Olivar is a great tool, thanks for creating and maintaining it. I'm using it to design primers for Hep A. This is the command I am running:
olivar tiling \
output/4.olivar_reference/olivar-ref.olvr \
-o output/5.olivar_primers \
--max-amp-len 1200 \
--min-amp-len 1000 \
--seed 1995 \
--fp-prefix HAVSeq \
--rp-prefix HAVSeq \
--check-var
Successfully loaded reference file output/4.olivar_reference/olivar-ref.olvr
reference sequence length: 7478
design region: 16:7463
region length: 7448
number of PDR sets to be tested: 3115
Designing PDRs...
100%|>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>| 3115/3115 [01:19<00:00, 38.98it/s]
Finished in 79.921s
Best total risk: 1151.410
total amplicons: 10
covered region: 90:7217
coverage of reference sequence: 95.320%
Generating primer candidates...
0%| | 0/10 [00:00<?, ?it/s]ta
Traceback (most recent call last):
File "micromamba/bin/olivar", line 156, in <module>
tiling(
File "micromamba/lib/python3.10/site-packages/olivar/main.py", line 793, in tiling
all_plex_info_primer = get_primer(all_plex_info, config)
File "micromamba/lib/python3.10/site-packages/olivar/main.py", line 436, in get_primer
fP, fail = fP_generator.get(fP_design, fP_prefix, check_BLAST=check_BLAST, **fP_setting)
File "micromamba/lib/python3.10/site-packages/olivar/design.py", line 226, in get
primer_arr.append(basic.seq2arr(s))
File "micromamba/lib/python3.10/site-packages/olivar/basic.py", line 76, in seq2arr
seq_list = [dic[s] for s in list(seq_str)]
File "micromamba/lib/python3.10/site-packages/olivar/basic.py", line 76, in <listcomp>
seq_list = [dic[s] for s in list(seq_str)]
KeyError: 'H'
ct
gc
gg
ag
ta
ct
cc
gc
tg
tt
tt
gt
cg
cc
gc
cg
HAVSeqcgccgtttgcctaggcta
I am running on Linux Mint 21, with micromamba installing Olivar version 1.1.1. Also tested with the latest version 1.1.2, same issue.
Not a huge deal as the Olivar still runs, just need to manually rename the outputs.