New column type for DNA sequences. Only for those coded on 2 bits (only

'ATGCatgc') for now.

src/encode.c

@@ -0,0 +1,180 @@
+/****************************************************************************
+ * Encoding functions                                                       *
+ ****************************************************************************/
+
+/**
+ * @file encode.c
+ * @author Celine Mercier
+ * @date November 18th 2015
+ * @brief Functions encoding DNA sequences.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <math.h>
+
+#include "encode.h"
+#include "obiarray.h"
+#include "obidebug.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+// TODO: endianness problem?
+
+
+
+bool only_ATGC(char* seq)
+{
+	char* c = seq;
+
+	while (*c)
+	{
+		if (!((*c == 'A') || \
+			  (*c == 'T') || \
+			  (*c == 'G') || \
+			  (*c == 'C') || \
+			  (*c == 'a') || \
+			  (*c == 't') || \
+			  (*c == 'g') || \
+			  (*c == 'c')))
+		{
+			return 0;
+		}
+		else
+		{
+			c++;
+		}
+	}
+	return 1;
+}
+
+
+byte_t* encode_seq_on_2_bits(char* seq, int32_t length)		// TODO shift = 2
+{
+	byte_t*  seq_b;
+	uint8_t  shift;
+	int32_t  length_b;
+	int32_t   i;
+
+//	fprintf(stderr, "\n>>>>>>>>>>>>>>>>>>Encoding sequence %s", seq);
+
+	length_b = ceil((double) length / (double) 4.0);
+
+//	fprintf(stderr, "\nLength: %d", length_b);
+
+	seq_b = (byte_t*) malloc(length_b * sizeof(byte_t));
+
+	memset(seq_b, 0, length_b);
+
+	for (i=0; i<length; i++)
+	{
+		shift = 6 - 2*(i%4);
+//		fprintf(stderr, "\nshift: %u", shift);
+
+		switch (seq[i])
+		{
+		case 'a':
+		case 'A':
+			seq_b[i/4] |= NUC_A << shift;
+//			fprintf(stderr, "\nIn byte %d, writing A:", i/4);
+//			print_bits(seq_b, length_b);
+			break;
+		case 'c':
+		case 'C':
+			seq_b[i/4] |= NUC_C << shift;
+//			fprintf(stderr, "\nIn byte %d, writing C:", i/4);
+//			print_bits(seq_b, length_b);
+			break;
+		case 'g':
+		case 'G':
+			seq_b[i/4] |= NUC_G << shift;
+//			fprintf(stderr, "\nIn byte %d, writing G:", i/4);
+//			print_bits(seq_b, length_b);
+			break;
+		case 't':
+		case 'T':
+			seq_b[i/4] |= NUC_T << shift;
+//			fprintf(stderr, "\nIn byte %d, writing T:", i/4);
+//			print_bits(seq_b, length_b);
+			break;
+		default:
+			obidebug(1, "\nInvalid nucleotide base when encoding (not [atgcATGC])");
+			return NULL;
+		}
+	}
+
+//	fprintf(stderr, "\n>>>>>>>>>Encoded:");
+//	print_bits(seq_b, length_b);
+
+	return seq_b;
+}
+
+
+char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq)
+{
+	char*   seq;
+	int32_t  i;
+	uint8_t shift;
+	uint8_t mask;
+	uint8_t nuc;
+
+	seq = (char*) malloc((length_seq+1) * sizeof(char));
+
+	for (i=0; i<length_seq; i++)
+	{
+		shift = 6 - 2*(i % 4);
+		mask = NUC_MASK << shift;
+		nuc = (seq_b[i/4] & mask) >> shift;
+
+		switch (nuc)
+		{
+		case NUC_A:
+			seq[i] = 'a';
+			break;
+		case NUC_C:
+			seq[i] = 'c';
+			break;
+		case NUC_G:
+			seq[i] = 'g';
+			break;
+		case NUC_T:
+			seq[i] = 't';
+			break;
+		default:
+			obidebug(1, "\nInvalid nucleotide base when decoding");
+			return NULL;
+		}
+	}
+
+	seq[length_seq] = '\0';
+
+	return seq;
+}
+
+
+////////// FOR DEBUGGING ///////////
+
+// little endian
+void print_bits(void* ptr, int32_t size)
+{
+	uint8_t* b = (uint8_t*) ptr;
+	uint8_t byte;
+    int32_t i, j;
+
+    fprintf(stderr, "\n");
+    for (i=0;i<size;i++)
+    {
+        for (j=7;j>=0;j--)
+        {
+            byte = b[i] & (1<<j);
+            byte >>= j;
+            fprintf(stderr, "%u", byte);
+        }
+        fprintf(stderr, " ");
+    }
+    fprintf(stderr, "\n");
+}