maker2jbrowse error: Don't know how to format iprscan tracks, skipping

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maker2jbrowse error: Don't know how to format iprscan tracks, skipping

joel
Hello,

I've been attempting to include the iprscan results with my maker gff file.

I used the   script below to add the iprscan results to my maker gff:

ipr_update_gff maker.gff iprscan.tsv > makeriprscan.gff

I also used the script below to generate a gff of iprscan domains

iprscan2gff3 iprscan.tsv maker.gff > iprscandomain.gff

At this point, I wasn't sure how to proceed.
I concatenated the iprscandomain.gff to the end of the makeriprscan.gff.

And then ran maker2jbrowse, everything seems to work except I get error message

 "Don't know how to format iprscan tracks, skipping"

If I view the file under jbrowse I can certainly see the iprscan results when I
click on a transcript, but there are no tracks of iprscan results in the
jbrowse.

Sorry, this is a bit long winded.

I suspect perhaps that concatenating the two GFFs was perhaps not the right way
to proceed?

Thanks
Joel
--
Dr. Joel S. Shore
Prof. Biology
York University

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Re: maker2jbrowse error: Don't know how to format iprscan tracks, skipping

Carson Holt-2
The maker2jbrowse inside maker is just an alias that launches the maker2jbrowse script inside of jbrowse itself (i.e. …/jbrowse-1.16.8-release/bin/maker2jbrowse). No longer maintained by us, but rather by the jbrowse team.

You can edit the maker2jbrowse script yourself to add an ‘iprscan' line or any other feature type you want by copying an existing feature in this section (image attached) and renaming values such as ‘blastn’ to be ‘iprscan’ (these are the command line options that get sent to flatfile-to-json.pl just as if you were runninging it manually) —> 


For '--type’, I believe ‘iprscan’ uses ‘match’ in the GFF3 column, so instead of ‘protein_match’ or ‘expressed_sequence_match’, just trim it to ‘match’ in the maker2jbrowse section as well.


You also must edit the …/jbrowse/css/maker.scss file to choose what colors you want the feature display to have. Similar to the example above, just copy an existing feature and make a new one where you replace names like ‘blastn' with ‘iprscan’ (image attached) —>


—Carson




On Mar 6, 2020, at 11:32 AM, [hidden email] wrote:

Hello,

I've been attempting to include the iprscan results with my maker gff file.

I used the   script below to add the iprscan results to my maker gff:

ipr_update_gff maker.gff iprscan.tsv > makeriprscan.gff

I also used the script below to generate a gff of iprscan domains

iprscan2gff3 iprscan.tsv maker.gff > iprscandomain.gff

At this point, I wasn't sure how to proceed.
I concatenated the iprscandomain.gff to the end of the makeriprscan.gff.

And then ran maker2jbrowse, everything seems to work except I get error message

"Don't know how to format iprscan tracks, skipping"

If I view the file under jbrowse I can certainly see the iprscan results when I
click on a transcript, but there are no tracks of iprscan results in the
jbrowse.

Sorry, this is a bit long winded.

I suspect perhaps that concatenating the two GFFs was perhaps not the right way
to proceed?

Thanks
Joel
--
Dr. Joel S. Shore
Prof. Biology
York University

_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org