Tb-profiler fasta_profile feature

[Ankitapal1995]

Hello, I have been using Tb-profiler from last 1 year for my research work. I am analysing AMR properties in M.tb using whole genome sequences in FASTA format. Till now I was using "fasta_profile" parameter to do all of my analysis but recently this features is replaced with "vcf_profile", now I am in big trouble as I am not able to use those fasta sequences for my analysis. If it is possible could you please give me your previous "fasta_profile" analysis code so that I can continue my analysis. Last but not the least, thank you so much for making such a great tool.

[jodyphelan]

Hi @Ankitapal1995

The fasta_profile function should still be available. Does it give an error if you try to run it?

[Ankitapal1995]

I am using TBProfiler version 2.3.0

[Ankitapal1995]

when i am using fasta_profile command:
tb-profiler fasta_profile 1733.5787.fna --dir test --csv

output error:
usage: tb-profiler [-h] {profile,vcf_profile,reprofile,reformat,load_library,update_tbdb,lineage,collate,version} ...
tb-profiler: error: invalid choice: 'fasta_profile' (choose from 'profile', 'vcf_profile', 'reprofile', 'reformat', 'load_library', 'update_tbdb', 'lineage', 'collate', 'version')

[jodyphelan]

I think this might be an older version of tb-profiler which has installed (I also can't see the create_db function which should be present). Sometimes conda will downgrade an installation to a previous version when you install something new due to clashes with dependancies. You can check the version with tb-profiler --version. If it is not the most recent I would recommend forcing the latest version with conda install tb-profiler=3.0.8.

[Ankitapal1995]

I installed 3.08 version. Now It has fasta_profile parameter and working properly. Thank you so much for solving my issue.

[jodyphelan]

Great no problem!

[Ankitapal1995]

/anaconda3/lib/python3.9/site-packages/tbprofiler/text.py script has an error in line number 119 of tb-profiler lastest version 4.0.3, just because of this, it is throwing an error while processing the result in csv format.
Please replace this below line in your script (line number : 119)

text_strings["med_dp"] = json_results["qc"]["median_coverage"]

with following line (by adding a comma between two keys)

text_strings["med_dp"] = json_results["qc"],["median_coverage"]

Regards,