Comments (2)
ChaochihL
commented on August 16, 2024
When running the following code:
./BAD_Mutations.py -v DEBUG \
> setup \
> -b ./BAD_Mutations_Data \
> -d ./BAD_Mutations_Deps \
> -t 'Hordeum_vulgare' \
> -e 0.05 \
> -m 0.2 \
> -c BAD_Mutations_Config.txt 2> Setup.logSetup.log does not form correctly:
After running less Setup.log to view the file, here is the contents:
usage: BAD_Mutations.py setup [-h] [--list-species] [--config CONFIG]
[--base BASE] [--deps-dir DEPS_DIR]
[--target TARGET] [--evalue EVALUE]
[-m MIN_SEQS] [--codon]
BAD_Mutations.py setup: error: argument -m/--min-seqs: invalid int value: '0.2'
from bad_mutations.
TomJKono
commented on August 16, 2024
Ah yes, need to change the missingness threshold to an integer value, since it is a number of sequences rather than a proportion of sequences.
from bad_mutations.
Related Issues (20)
- Skip sequences with ambiguous nucleotides HOT 1
- Off-by-one error in HyPhy script? HOT 1
- Add command for dowloading in Mannual HOT 1
- Fail gracefully when no BLAST hits HOT 1
- makeblastdb HOT 1
- No output written to output dir with silent error HOT 3
- Fail nicely when "required" arguments are not specified
- Add Filtering of Species Databases
- Sanitize sequence names before alignment HOT 1
- Add Logistic Regression to Prediction
- Doesn't find HyPhy properly
- BAD_Mutations Incorrectly Back-translates from PASTA HOT 1
- The logistic P value is only valid for the 41 genomes
- Fetch XML ParseError HOT 5
- Multiple Trees in File HOT 6
- Fetch only the latest CDS for each species
- The XML document has moved HOT 2
- Compile Bug - Won't work on test data HOT 5
- Compile - include SNP names? HOT 1
- BUG: HOT 3
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