diff --git a/c/nucleotide-count/GNUmakefile b/c/nucleotide-count/GNUmakefile new file mode 100644 index 0000000..ec085d0 --- /dev/null +++ b/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 diff --git a/c/nucleotide-count/README.md b/c/nucleotide-count/README.md new file mode 100644 index 0000000..eef8d96 --- /dev/null +++ b/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 diff --git a/c/nucleotide-count/makefile b/c/nucleotide-count/makefile new file mode 100644 index 0000000..f34535a --- /dev/null +++ b/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) diff --git a/c/nucleotide-count/src/nucleotide_count.c b/c/nucleotide-count/src/nucleotide_count.c new file mode 100644 index 0000000..992bb7d --- /dev/null +++ b/c/nucleotide-count/src/nucleotide_count.c @@ -0,0 +1,68 @@ +#include +#include +#include +#include +#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 +#include +#endif +#ifdef TESTALL +#undef TEST_IGNORE +#define TEST_IGNORE() {} +#endif + +#endif diff --git a/c/rna-transcription/GNUmakefile b/c/rna-transcription/GNUmakefile new file mode 100644 index 0000000..ec085d0 --- /dev/null +++ b/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 diff --git a/c/rna-transcription/README.md b/c/rna-transcription/README.md new file mode 100644 index 0000000..bf475f1 --- /dev/null +++ b/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 diff --git a/c/rna-transcription/makefile b/c/rna-transcription/makefile new file mode 100644 index 0000000..f34535a --- /dev/null +++ b/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) diff --git a/c/rna-transcription/src/rna_transcription.c b/c/rna-transcription/src/rna_transcription.c new file mode 100644 index 0000000..dd50604 --- /dev/null +++ b/c/rna-transcription/src/rna_transcription.c @@ -0,0 +1,37 @@ +#include +#include +#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 +#include +#endif +#ifdef TESTALL +#undef TEST_IGNORE +#define TEST_IGNORE() {} +#endif + +#endif