Custom resistance probes

[arnoldbain]

Am trying to create custom resistance probes using this command: "mykrobe variants make-probes -t gene1.txt -g refe/H37Rv4.gbk refe/H37Rv.fasta > probes4.gene.fa" but i get the error below. What might be the issue?
[mykrobe 2021-10-31T15:59:00 WARNING] Could not connect to database. Continuing without using genetic backgrounds
/mnt/transient_data/conda/envs/mykrobe/lib/python3.6/site-packages/Bio/GenBank/Scanner.py:215: BiopythonParserWarning: Over indented /inference="protein feature?
BiopythonParserWarning,
/mnt/transient_data/conda/envs/mykrobe/lib/python3.6/site-packages/Bio/GenBank/init.py:1267: BiopythonParserWarning: Couldn't parse feature location: 'motif:PROSITE:PS00599"'
"Couldn't parse feature location: %r" % location_line
Traceback (most recent call last):
File "/mnt/transient_data/conda/envs/mykrobe/bin/mykrobe", line 11, in
sys.exit(main())
File "/mnt/transient_data/conda/envs/mykrobe/lib/python3.6/site-packages/mykrobe/cli.py", line 8, in main
args.func(parser, args)
File "/mnt/transient_data/conda/envs/mykrobe/lib/python3.6/site-packages/mykrobe/parser.py", line 53, in run_subtool
run(parser, args)
File "/mnt/transient_data/conda/envs/mykrobe/lib/python3.6/site-packages/mykrobe/cmds/makeprobes.py", line 70, in run
gene, mutation_string, protein_coding_var
File "/mnt/transient_data/conda/envs/mykrobe/lib/python3.6/site-packages/mykrobe/annotation/genes/models.py", line 180, in get_variant_names
ref, start, alt = split_var_name(mutation)
File "/mnt/transient_data/conda/envs/mykrobe/lib/python3.6/site-packages/mykrobe/utils.py", line 29, in split_var_name
items = re.match(r"([A-Z]+)([-0-9]+)([A-Z/]+)", name, re.I).groups()
AttributeError: 'NoneType' object has no attribute 'groups'

[iqbal-lab]

Cc @martinghunt

[martinghunt]

I'd guess that the file gene1.txt is not the right format. The error is being thrown when trying to read a line of that file. Example line:

ileS	D2E	PROT

The error because the second column is not in the expected format of <amino acid><number><amino acid>.

If that's not the reason, then could you please share the input files so I can debug?

[arnoldbain]

@martinghunt could it be the deletions? thx

gene1.txt

[martinghunt]

deletions should be ok. Definitely a * in the variant causes that error. If you want * to mean "any other amino acid other than the ref", then use X instead. If you want it to mean "stop codon", then sorry but the only way to do that in mykrobe is to provide the dna variants.

[mbhall88]

Stop codons are now supported with *. This is on the tip of master and will be in the next release.

[iqbal-lab]

Sorry, how do you encode a deletion with *?. Is this amino, nucleotide or both?

[mbhall88]

Typo sorry. I meant stop codons. I've edited the above comment.