request to add argument to print the version

[Rohit-Satyam]

@liaoherui I was wondering if you can add a parameter to print the version of the tool because I am not sure if I downloaded the latest version.

Besides I keep on getting this error message while building the database:

Newly added sites number:  0 / 0
Kmer POS-Snp file done! Start generating matrix.
Traceback (most recent call last):
  File "bin/S2_remove_redundant_For_Me.py", line 25, in <module>
    if int(c) not in carr:
ValueError: invalid literal for int() with base 10: ''

Most of the files are of 0kb

python VirStrain_build.py --i denv.mafft.aln -d denv_virstrain_s0.6_revised -s 0.6

I have 15788 sequences in MSA so is it because of that?

[liaoherui]

Sorry for late reply. I am very busy these days.

Can you check the head name of your input strains? E.g. Whether there are duplicate names or special characters? Please make sure all head name of your input strains are in the format as suggested.

[Rohit-Satyam]

Yes @liaoherui I checked the names of the sequence and they are without spaces or special characters. They are just accession IDs without versions. I saw that when I remove some sequences based on length (now I take genomes with lengths of 8-12Kb rather than 5-12kb previously), the error disappears. So I will close this issue for now. Besides, could you kindly add a --version argument so that in the future it's easy to see if I downloaded the correct version?

[liaoherui]

Hi, @Rohit-Satyam I added the parameter. Now, you can use "-v" to check the version.

[Rohit-Satyam]

I tried using the -v option after installing latest version through conda and it doesn't work

virstrain_merge -v
usage: VirStrain_contigDB_merge.py [-h] -i MERGE_DB [-o OUT_DIR]
VirStrain_contigDB_merge.py: error: the following arguments are required: -i/--merge_db
(temp) satyamr@KW61512:~/miniconda3/envs/virstrain/bin$ virstrain --version
usage: VirStrain.py [-h] -i INPUT_READS [-p INPUT_READS2] -d DB_DIR
                    [-o OUT_DIR] [-c SF_CUTOFF] [-s RK_SITE] [-f CLOSE_FIG]
                    [-m [HM_VIRUS]]
VirStrain.py: error: the following arguments are required: -i/--input_reads, -d/--database_dir

[liaoherui]

Hi, thanks for using VirStrain!

Currently, the -v parameter is only supported by virstrain -v and virstrain_build -v.

[Rohit-Satyam]

Even that doesn't work. Tried that too 🥹

[liaoherui]

Oh, sorry, after testing by myself, I just realized that this parameter is only updated in the GitHub version, not in the Bioconda version. I’ve revised the README to clarify this.

Well, if you’d like to check the version number, you can use the following command:: conda list |grep 'virstrain'