Rosalind Command Line CLI.hs
Run with
❯ cabal run rosalind-cli -- --help
Up to date
Rosalind CLI
Usage: rosalind-cli COMMAND
Runs Rosalind problems and commands
Available options:
-h,--help Show this help text
Available commands:
server server commands
problem run problem
solver run solver
❯ cabal run rosalind-cli -- problem --help
Usage: rosalind-cli problem COMMAND
run problem
Available options:
-h,--help Show this help text
Problem commands:
hamm Execute problem hamm
rna Execute problem rna
revc Execute problem revc
revc2 Execute problem revc
prot Execute problem prot
tran Execute problem tran
frmt Execute problem frmt
orf Execute problem orf
cons Execute problem cons
An example help for a problem command
❯ cabal run rosalind-cli -- problem --help hamm
Usage: rosalind-cli problem hamm [(-e|--example) | (-i|--input FILE)]
[-o|--output-dir OUTPUT_DIR]
Execute problem hamm
Available options:
-e,--example Override input FILE option to use the example input
for the problem
-i,--input FILE File input (default: "input.txt")
-o,--output-dir OUTPUT_DIR
Write output to FILE with path (default: "./out.txt")
An example of running a problem.
❯ cabal run rosalind-cli -- problem hamm
Dataset option: SpecifiedInputFile "input.txt"
Evaluating hamm -> input.txt
Done -> ./out.txt
An example of running a solver.
❯ cabal run rosalind-cli -- solver --help
Usage: rosalind-cli solver COMMAND
run solver
Available options:
-h,--help Show this help text
Available commands:
dna2rna Convert DNA to RNA
dnas2rna Convert multiple DNA to RNA
revc Calculate the reverse complement of DNA
hamm Calculate the hamm of 2 DNA sequences
❯ cabal run rosalind-cli -- solver --help dna2rna
Usage: rosalind-cli solver dna2rna (-d|--dnaInput DNA)
Convert DNA to RNA
Available options:
-d,--dnaInput DNA DNA input
❯ cabal run rosalind-cli -- solver dna2rna -d ACGTAACCGGTT
DNA: ACGTAACCGGTT
RNA: ACGUAACCGGUU
An example running the server
❯ cabal run rosalind-cli -- run
Up to date
runserver
Listening on port 8081
Converted AAGCT to AGCTT
127.0.0.1 - - [19/Jan/2022:16:13:42 +0000] "GET /revc/AAGCT HTTP/1.1" 200 -
❯ curl http://localhost:8081/revc/AAGCT
"AGCTT"%
Run with
cabal test all --test-show-details=direct
Running 1 test suites...
Test suite Rosalind-test: RUNNING...
test/Driver.hs
Unit tests Rosalind Rna Hedgehog
test Motif tripping: OK (0.38s)
✓ test Motif tripping passed 100 tests.
Unit tests Rosalind Rna Hedgehog
test Fast tripping: OK (0.02s)
✓ test Fast tripping passed 100 tests.
Tests Rosalind
Unit tests Rosalind Revc
check sample result: OK
✓ check sample result passed 100 tests.
check revc applied twice is the same as original : OK
✓ check revc applied twice is the same as original passed 100 tests.
check revc by checking every conversion : OK
✓ check revc by checking every conversion passed 100 tests.
Unit tests Rosalind Rna Hedgehog
check sample result: OK
✓ check sample result passed 100 tests.
tran file expected : OK
Tests Rosalind
Unit tests Rosalind hamm
hamm : OK
check hamm with given mutations: OK
+++ OK, passed 100 tests.
Unit tests Rosalind Rna Hedgehog
check sample result: OK
✓ check sample result passed 100 tests.
gc file : OK
Unit tests Rosalind hamm (Hedgehog)
check sample result: OK
✓ check sample result passed 100 tests.
check hamm with given mutations: OK (0.04s)
✓ check hamm with given mutations passed 100 tests.
check hamm with same =0 mutations: OK
✓ check hamm with same =0 mutations passed 100 tests.
check hamm mutations in every base has mutation count of length : OK
✓ check hamm mutations in every base has mutation count of length passed 100 tests.
hamm file : OK
hamm file expected : OK
Unit tests Rosalind Rna Hedgehog
check sample result: OK
✓ check sample result passed 100 tests.
check if a T exists in the dna strand a U exists in the result: OK
✓ check if a T exists in the dna strand a U exists in the result passed 100 tests.
check each dnabase is correctly converted to rna: OK
✓ check each dnabase is correctly converted to rna passed 100 tests.
Unit tests Rosalind hamm (Hedgehog)
check sample result: OK
✓ check sample result passed 100 tests.
prot file expected : OK
Unit tests Rosalind Orf (Hedgehog)
check sample result: OK
✓ check sample result passed 100 tests.
Unit tests Rosalind Subs (Hedgehog)
check sample result: OK
✓ check sample result passed 100 tests.
Tests Rosalind
Unit tests Rosalind Recv QC
revc : OK
check sample result: OK
+++ OK, passed 1 test.
check revc applied twice is the same as original : OK
+++ OK, passed 100 tests.
check revc' applied twice is the same as original : OK
+++ OK, passed 100 tests.
All 28 tests passed (0.49s)
Test suite Rosalind-test: PASS
Test suite logged to:
1 of 1 test suites (1 of 1 test cases) passed.