New command: obi ecopcr

src/libecoPCR/ecodna.c

@@ -0,0 +1,156 @@
+#include <string.h>
+#include "ecoPCR.h"
+
+/*
+ * @doc: DNA alphabet (IUPAC)
+ */
+#define LX_BIO_DNA_ALPHA   "ABCDEFGHIJKLMNOPQRSTUVWXYZ#![]"
+
+/*
+ * @doc: complementary DNA alphabet (IUPAC)
+ */
+#define LX_BIO_CDNA_ALPHA  "TVGHEFCDIJMLKNOPQYSAABWXRZ#!]["
+
+
+static char sNuc[]     = LX_BIO_DNA_ALPHA;
+static char sAnuc[]    = LX_BIO_CDNA_ALPHA;
+
+static char LXBioBaseComplement(char nucAc);
+static char *LXBioSeqComplement(char *nucAcSeq);
+static char *reverseSequence(char *str,char isPattern);
+
+ 
+/* ---------------------------- */
+
+char LXBioBaseComplement(char nucAc)
+{
+    char *c;
+
+    if ((c = strchr(sNuc, nucAc)))
+        return sAnuc[(c - sNuc)];
+    else
+        return nucAc;
+}
+
+/* ---------------------------- */
+
+char *LXBioSeqComplement(char *nucAcSeq)
+{
+    char *s;
+
+    for (s = nucAcSeq ; *s ; s++)
+        *s = LXBioBaseComplement(*s);
+
+    return nucAcSeq;
+}
+
+
+char *reverseSequence(char *str,char isPattern)
+{
+        char *sb, *se, c;
+
+        if (! str)
+            return str;
+            
+        sb = str;
+        se = str + strlen(str) - 1;
+
+        while(sb <= se) {
+           c    = *sb;
+          *sb++ = *se;
+          *se-- = c;
+        }
+
+		sb = str;
+		se = str + strlen(str) - 1;
+		
+		if (isPattern)
+			for (;sb < se; sb++)
+			{
+				if (*sb=='#')
+				{
+					if (((se - sb) > 2) && (*(sb+2)=='!'))
+					{
+						*sb='!';
+						sb+=2;
+						*sb='#';
+					}
+					else
+					{
+						*sb=*(sb+1);
+						sb++;
+						*sb='#';
+					}
+				}
+				else if (*sb=='!')
+					{
+						*sb=*(sb-1);
+						*(sb-1)='!';
+					}
+			}
+
+        return str;
+}
+
+char *ecoComplementPattern(char *nucAcSeq)
+{
+    return reverseSequence(LXBioSeqComplement(nucAcSeq),1);
+}
+
+char *ecoComplementSequence(char *nucAcSeq)
+{
+    return reverseSequence(LXBioSeqComplement(nucAcSeq),0);
+}
+
+
+char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end)
+/*
+   extract subsequence from nucAcSeq [begin,end[
+*/
+{
+	static char *buffer  = NULL;
+	static int32_t buffSize= 0;
+	int32_t length;
+	
+	if (begin < end)
+	{
+		length = end - begin;
+		
+		if (length >= buffSize)
+		{
+			buffSize = length+1;
+			if (buffer)
+				buffer=ECOREALLOC(buffer,buffSize,
+						   	      "Error in reallocating sub sequence buffer");
+			else
+				buffer=ECOMALLOC(buffSize,
+				          		 "Error in allocating sub sequence buffer");
+				
+		}
+		
+		strncpy(buffer,nucAcSeq + begin,length);
+		buffer[length]=0;
+	}
+	else
+	{
+		length = end + strlen(nucAcSeq) - begin;
+		
+		if (length >= buffSize)
+		{
+			buffSize = length+1;
+			if (buffer)
+				buffer=ECOREALLOC(buffer,buffSize,
+						   	      "Error in reallocating sub sequence buffer");
+			else
+				buffer=ECOMALLOC(buffSize,
+				          		 "Error in allocating sub sequence buffer");
+				
+		}
+		strncpy(buffer,nucAcSeq+begin,length - end);
+		strncpy(buffer+(length-end),nucAcSeq ,end);
+		buffer[length]=0;
+	}
+	
+	return buffer;
+}
+