_4.gff.gz" target="_blank">ftp://ftp.jgi-psf.org/pub/JGI_data/Sorghum_bicolor/v1.0/Sorbi1_GeneModels_Sbi1_4_Sbi1_4.gff.gz</a><br>
<br>
</div>is definitely not GFF3. The first couple of lines look like this:<br>
<br>
chr_1 JGI exon 2164 2829 . + . name<br>
"Sb01g000200"; transcriptId 5257096<br>
chr_1 JGI CDS 2164 2829 . + 0 name<br>
"Sb01g000200"; proteinId 5027909; exonNumber 1<br>
<br>
The 9th column needs to be in "tag=value" format and "name" should be<br>
capitalized, and it would be nice to have gene and mRNA features to go<br>
with the exon and CDS features, rather than depending on inferring<br>
their existance (the Chado loader will fail to do that, and the<br>
Bio::DB::SeqFeature::Store will probably be successful, but getting<br>
GBrowse to display it properly will likely not be easy).<br>
<font color="#888888"><br>
Scott<br>
</font><div><div></div><div><br>
<br>
On Aug 14, 2009, at 4:35 PM, Shengqiang Shu wrote:<br>
<br>
> This file is in format of GFF3, Is this loading problem due to file<br>
> not conforming to GFF3 standard? In term of SO terms, it uses gene,<br>
> mRNA, exon, CDS. No problem, is there?<br>
><br>
> Only thing looks like missing is Name attribute. Is Name attribute<br>
> required? From scanning through doc on sequence ontology site, it<br>
> did not say Name is required.<br>
><br>
> I know this file is produced by one of our members. If you guys<br>
> point out what is the problem with file in term of conforming to<br>
> GFF3 standard, it would be very helpful.<br>
><br>
> By the way, FASTA in GFF3 is optional, isn't? Don't know why loader<br>
> can not handle it? ah, the file is annotation GFF3 file, it does not<br>
> contain genomic features. Is this causing the loading problem?<br>
><br>
><br>
> Shu<br>
><br>
><br>
> On Aug 14, 2009, at 12:54 PM, Chris Fields wrote:<br>
><br>
>> Yikes, another GFF2 variant?<br>
>><br>
>> chris<br>
>><br>
>> On Aug 14, 2009, at 2:50 PM, Jason Stajich wrote:<br>
>><br>
>>> I also have these script jg_gff2gff3.pl in gff_tools of <a href="http://github.com/hyphaltip/genome-scripts/tree/master" target="_blank">http://github.com/hyphaltip/genome-scripts/tree/master</a><br>
>>> and<br>
>>> gff3_to_JGIgff.pl for converting back into JGI gff from GFF3.<br>
>>><br>
>>> -jason<br>
>>><br>
>>> On Aug 14, 2009, at 11:01 AM, Don Gilbert wrote:<br>
>>><br>
>>>><br>
>>>>> Has anyone out there written a JGI GFF2 to GFF3 parser<br>
>>>><br>
>>>> I've written both ways: jgi to gff3, and gff3 to jgi-gff (which<br>
>>>> is a<br>
>>>> variant of gff2).<br>
>>>> Find here<br>
>>>> <a href="http://wfleabase.org/release1/current_release/supplement/jgi_gff/" target="_blank">http://wfleabase.org/release1/current_release/supplement/jgi_gff/</a><br>
>>>> as jgi2gff.pl (and dpulex_gff2jgi.pl for the other way)<br>
>>>><br>
>>>> This script will want some revision for your data, and the variant<br>
>>>> of JGI's gff<br>
>>>> I worked with may differ from yours. Look at the sample at the top<br>
>>>> of the<br>
>>>> script to see if it matches yours.<br>
>>>><br>
>>>> - Don<br>
>>>><br>
>>>> ------------------------------------------------------------------------------<br>
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>>><br>
>>> --<br>
>>> Jason Stajich<br>
>>> <a href="mailto:jason.stajich@gmail.com" target="_blank">jason.stajich@gmail.com</a><br>
>>> <a href="mailto:jason@bioperl.org" target="_blank">jason@bioperl.org</a><br>
>>><br>
>>><br>
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Ontario Institute for Cancer Research<br>
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