apply_to_db.py does not update metadata.tsv file

[Edouard94]

Hello PhyloFisher team,

I have an issue where, after running _apply_todb.py script, the metadata.tsv and _treecolors.tsv files are not updated, when the other folders and files seem to be.

Could you give me some insight regarding this issue? Should I update the files manually or use the _selecttaxa.py script, knowing that I want all taxa.

Thank you for your help, Edouard

[atice]

Hi @Edouard94

Thank you for the message. Would you be willing to share your input_metadata.tsv, parsed.tsv files, config_ini, and the command you are running? These should be all we need to diagnose the issue thoroughly.

Alex

[Edouard94]

Hello Alex,

Thank you for getting back to me so quickly.

I am attaching here the requested files and the commands I used after parsing: https://we.tl/t-Zi9c6dtXnn

apply_to_db.py -i forest_out_date/ -fi fisher_out_date/ -t 10 prep_final_dataset.py matrix_constructor.py -i prep_final_dataset_date -t 10

Thank you for your help.

Best wishes, Edouard

[atice]

Hi @Edouard94

Looking in your forest_out_Oct.03.2023 directory I do not see any _parsed.tsv files. Even if you do not make changes to the ortholog/paralog decisions automatically made by fisher.py the original .tsv files output by forest.py need to be saved {gene}_parsed.tsv after being viewed as is automaticly done by ParaSorter when you click "Save to TSV." Would you go back and either rename your files with a script/by hand/opening and saving in ParaSorter so they fit this format and run apply_db.py again and let us know the results. Our guess is none of the sequences from the taxon you added are in the ortholog and paralog files. Those directories and files were just touched as the script was running though sequences already present in the database.

As for tree_colors.tsv, is this the first time you are using either Microsporidia or IncertaeSedis as taxonomic designations? Could you provide us with more information about what behavior are you expecting?

Alex

[atice]

Hi @Edouard94 ,

Just wanted to follow up to see if this solved your issue or not? Thanks for any update you can provide.

Alex

[Edouard94]

Hi Alex,

Sorry for my late reply.

Ok yes, I see that I went to fast here at the parsing step. All looked correct so I did not do the manual parsing. But eventually I did and rerun the apply_db.py and constructed my matrix and I had the expected changes and results where my new proteome has been added.

Regarding the tree_colors.tsv I don't really know how to use it with the produced matrix, but yes it would be the first time I use this file with those new taxonomical ranks.

Thank you for your help!

Best, Edouard