C: nucleotide-count & rna-transcription

c/nucleotide-count/GNUmakefile

@@ -0,0 +1,51 @@
+# The original 'makefile' has a flaw:
+# 1) it overrides CFLAGS
+# 2) it does not pass extra "FLAGS" to $(CC) that could come from environment
+#
+# It means :
+# - we need to edit 'makefile' for different builds (DEBUG, etc...), which is
+#   not practical at all.
+# - Also, it does not allow to run all tests without editing the test source
+#   code.
+#
+# To use this makefile (GNU make only):
+#   "make": build with all predefined tests (without editing test source code)
+#   "make debugall": build with all predefined tests and debug code
+#   "make mem": perform memcheck with all tests enabled
+#   "make unit": build standalone (unit) test
+#   "make debug": build standalone test with debugging code
+#
+# Original 'makefile' targets can be used (test, memcheck, clean, ...)
+
+.PHONY: default all mem unit debug std debugtest
+
+default: all
+
+# default is to build with all predefined tests
+BUILD := teststall
+
+include makefile
+
+all: CFLAGS+=-DTESTALL
+all: clean test
+
+debugall: CFLAGS+=-DDEBUG
+debugall: all
+
+debugtest: CFLAGS+=-DDEBUG
+debugtest: test
+
+mem: CFLAGS+=-DTESTALL
+mem: clean memcheck
+
+unit: CFLAGS+=-DUNIT_TEST
+unit: clean std
+
+debug: CFLAGS+=-DUNIT_TEST -DDEBUG
+debug: clean std
+
+debugtest: CFLAGS+=-DDEBUG
+debugtest: test
+
+std: src/*.c src/*.h
+	$(CC) $(CFLAGS) src/*.c -o test.out

c/nucleotide-count/README.md

@@ -0,0 +1,59 @@
+# Nucleotide Count
+
+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:
+
+```
+"GATTACA" -> 'A': 3, 'C': 1, 'G': 1, 'T': 2
+"INVALID" -> error
+```
+
+## Getting Started
+
+Make sure you have read the "Guides" section of the
+[C track][c-track] on the Exercism site. This covers
+the basic information on setting up the development environment expected
+by the exercises.
+
+## Passing the Tests
+
+Get the first test compiling, linking and passing by following the [three
+rules of test-driven development][3-tdd-rules].
+
+The included makefile can be used to create and run the tests using the `test`
+task.
+
+    make test
+
+Create just the functions you need to satisfy any compiler errors and get the
+test to fail. Then write just enough code to get the test to pass. Once you've
+done that, move onto the next test.
+
+As you progress through the tests, take the time to refactor your
+implementation for readability and expressiveness and then go on to the next
+test.
+
+Try to use standard C99 facilities in preference to writing your own
+low-level algorithms or facilities by hand.
+
+## Source
+
+The Calculating DNA Nucleotides_problem at Rosalind [http://rosalind.info/problems/dna/](http://rosalind.info/problems/dna/)
+
+## Submitting Incomplete Solutions
+It's possible to submit an incomplete solution so you can see how others have completed the exercise.
+
+[c-track]: https://exercism.io/my/tracks/c
+[3-tdd-rules]: http://butunclebob.com/ArticleS.UncleBob.TheThreeRulesOfTdd

c/nucleotide-count/makefile

@@ -0,0 +1,37 @@
+### If you wish to use extra libraries (math.h for instance),
+### add their flags here (-lm in our case) in the "LIBS" variable.
+
+LIBS = -lm
+
+###
+CFLAGS  = -std=c99
+CFLAGS += -g
+CFLAGS += -Wall
+CFLAGS += -Wextra
+CFLAGS += -pedantic
+CFLAGS += -Werror
+CFLAGS += -Wmissing-declarations
+CFLAGS += -DUNITY_SUPPORT_64
+
+ASANFLAGS  = -fsanitize=address
+ASANFLAGS += -fno-common
+ASANFLAGS += -fno-omit-frame-pointer
+
+.PHONY: test
+test: tests.out
+	@./tests.out
+
+.PHONY: memcheck
+memcheck: test/*.c src/*.c src/*.h
+	@echo Compiling $@
+	@$(CC) $(ASANFLAGS) $(CFLAGS) src/*.c test/vendor/unity.c test/*.c -o memcheck.out $(LIBS)
+	@./memcheck.out
+	@echo "Memory check passed"
+
+.PHONY: clean
+clean:
+	rm -rf *.o *.out *.out.dSYM
+
+tests.out: test/*.c src/*.c src/*.h
+	@echo Compiling $@
+	@$(CC) $(CFLAGS) src/*.c test/vendor/unity.c test/*.c -o tests.out $(LIBS)

c/nucleotide-count/src/nucleotide_count.c

@@ -0,0 +1,68 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include "nucleotide_count.h"
+
+typedef unsigned char uchar;
+
+static int C[256] = {
+    ['A']=1, ['C']=2, ['G']=3, ['T']=4
+};
+
+/* not in C99: we implement asprintf */
+static char *asprintf(const char *fmt, ...)
+{
+    int n = 0;
+    char *p = NULL;
+    va_list ap;
+
+    va_start(ap, fmt);
+    n = vsnprintf(p, 0, fmt, ap);
+    va_end(ap);
+
+    if (n < 0 || !(p=malloc(n+1)))
+        return NULL;
+
+    va_start(ap, fmt);
+    n = vsnprintf(p, n+1, fmt, ap);
+    va_end(ap);
+    if (n < 0) {
+        free(p);
+        return NULL;
+    }
+
+    return p;
+}
+
+char *count(const char *dna)
+{
+    int res[4]={ 0 };
+
+    if (!dna)
+        return NULL;                              /* should it be "" ? */
+
+    for (const uchar *p=(uchar *)dna; *p; ++p) {
+        if (!C[*p])
+            return asprintf("");
+        res[C[*p]-1]++;
+    }
+    return asprintf("A:%d C:%d G:%d T:%d", res[0], res[1], res[2], res[3]);
+}
+
+/* See GNUmakefile below for explanation
+ * https://github.com/braoult/exercism/blob/master/c/templates/GNUmakefile
+ */
+#ifdef UNIT_TEST
+int main(int ac, char **av)
+{
+    int arg=1;
+    char *p;
+
+    //printf("%s: %s\n", asprintf("%d %d %d %d %s", (long)av-(long)av, ac, arg, 1000, "foobar"));
+    for (; arg<ac; ++arg) {
+        p=count(av[arg]);
+        printf("%s: [%s] len=%lu\n", av[arg], p, strlen(p));
+    }
+}
+#endif

c/nucleotide-count/src/nucleotide_count.h

@@ -0,0 +1,18 @@
+#ifndef _NUCLEOTIDE_COUNT_H
+#define _NUCLEOTIDE_COUNT_H
+
+char *count(const char *dna_strand);
+
+/* See GNUmakefile below for explanation
+ * https://github.com/braoult/exercism/blob/master/c/templates/GNUmakefile
+ */
+#if defined UNIT_TEST || defined DEBUG
+#include <stdio.h>
+#include <stdlib.h>
+#endif
+#ifdef  TESTALL
+#undef  TEST_IGNORE
+#define TEST_IGNORE() {}
+#endif
+
+#endif

c/rna-transcription/GNUmakefile

@@ -0,0 +1,51 @@
+# The original 'makefile' has a flaw:
+# 1) it overrides CFLAGS
+# 2) it does not pass extra "FLAGS" to $(CC) that could come from environment
+#
+# It means :
+# - we need to edit 'makefile' for different builds (DEBUG, etc...), which is
+#   not practical at all.
+# - Also, it does not allow to run all tests without editing the test source
+#   code.
+#
+# To use this makefile (GNU make only):
+#   "make": build with all predefined tests (without editing test source code)
+#   "make debugall": build with all predefined tests and debug code
+#   "make mem": perform memcheck with all tests enabled
+#   "make unit": build standalone (unit) test
+#   "make debug": build standalone test with debugging code
+#
+# Original 'makefile' targets can be used (test, memcheck, clean, ...)
+
+.PHONY: default all mem unit debug std debugtest
+
+default: all
+
+# default is to build with all predefined tests
+BUILD := teststall
+
+include makefile
+
+all: CFLAGS+=-DTESTALL
+all: clean test
+
+debugall: CFLAGS+=-DDEBUG
+debugall: all
+
+debugtest: CFLAGS+=-DDEBUG
+debugtest: test
+
+mem: CFLAGS+=-DTESTALL
+mem: clean memcheck
+
+unit: CFLAGS+=-DUNIT_TEST
+unit: clean std
+
+debug: CFLAGS+=-DUNIT_TEST -DDEBUG
+debug: clean std
+
+debugtest: CFLAGS+=-DDEBUG
+debugtest: test
+
+std: src/*.c src/*.h
+	$(CC) $(CFLAGS) src/*.c -o test.out

c/rna-transcription/README.md

@@ -0,0 +1,57 @@
+# RNA Transcription
+
+Given a DNA strand, return its RNA complement (per RNA transcription).
+
+Both DNA and RNA strands are a sequence of nucleotides.
+
+The four nucleotides found in DNA are adenine (**A**), cytosine (**C**),
+guanine (**G**) and thymine (**T**).
+
+The four nucleotides found in RNA are adenine (**A**), cytosine (**C**),
+guanine (**G**) and uracil (**U**).
+
+Given a DNA strand, its transcribed RNA strand is formed by replacing
+each nucleotide with its complement:
+
+* `G` -> `C`
+* `C` -> `G`
+* `T` -> `A`
+* `A` -> `U`
+
+## Getting Started
+
+Make sure you have read the "Guides" section of the
+[C track][c-track] on the Exercism site. This covers
+the basic information on setting up the development environment expected
+by the exercises.
+
+## Passing the Tests
+
+Get the first test compiling, linking and passing by following the [three
+rules of test-driven development][3-tdd-rules].
+
+The included makefile can be used to create and run the tests using the `test`
+task.
+
+    make test
+
+Create just the functions you need to satisfy any compiler errors and get the
+test to fail. Then write just enough code to get the test to pass. Once you've
+done that, move onto the next test.
+
+As you progress through the tests, take the time to refactor your
+implementation for readability and expressiveness and then go on to the next
+test.
+
+Try to use standard C99 facilities in preference to writing your own
+low-level algorithms or facilities by hand.
+
+## Source
+
+Hyperphysics [http://hyperphysics.phy-astr.gsu.edu/hbase/Organic/transcription.html](http://hyperphysics.phy-astr.gsu.edu/hbase/Organic/transcription.html)
+
+## Submitting Incomplete Solutions
+It's possible to submit an incomplete solution so you can see how others have completed the exercise.
+
+[c-track]: https://exercism.io/my/tracks/c
+[3-tdd-rules]: http://butunclebob.com/ArticleS.UncleBob.TheThreeRulesOfTdd

c/rna-transcription/makefile

@@ -0,0 +1,37 @@
+### If you wish to use extra libraries (math.h for instance),
+### add their flags here (-lm in our case) in the "LIBS" variable.
+
+LIBS = -lm
+
+###
+CFLAGS  = -std=c99
+CFLAGS += -g
+CFLAGS += -Wall
+CFLAGS += -Wextra
+CFLAGS += -pedantic
+CFLAGS += -Werror
+CFLAGS += -Wmissing-declarations
+CFLAGS += -DUNITY_SUPPORT_64
+
+ASANFLAGS  = -fsanitize=address
+ASANFLAGS += -fno-common
+ASANFLAGS += -fno-omit-frame-pointer
+
+.PHONY: test
+test: tests.out
+	@./tests.out
+
+.PHONY: memcheck
+memcheck: test/*.c src/*.c src/*.h
+	@echo Compiling $@
+	@$(CC) $(ASANFLAGS) $(CFLAGS) src/*.c test/vendor/unity.c test/*.c -o memcheck.out $(LIBS)
+	@./memcheck.out
+	@echo "Memory check passed"
+
+.PHONY: clean
+clean:
+	rm -rf *.o *.out *.out.dSYM
+
+tests.out: test/*.c src/*.c src/*.h
+	@echo Compiling $@
+	@$(CC) $(CFLAGS) src/*.c test/vendor/unity.c test/*.c -o tests.out $(LIBS)

c/rna-transcription/src/rna_transcription.c

@@ -0,0 +1,37 @@
+#include <malloc.h>
+#include <string.h>
+#include "rna_transcription.h"
+
+static char C[256]={
+    ['G']='C', ['C']='G', ['T']='A', ['A']='U',
+};
+
+char *to_rna(const char *dna)
+{
+    char *rna=malloc(strlen(dna+1)), *p;
+
+    if (rna) {
+        for (p=rna; *dna; p++, dna++) {
+            if (!(*p=C[(int)*dna])) {
+                free(rna);
+                return NULL;
+            }
+        }
+        *p=0;
+    }
+    return rna;
+}
+
+/* See GNUmakefile below for explanation
+ * https://github.com/braoult/exercism/blob/master/c/templates/GNUmakefile
+ */
+#ifdef UNIT_TEST
+int main(int ac, char **av)
+{
+    int arg=1;
+
+    for (; arg<ac; ++arg) {
+        printf("rna(%s)=%s\n", av[arg], to_rna(av[arg]));
+    }
+}
+#endif

c/rna-transcription/src/rna_transcription.h

@@ -0,0 +1,18 @@
+#ifndef RNA_TRANSCRIPTION_H
+#define RNA_TRANSCRIPTION_H
+
+char *to_rna(const char *dna);
+
+/* See GNUmakefile below for explanation
+ * https://github.com/braoult/exercism/blob/master/c/templates/GNUmakefile
+ */
+#if defined UNIT_TEST || defined DEBUG
+#include <stdio.h>
+#include <stdlib.h>
+#endif
+#ifdef  TESTALL
+#undef  TEST_IGNORE
+#define TEST_IGNORE() {}
+#endif
+
+#endif