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