A kmer counter for directories of FASTA files.
Implemented in Rust as an exercise.
-
Clone repository and build
git clone https://github.com/yamad/kmer-count cd kmer-count cargo build --release -
Run, e.g.
target/release/kmer -vv -k 4 fasta-directory output-directory -
For help and usage:
kmer --help
Run:
cargo test
Current results:
running 11 tests
test tests::test_check_bases_success ... ok
test tests::test_check_bases_bad_base ... ok
test tests::test_count_kmers ... ok
test tests::test_find_files_dir_is_file - should panic ... ok
test tests::test_kmer_0 ... ok
test tests::test_kmer_empty_string ... ok
test tests::test_kmer_k_too_big ... ok
test tests::test_kmers_fn_basic ... ok
test tests::test_kmers_vec_helper_demo ... ok
test tests::test_output_path_from_input ... ok
test tests::test_find_files ... ok
test result: ok. 11 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
kmer count 0.1.0
Count frequency of all kmers for all fasta files in directory
USAGE:
kmer [FLAGS] [OPTIONS] -k <k> [--] [ARGS]
FLAGS:
-h, --help
Prints help information
-q, --quiet
Pass many times for less log output
-V, --version
Prints version information
-v, --verbose
Pass many times for more log output
By default, it'll only report errors. Passing `-v` one time also prints warnings, `-vv` enables info
logging, `-vvv` debug, and `-vvvv` trace.
OPTIONS:
-e, --extensions <extensions>...
input file extensions to find [default: fasta]
-k <k>
length of kmer
ARGS:
<directory>
input directory [default: .]
<output-root>
output directory root [default: ./output]