Score value in Primary Data

[hkmoon]

Hi,

Is there a way to show score in primary data? I have match data with e-value in the column of score in GFF3 format. Currently, biodb-to-json.pl and json are used for importing gff3 file.

For example, be_v1 e-value BlastHit 259 1233 3e-128 - . ID=be_S_v1;Parent=be_v1;Name=NP_001157823.1;Target=NP_001157823.1 1 324;Species=;Note="factor 3, subunit I"

How can I show the score in "Primary data" section? Currently, I treat this data as "FeatureTrack" type and "Transcript" class for the display.

Regards, HongKee

[rbuels]

You could either:

a. Put the e-value in the score column of the gff3 you're loading, in which case it would show up as Score under primary data

b. Make the dialog be a custom popup that shows anything you want, by implementing a custom left-click behavior for that track in the trackList.json. An example of that can be seen at https://github.com/GMOD/jbrowse/blob/16c50d5de1a4a31f1e7a97c862bf84476ed6461d/docs/tutorial/conf_files/volvox.json#L93

Does this work for you? Just reopen the issue to continue the conversation if not.

[hkmoon]

Hi, Thank you for the reply. Still, I'm not able to see stored score value inside trackData.json. Probably, does bin/biodb-to-json.pl check the "type" column if it needs score value or not, during importing process? In my gff3 file, I named "BlastHit" in the "type" column.

Do you have any clue?

[rbuels]

It's definitely not related to the type column.

Have you tried clearing your browser's cache when reloading? Your browser could be caching on old version of the feature data.

[hkmoon]

Hi,

gff3 data looks like: ox_Smed_v1_00001 e-value BlastHit 211 528 9e-19 + . ID=ox_Smed_v1_00001bmatch001;Parent=ox_Smed_v1_00001;Name=XP_004069140.1;Target=XP_004069140.1 51 155;Species=Japanese medaka;Note="bcl-2-like protein 1-like" ox_Smed_v1_00001 e-value BlastHit 172 528 3e-16 + . ID=ox_Smed_v1_00001bmatch002;Parent=ox_Smed_v1_00001;Name=XP_003457009.1;Target=XP_003457009.1 68 185;Species=Oreochromis niloticus (Linnaeus, 1758);Note="bcl-2-like protein 1-like" ox_Smed_v1_00001 e-value BlastHit 139 528 2e-15 + . ID=ox_Smed_v1_00001bmatch003;Parent=ox_Smed_v1_00001;Name=NP_571882.1;Target=NP_571882.1 63 191;Species=Danio rerio (Hamilton, 1822);Note="bcl2-like 1"

trackData.json looks like: "histograms":{"stats":[{"basesPerBin":"500","max":3,"mean":3}],"meta":[{"basesPerBin":"500","arrayParams":{"length":2,"chunkSize":10000,"urlTemplate":"hist-500-{Chunk}.json"}}]},"featureCount":3,"intervals":{"nclist":[[1,138,528,1,"e-value"," 1822)","ox_Smed_v1_00001","ox_Smed_v1_00001bmatch003","NP_571882.1","Danio rerio (Hamilton","\"bcl2-like 1\"\r","ox_Smed_v1_00001","NP_571882.1 63 191","BlastHit"],[1,171,528,1,"e-value"," 1758)","ox_Smed_v1_00001","ox_Smed_v1_00001bmatch002","XP_003457009.1","Oreochromis niloticus (Linnaeus","\"bcl-2-like protein 1-like\"\r","ox_Smed_v1_00001","XP_003457009.1 68 185","BlastHit"],[0,210,528,1,"e-value","ox_Smed_v1_00001","ox_Smed_v1_00001bmatch001","XP_004069140.1","Japanese medaka","\"bcl-2-like protein 1-like\"\r","ox_Smed_v1_00001","XP_004069140.1 51 155","BlastHit"]],"classes":[{"isArrayAttr":{},"attributes":["Start","End","Strand","Source","Seq_id","Load_id","Name","Species","Note","Parent_id","Target","Type"]},{"isArrayAttr":{},"attributes":["Start","End","Strand","Source","Species2","Seq_id","Load_id","Name","Species","Note","Parent_id","Target","Type"]},{"isArrayAttr":{"Sublist":1},"attributes":["Start","End","Chunk"]}],"maxEnd":528,"count":3,"lazyClass":2,"urlTemplate":"lf-{Chunk}.json","minStart":138},"formatVersion":1}

I couldn't see any score here.

Thank you so much!

[rbuels]

Hmm, I think there is a bug somewhere in here. I'll look into it.

[rbuels]

Fixed in git, the fix will come out in 1.10.7. Thanks for reporting it!

[hkmoon]

Thanks a lot, Robert!