Add nucleotide-count exercise

config.json

@@ -142,6 +142,18 @@
           "filtering"
         ]
       },
+      {
+        "uuid": "2ef7f926-e6f1-4828-94ed-5aee5930987a",
+        "slug": "nucleotide-count",
+        "name": "Nucleotide Count",
+        "practices": [],
+        "prerequisites": [],
+        "difficulty": 3,
+        "topics": [
+          "arrays",
+          "strings"
+        ]
+      },
       {
         "slug": "rotational-cipher",
         "name": "Rotational Cipher",

exercises/practice/nucleotide-count/.docs/instructions.md

@@ -0,0 +1,23 @@
+# Instructions
+
+Each of us inherits from our biological parents a set of chemical instructions known as DNA that influence how our bodies are constructed.
+All known life depends on DNA!
+
+> Note: You do not need to understand anything about nucleotides or DNA to complete this exercise.
+
+DNA is a long chain of other chemicals and the most important are the four nucleotides, adenine, cytosine, guanine and thymine.
+A single DNA chain can contain billions of these four nucleotides and the order in which they occur is important!
+We call the order of these nucleotides in a bit of DNA a "DNA sequence".
+
+We represent a DNA sequence as an ordered collection of these four nucleotides and a common way to do that is with a string of characters such as "ATTACG" for a DNA sequence of 6 nucleotides.
+'A' for adenine, 'C' for cytosine, 'G' for guanine, and 'T' for thymine.
+
+Given a string representing a DNA sequence, count how many of each nucleotide is present.
+If the string contains characters that aren't A, C, G, or T then it is invalid and you should signal an error.
+
+For example:
+
+```text
+"GATTACA" -> 'A': 3, 'C': 1, 'G': 1, 'T': 2
+"INVALID" -> error
+```

exercises/practice/nucleotide-count/.gitignore

@@ -0,0 +1,2 @@
+*.o
+tests

exercises/practice/nucleotide-count/.meta/config.json

@@ -0,0 +1,19 @@
+{
+  "authors": [
+    "keiravillekode"
+  ],
+  "files": {
+    "solution": [
+      "nucleotide_count.asm"
+    ],
+    "test": [
+      "nucleotide_count_test.c"
+    ],
+    "example": [
+      ".meta/example.asm"
+    ]
+  },
+  "blurb": "Given a DNA string, compute how many times each nucleotide occurs in the string.",
+  "source": "The Calculating DNA Nucleotides_problem at Rosalind",
+  "source_url": "https://rosalind.info/problems/dna/"
+}

exercises/practice/nucleotide-count/.meta/example.asm

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+section .text
+global nucleotide_counts
+
+; rdi - address of strand string
+; rsi - address of counts array
+; cl - current character
+; r8 - adenine count
+; r9 - cytosine count
+; r10 - guanine count
+; r11 - thymine count
+nucleotide_counts:
+    xor r8, r8                ; Current adenine count is 0
+    xor r9, r9                ; Current cytosine count is 0
+    xor r10, r10              ; Current guanine count is 0
+    xor r11, r11              ; Current thymine count is 0
+    jmp .read
+
+.adenine:
+    inc r8
+    jmp .read
+
+.cytosine:
+    inc r9
+    jmp .read
+
+.guanine:
+    inc r10
+    jmp .read
+
+.thymine:
+    inc r11
+
+.read:
+    mov cl, byte [rdi]        ; Load strand character
+    inc rdi
+    cmp cl, 'A'
+    je .adenine
+    cmp cl, 'C'
+    je .cytosine
+    cmp cl, 'G'
+    je .guanine
+    cmp cl, 'T'
+    je .thymine
+    cmp cl, 0
+    je .report                ; Check if we have reached end of string
+    mov r8, -1
+    mov r9, -1
+    mov r10, -1
+    mov r11, -1
+
+.report:
+    mov qword [rsi], r8       ; Report adenine count
+    mov qword [rsi + 4], r9   ; Report cytosine count
+    mov qword [rsi + 8], r10  ; Report guanine count
+    mov qword [rsi + 12], r11 ; Report thymine count
+    ret
+
+%ifidn __OUTPUT_FORMAT__,elf64
+section .note.GNU-stack noalloc noexec nowrite progbits
+%endif

exercises/practice/nucleotide-count/.meta/tests.toml

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+# This is an auto-generated file.
+#
+# Regenerating this file via `configlet sync` will:
+# - Recreate every `description` key/value pair
+# - Recreate every `reimplements` key/value pair, where they exist in problem-specifications
+# - Remove any `include = true` key/value pair (an omitted `include` key implies inclusion)
+# - Preserve any other key/value pair
+#
+# As user-added comments (using the # character) will be removed when this file
+# is regenerated, comments can be added via a `comment` key.
+
+[3e5c30a8-87e2-4845-a815-a49671ade970]
+description = "empty strand"
+
+[a0ea42a6-06d9-4ac6-828c-7ccaccf98fec]
+description = "can count one nucleotide in single-character input"
+
+[eca0d565-ed8c-43e7-9033-6cefbf5115b5]
+description = "strand with repeated nucleotide"
+
+[40a45eac-c83f-4740-901a-20b22d15a39f]
+description = "strand with multiple nucleotides"
+
+[b4c47851-ee9e-4b0a-be70-a86e343bd851]
+description = "strand with invalid nucleotides"

exercises/practice/nucleotide-count/Makefile

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+AS = nasm
+
+CFLAGS = -g -Wall -Wextra -pedantic -Werror
+LDFLAGS =
+ASFLAGS = -g -F dwarf -Werror
+
+ifeq ($(shell uname -s),Darwin)
+ifeq ($(shell sysctl -n hw.optional.arm64 2>/dev/null),1)
+	ALL_CFLAGS = -target x86_64-apple-darwin
+endif
+	ALL_LDFLAGS = -Wl,-pie -Wl,-fatal_warnings
+	ALL_ASFLAGS = -f macho64 --prefix _
+else
+	ALL_LDFLAGS = -pie -Wl,--fatal-warnings
+	ALL_ASFLAGS = -f elf64
+endif
+
+ALL_CFLAGS += -std=c99 -fPIE -m64 $(CFLAGS)
+ALL_LDFLAGS += $(LDFLAGS)
+ALL_ASFLAGS += $(ASFLAGS)
+
+C_OBJS = $(patsubst %.c,%.o,$(wildcard *.c))
+AS_OBJS = $(patsubst %.asm,%.o,$(wildcard *.asm))
+ALL_OBJS = $(filter-out example.o,$(C_OBJS) $(AS_OBJS) vendor/unity.o)
+
+CC_CMD = $(CC) $(ALL_CFLAGS) -c -o $@ $<
+
+all: tests
+	@./$<
+
+tests: $(ALL_OBJS)
+	@$(CC) $(ALL_CFLAGS) $(ALL_LDFLAGS) -o $@ $(ALL_OBJS)
+
+%.o: %.asm
+	@$(AS) $(ALL_ASFLAGS) -o $@ $<
+
+%.o: %.c
+	@$(CC_CMD)
+
+vendor/unity.o: vendor/unity.c vendor/unity.h vendor/unity_internals.h
+	@$(CC_CMD)
+
+clean:
+	@rm -f *.o vendor/*.o tests
+
+.PHONY: all clean

exercises/practice/nucleotide-count/nucleotide_count.asm

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+section .text
+global nucleotide_counts
+nucleotide_counts:
+    ; Provide your implementation here
+    ret
+
+%ifidn __OUTPUT_FORMAT__,elf64
+section .note.GNU-stack noalloc noexec nowrite progbits
+%endif

exercises/practice/nucleotide-count/nucleotide_count_test.c

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+// Version: 1.0.0
+
+#include "vendor/unity.h"
+
+enum nucleotide {
+    ADENINE,
+    CYTOSINE,
+    GUANINE,
+    THYMINE
+};
+
+extern void nucleotide_counts(const char* strand, int* counts);
+
+void setUp(void) {
+}
+
+void tearDown(void) {
+}
+
+
+void test_empty_strand(void) {
+    int counts[4];
+
+    nucleotide_counts("", counts);
+    TEST_ASSERT_EQUAL_INT(0, counts[ADENINE]);
+    TEST_ASSERT_EQUAL_INT(0, counts[CYTOSINE]);
+    TEST_ASSERT_EQUAL_INT(0, counts[GUANINE]);
+    TEST_ASSERT_EQUAL_INT(0, counts[THYMINE]);
+}
+
+void test_can_count_one_nucleotide_in_single_character_input(void) {
+    TEST_IGNORE();
+    int counts[4];
+
+    nucleotide_counts("G", counts);
+    TEST_ASSERT_EQUAL_INT(0, counts[ADENINE]);
+    TEST_ASSERT_EQUAL_INT(0, counts[CYTOSINE]);
+    TEST_ASSERT_EQUAL_INT(1, counts[GUANINE]);
+    TEST_ASSERT_EQUAL_INT(0, counts[THYMINE]);
+}
+
+void test_strand_with_repeated_nucleotide(void) {
+    TEST_IGNORE();
+    int counts[4];
+
+    nucleotide_counts("GGGGGGG", counts);
+    TEST_ASSERT_EQUAL_INT(0, counts[ADENINE]);
+    TEST_ASSERT_EQUAL_INT(0, counts[CYTOSINE]);
+    TEST_ASSERT_EQUAL_INT(7, counts[GUANINE]);
+    TEST_ASSERT_EQUAL_INT(0, counts[THYMINE]);
+}
+
+void test_strand_with_multiple_nucleotides(void) {
+    TEST_IGNORE();
+    int counts[4];
+
+    nucleotide_counts("AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC", counts);
+    TEST_ASSERT_EQUAL_INT(20, counts[ADENINE]);
+    TEST_ASSERT_EQUAL_INT(12, counts[CYTOSINE]);
+    TEST_ASSERT_EQUAL_INT(17, counts[GUANINE]);
+    TEST_ASSERT_EQUAL_INT(21, counts[THYMINE]);
+}
+
+void test_strand_with_invalid_nucleotides(void) {
+    TEST_IGNORE();
+    int counts[4];
+
+    nucleotide_counts("AGXXACT", counts);
+    TEST_ASSERT_EQUAL_INT(-1, counts[ADENINE]);
+    TEST_ASSERT_EQUAL_INT(-1, counts[CYTOSINE]);
+    TEST_ASSERT_EQUAL_INT(-1, counts[GUANINE]);
+    TEST_ASSERT_EQUAL_INT(-1, counts[THYMINE]);
+}
+
+int main(void) {
+    UNITY_BEGIN();
+    RUN_TEST(test_empty_strand);
+    RUN_TEST(test_can_count_one_nucleotide_in_single_character_input);
+    RUN_TEST(test_strand_with_repeated_nucleotide);
+    RUN_TEST(test_strand_with_multiple_nucleotides);
+    RUN_TEST(test_strand_with_invalid_nucleotides);
+    return UNITY_END();
+}