kennthshang / phatyp Goto Github PK

hi, I just want to know if the higher prediction score in the result table means more accurate? Can it be considered that reliable results require a score greater than 0.9? or 0.8? Is there an empirical value for this?

HI,

I get the following error when running PhaTYP:

Opening the database file... No such file or directory
 [0.004s]
Error: Error calling stat on file database/database.fa
Running prodigal-gv...


---------------------------------Diamond BLASTp---------------------------------
Creating Diamond database and running Diamond...
Creating Diamond database...
create database failed
Traceback (most recent call last):
  File "/data/umcg-llnext/python_venvs/PhaTYP_venv/PhaTYP/PhaTYP.py", line 37, in <module>
    id2contig = pkl.load(open(f'{transformer_fn}/sentence_id2contig.dict', 'rb'))
FileNotFoundError: [Errno 2] No such file or directory: 'phatyp//sentence_id2contig.dict'

Do I need to add the location of the database to the path? Or is there any options/flags to add the database path when running thepreprocessing.py script?

Hi,

Thanks for developing the tool! Is the pre-trained model (without any fine-tuning, but the same that was used for fine-tuning later) available? Could you maybe also share it?

Thank you!

Dear PhaTYPer,
Hope this mail find you well.
It seems the phatyp.yaml file has a formatting error at line 28, the log showed ruamel.yaml.scanner.ScannerError when I run conda create.

ruamel.yaml.scanner.ScannerError: mapping values are not allowed here
  in "<unicode string>", line 28, column 66:
     ... le" content="{&quot;groups&quot;: [], &quot;environmentKey&quot; ...
                                         ^ (line: 28)

Best,
Panpan

Hi!

Thanks for the great tool! I was wondering whether you are planning to update the current version of prodigal used by PhaTYP to prodigal-gv to improve gene calling for viruses with alternative genetic codes.

Best,

Asier

Hello,

Thanks for the excellent tool. Is it possible that the life styles of some viral contigs are undetermined (absence in the output csv file)?

Hello, thank you for the excellent tool. I used Phatyp to compare my metagenomic data with BACPHLIP. To be more stringent I used the following criteria:

1. CheckV was performed on the tested viral contigs to ensure that they were complete and free of contamination.
2. Phatyp and BACPHLIP were run using default parameters.
3. Only contigs from both predictions with a probability score of >= 0.95 were taken into account for the final analysis.

Here, are the results:

It seems like there is a significant difference between the output of the two classifiers.

When testing the tool with the test_contigs.fa file, I get the following error when it tries to build the DIAMOND database:

---------------------------------Diamond BLASTp---------------------------------
Creating Diamond database and running Diamond...
Creating Diamond database...
create database failed

I have tried installing different versions of DIAMOND (2.0.13, 4.0.515) but I get the same error. Which is the version you recommend?

Thanks!