Demo annotation occurred in my own json file.

[wh960823]

Hi, I am interested in your work on genome comparison visulization. However, when I creat my own json file using my own data and annotation tsv. file, the ndh, invert repeat annoatations in demo occurred instead of my annotations. Could you please guide me to solve this problem ?
Sincerely,
Hao

[iimog]

Hi Hao,
I think this is related to AliTVTeam/AliTV#123. My guess is, that your json is just fine, containing none of the demo features and only the annotation you provided. The problem is, that the web interface does not by default change the visibility of features when you load a new json file. You should be able to click on "Show/Hide Annotations" (see screenshot below) to hide the annotations you don't need and select a style for the annotations you want to show.
If there is really an issue with the json file, it would be awesome if you could share the command you used for creation and the output json for inspection.

[iimog]

[wh960823]

Thanks for your reply! I tried to show annotations in the web interface, but no list of my annotations in the list. Please see the yaml file attached below.

command: alitv.pl --project test /home/bioinfo/Crabs/hcl/test_AliTV/a.yaml --overwrite

a.yaml

genomes: 
   -
    name: Bradyrhizobium_canariense_WSM471
    sequence_files:
      - /home/bioinfo/Crabs/hcl/test_AliTV/Bradyrhizobium_canariense_WSM471.fasta
    feature_files:
      nif: 
             - /home/bioinfo/Crabs/hcl/test_AliTV/nif.tsv           
   - 
    name: Bradyrhizobium_daqingense_CCBAU15774
    sequence_files:
      - /home/bioinfo/Crabs/hcl/test_AliTV/Bradyrhizobium_daqingense_CCBAU15774.fasta
    feature_files:
      nif: 
             - /home/bioinfo/Crabs/hcl/test_AliTV/nif.tsv 
features:
  nif:
    color: "#ff006e"
    form: arrow
    height: 30
    visible: 1
alignment:
   program: lastz
   parameter:
       - "--format=maf"
       - "--noytrim"
       - "--ambiguous=iupac"
       - "--gapped"
       - "--strand=both"

[iimog]

This looks good. If all files are in the correct format and sequence IDs in the fasta and tsv files match, the nif features should end up in the json file. Is it possilble to share the output json file for debugging (you can use dummy or public sequences if your data is confidential)?

[bio-tombow]

This looks good. If all files are in the correct format and sequence IDs in the fasta and tsv files match, the nif features should end up in the json file. Is it possilble to share the output json file for debugging (you can use dummy or public sequences if your data is confidential)?

Here is the files, the Github not allowed uploading json, tsv files, so I add virtual txt extension to files, please check the files. Thanks you so much for helping me debugg.
nif.tsv.txt
test.json.txt
Bradyrhizobium_daqingense_CCBAU15774.fasta.txt

[iimog]

It looks like your tsv file has an additional first column with just nif in it. According to the documentation:

The easiest feature annotation file format is a tab separated *.tsv file containing the following fields: sequence ID, start coordinate, end coordinate, strand (1/-1), and a name for that feature instance.

Therefore, AliTV tries to find sequences with id nif, which don't exist and are silently ignored (by design). All other columns would be shifted by one as well.

Please remove the first column from the tsv file and try again.

[wh960823]

Thanks so much ! The annotation was successfully added.

[iimog]

Awesome! 🎉