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faf2snp.c
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faf2snp.c
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/* faf2snp.c Fist two sequence FASTA alignment checker:
* Mnemnic fa: fasta alignment, f2: first two (sequences) snp: because the alignments are usually of SNPs
* The rationale is that in pairwise comparisons, there are usually 3 sequences. The third being the reference
* provided out of comfort */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#if defined DBG || defined DBG2
#define GBUF 4
#else
#define GBUF 128
#endif
#define SSZ 2 /* CG count, first, AT count second, third are the anomalous characters */
#define HISTBUCKETSZ 10
#define HTCOLWIDTH 120
#define NAMESTRSZ 256 // an arbitrary size for a name.
#define F2 2 // F2 the first two sequences!
#define CONDREALLOC(x, b, c, a, t); \
if((x)==((b)-1)) { \
(b) += (c); \
(a)=realloc((a), (b)*sizeof(t)); \
memset((a)+(b)-(c), '\0', (c)*sizeof(t)); \
}
#define CONDREALLOC2(x, b, c, a1, a2, t); \
if((x)==((b)-1)) { \
(b) += (c); \
(a1)=realloc((a1), (b)*sizeof(t)); \
memset((a1)+(b)-(c), '\0', (c)*sizeof(t)); \
(a2)=realloc((a2), (b)*sizeof(t)); \
memset((a2)+(b)-(c), '\0', (c)*sizeof(t)); \
}
typedef struct /* onefa */
{
char *id;
char *sq;
unsigned idz, sqz;
} onefa;
typedef struct /* i_s; sequence index and number of symbols */
{
unsigned idx;
size_t sylen; /* this is the precise symbol length of the sequence */
size_t sy[SSZ]; /* used to hold counts of symbols */
float cgp;
unsigned ambano[2]; /* number of ambiguous symbols (first), then number of anomalous symbols */
char *id; // the ID name
char *sq; // the sequence itself
unsigned ibf, sbf; // buffers for ID and SQ strings
unsigned idz, sqz; // actual size of the ID and SQ strings. Is almost a duplication of sylen, can be removed if memory is a consideration.
} i_s; /* sequence index and number of symbols */
typedef struct /* ou uov */
{
unsigned *ua;
unsigned ub;
unsigned *oa;
} uo;
int f2uniquelens(i_s *sqi, unsigned numsq) /* first two sequences must have same length */
{
unsigned char new;
unsigned i, j;
unsigned ai=0;
uo uov;
uov.ub=GBUF;
uov.ua=calloc(uov.ub, sizeof(unsigned));
uov.oa=calloc(uov.ub, sizeof(unsigned));
// for(i=0; i<numsq;++i) {
for(i=0; i<F2;++i) {
new=1;
for(j=0; j<=ai;++j) {
if(uov.ua[j] == sqi[i].sylen) {
uov.oa[j]++;
new=0;
break;
}
}
if(new) {
CONDREALLOC2(ai, uov.ub, GBUF, uov.ua, uov.oa, unsigned);
uov.ua[ai]=sqi[i].sylen;
uov.oa[ai]++;
ai++;
}
}
if(ai != 1) {
printf("Sorry, this program is for alignments, all sequences must be the smae length\n");
exit (EXIT_FAILURE);
}
#if defined DBG || defined DBG2
printf("number of different sequence lengths: %u\n", ai);
printf("vals: ");
for(j=0; j<ai;++j)
printf("%5u ", uov.ua[j]);
printf("\n");
printf("ocs: ");
for(j=0; j<ai;++j)
printf("%5u ", uov.oa[j]);
printf("\n");
#endif
free(uov.ua);
free(uov.oa);
return sqi[0].sylen; // the first seuence length will do
}
void prtfa(onefa *fac)
{
printf(">");
printf("%s\n", fac->id);
printf("%s\n", fac->sq);
}
void prtfaf(onefa *fac, FILE *fp)
{
fprintf(fp, ">");
fprintf(fp, "%s\n", fac->id);
fprintf(fp, "%s\n", fac->sq);
}
void prtsq(i_s *sqisz, int sz)
{
int i;
for(i=0;i<sz;++i) {
printf("%s\n", sqisz[i].id);
printf("%s\n", sqisz[i].sq);
}
return;
}
void prtpwct(i_s *sqisz, int numsq, int *pwa, int nr, int nc, char *spapad)
{
int i, j, k, mi, mj;
printf("%*.*s", 12, 12, " ");
for(i=0;i<numsq;++i)
printf("%*.*s ", 12, 12, sqisz[i].id);
printf("\n");
mi=0;
for(i=0;i<nr;++i) {
mj=nc-i;
printf("%d) \"%*.*s\": ", i, 12, 12, sqisz[i].id);
for(k=0;k<i;++k)
printf("%s", spapad);
for(j=0;j<mj;++j) {
printf("%*d ", 12, pwa[mi+j]);
}
mi+=numsq-i-1; //multiplier for i
printf("\n");
}
}
void prtpwct2(i_s *sqisz, int numsq, int *pwa, int nr, int nc, char *spapad, char *htmlfn, int oneln)
{
int i, j, k, mi, mj;
FILE *fout=fopen(htmlfn, "w");
fprintf(fout, "<html>\n");
fprintf(fout, "\t<head>\n");
fprintf(fout, "\t\t<title>Pairwise SNP Distance Table</title>");
fprintf(fout, "\t\t<style>\n");
fprintf(fout, "\t\t\ttable\n");
fprintf(fout, "\t\t\t{\n");
// fprintf(fout, "\t\t\t\ttable-layout: fixed;\n");
// fprintf(fout, "\t\t\t\twidth: 100px;\n");
fprintf(fout, "\t\t\t\tborder: 1px solid black;\n");
fprintf(fout, "\t\t\t\tborder-collapse: collapse;\n");
fprintf(fout, "\t\t\t}\n");
fprintf(fout, "\t\t\ttd\n");
fprintf(fout, "\t\t\t{\n");
fprintf(fout, "\t\t\t\twidth: %dpx;\n", HTCOLWIDTH);
fprintf(fout, "\t\t\t\tborder: 1px solid black;\n");
fprintf(fout, "\t\t\t\ttext-align:right;\n");
fprintf(fout, "\t\t\t}\n");
fprintf(fout, "\t\t\tth\n");
fprintf(fout, "\t\t\t{\n");
fprintf(fout, "\t\t\t\twidth: %dpx;\n", HTCOLWIDTH);
fprintf(fout, "\t\t\t\tborder: 1px solid black;\n");
fprintf(fout, "\t\t\t\ttext-align:right;\n");
fprintf(fout, "\t\t\t}\n");
fprintf(fout, "\t\t</style>\n");
fprintf(fout, "\t</head>\n");
fprintf(fout, "\t<body>\n");
fprintf(fout, "\t\t<h3>Pairwise SNP Distance Table</h3>\n");
fprintf(fout, "\t\t<ul>\n");
fprintf(fout, "\t\t<li>In the first column of this table we have the list of sequence IDs</li>\n");
fprintf(fout, "\t\t<li>The names in the first row are those sequence which the names in the first column are measured against</li>\n");
fprintf(fout, "\t\t<li>A sequence is never measured against itself, only against the other sequences in the FASTA alignment file</li>\n");
fprintf(fout, "\t\t<li>A total of %d SNP sites were detected in the analysis (the being the uniform length of the sequences in the alignment)</li>", oneln);
fprintf(fout, "\t\t</ul>\n");
fprintf(fout, "\t\t<table>\n");
fprintf(fout, "\t\t\t<tr>");
fprintf(fout, "<td></td>"); // first col of first row empty
for(i=1;i<numsq;++i)
fprintf(fout, "<th>%s</th>", sqisz[i].id);
fprintf(fout, "</tr>\n");
mi=0;
for(i=0;i<nr;++i) {
fprintf(fout, "\t\t\t<tr>");
mj=nc-i;
fprintf(fout, "<td>%s</td>", sqisz[i].id);
for(k=0;k<i;++k)
fprintf(fout, "<td></td>");
for(j=0;j<mj;++j)
fprintf(fout, "<td>%d</td>", pwa[mi+j]);
mi+=numsq-i-1; //multiplier for i
fprintf(fout, "</tr>\n");
}
fprintf(fout, "\t\t</table>\n");
fprintf(fout, "\t</body>\n");
fprintf(fout, "</html>\n");
fclose(fout);
}
void prtfa2(onefa *fac)
{
int i;
printf("SQZ=%d:", fac->sqz);
for(i=0;i<3;++i)
putchar(fac->sq[i]);
printf("\n");
}
void prti_s(i_s *sqisz, int sz, float *mxcg, float *mncg)
{
int i;
char *sqgood;
*mxcg=.0;
*mncg=1.;
size_t tsz;
for(i=0;i<sz;++i) {
if(sqisz[i].ambano[1] != 0)
sqgood="AnoSQ";
else
sqgood="SQ";
tsz = sqisz[i].sy[0] + sqisz[i].sy[1];
sqisz[i].cgp=(float)sqisz[i].sy[0]/tsz;
if(sqisz[i].cgp>*mxcg)
*mxcg=sqisz[i].cgp;
if(sqisz[i].cgp<*mncg)
*mncg=sqisz[i].cgp;
printf("| %s#%i=TOT:%zu CG:%.4f ", sqgood, i, sqisz[i].sylen, sqisz[i].cgp);
}
printf("|\n");
}
void la_prti_s(i_s *sqisz, int sz, float *mxcg, float *mncg, char *titlestr) /* prints onto a beamer table, also calculates mx amnd min cg in passsing */
{
int i, cols=4;
printf("\\begin{frame}\n\t\\frametitle{%s}\n", titlestr);
char *h0[4]= {"Seq Idx", "Presence AmbSymbs", "Seq Length", "\\% CG Content"};
size_t tsz;
char *sqgood;
printf("\\begin{center}\n");
printf("\\small\n");
printf(" \\begin{tabular}{| l | r | r | r |}\n");
printf(" \\hline\n ");
for(i=0;i<cols;++i) {
printf("%s", h0[i]);
(i != cols-1)? printf(" & ") : printf(" \\\\\n");
}
printf(" \\hline\n");
for(i=0;i<sz;++i) {
if(sqisz[i].ambano[1] != 0)
sqgood="AnoSQ";
else
sqgood="SQ";
tsz = sqisz[i].sy[0] + sqisz[i].sy[1];
sqisz[i].cgp=(float)sqisz[i].sy[0]/tsz;
if(sqisz[i].cgp>*mxcg)
*mxcg=sqisz[i].cgp;
if(sqisz[i].cgp<*mncg)
*mncg=sqisz[i].cgp;
printf("%i & %s & %zu & %.3f \\\\\n", i, sqgood, sqisz[i].sylen, sqisz[i].cgp);
}
printf(" \\hline\n");
printf(" \\end{tabular}\n");
printf("\\end{center}\n");
printf("\\end{frame}\n\n");
return;
}
int main(int argc, char *argv[])
{
/* argument accounting: remember argc, the number of arguments, _includes_ the executable */
if(argc!=2) {
printf("faaln0, a program to calculate pairwise distances on a sequence alignment: input format is FASTA only\n");
printf("Error. Progam requires 1 argument: the fast input file name.\n");
exit(EXIT_FAILURE);
}
/* general declarations */
FILE *fin;
char *tp, *htmlfn=calloc(NAMESTRSZ, sizeof(char));
char IGLINE, begline;
size_t lidx, mxsylen, mnsylen;
unsigned mxamb, mnamb;
int i, j, k, c, sqidx;
int gbuf;
i_s *sqisz=NULL;
int whatint; // a number reflecting the type of symbol read
unsigned numsq, numano;
int ididx0=0;
int oneln, npwc, *pwa=NULL, nr, nc, mi, mj; // for the PWCT
char *spapad=" ";
// OK open the file
if(!(fin=fopen(argv[1], "r")) ) { /*should one check the extension of the fasta file ? */
printf("Error. Cannot open \"%s\" file.\n", argv[1]);
exit(EXIT_FAILURE);
}
tp=strrchr(argv[1], '.');
sprintf(htmlfn, "%.*s%s", (int)(tp-argv[1]), argv[1], ".html");
IGLINE=0, begline=1;
lidx=0, mxsylen=0, mnsylen=0XFFFFFFFFFFFFFFFF;
mxamb=0, mnamb=0xFFFFFFFF;
sqidx=-1; /* this is slightly dangerous, you need very much to know what you're doing */
gbuf=GBUF;
// sqisz=malloc(gbuf*sizeof(i_s));
sqisz=realloc(sqisz, gbuf*sizeof(i_s));
for(i=0;i<gbuf;++i) {
sqisz[i].ibf=GBUF;
sqisz[i].sbf=GBUF;
sqisz[i].id=calloc(sqisz[i].ibf, sizeof(char));
sqisz[i].sq=calloc(sqisz[i].sbf, sizeof(char));
}
for(i=gbuf-GBUF;i<gbuf;++i) {
sqisz[i].ambano[0]=0;
sqisz[i].ambano[1]=0;
}
whatint=0; /* needs explanation */
ididx0=0;
while( ( (c = fgetc(fin)) != EOF) ) {
if(c =='\n') {
IGLINE=0;
begline=1;
lidx++;
} else if( (begline==1) & (c == '>') ) { /* this condition catches the beginning of a new sequence, and uses it to prepare the nextsequence.*/
IGLINE =1;
begline=0;
if(sqidx>=0) { /* chancing my arm here ... operating on the past sequence */
if(sqisz[sqidx].sylen > mxsylen)
mxsylen = sqisz[sqidx].sylen;
if(sqisz[sqidx].sylen < mnsylen)
mnsylen = sqisz[sqidx].sylen;
if(sqisz[sqidx].ambano[0] > mxamb)
mxamb = sqisz[sqidx].ambano[0];
if(sqisz[sqidx].ambano[0] < mnamb)
mnamb = sqisz[sqidx].ambano[0];
CONDREALLOC(ididx0, sqisz[sqidx].ibf, GBUF, sqisz[sqidx].id, char);
sqisz[sqidx].id[ididx0]='\0';
CONDREALLOC(sqisz[sqidx].sylen, sqisz[sqidx].sbf, GBUF, sqisz[sqidx].sq, char);
sqisz[sqidx].sq[sqisz[sqidx].sylen]='\0';
sqisz[sqidx].idz=1+ididx0;
sqisz[sqidx].sqz=1+sqisz[sqidx].sylen;
}
sqidx++;
if(sqidx==gbuf) {
gbuf+=GBUF;
sqisz=realloc(sqisz, gbuf*sizeof(i_s));
for(i=gbuf-GBUF;i<gbuf;++i) {
sqisz[i].ibf=GBUF;
sqisz[i].sbf=GBUF;
sqisz[i].id=calloc(sqisz[i].ibf, sizeof(char));
sqisz[i].sq=calloc(sqisz[i].sbf, sizeof(char));
}
}
sqisz[sqidx].idx=sqidx;
/* resetting stuff */
sqisz[sqidx].sylen=0;
ididx0=0;
for(i=0;i<SSZ;++i)
sqisz[sqidx].sy[i]=0;
for(i=0;i<2;++i)
sqisz[sqidx].ambano[i]=0;
} else if (IGLINE==1) {
CONDREALLOC(ididx0, sqisz[sqidx].ibf, GBUF, sqisz[sqidx].id, char);
sqisz[sqidx].id[ididx0++]=c;
} else if (IGLINE==0) {
CONDREALLOC(sqisz[sqidx].sylen, sqisz[sqidx].sbf, GBUF, sqisz[sqidx].sq, char);
sqisz[sqidx].sq[sqisz[sqidx].sylen]=c;
sqisz[sqidx].sylen++;
switch(c) {
case 'A': case 'a':
whatint=1; break;
case 'C': case 'c':
whatint=2; break;
case 'G': case 'g':
whatint=3; break;
case 'T': case 't':
whatint=4; break;
case 'R': case 'r':
whatint=5; break;
case 'Y': case 'y':
whatint=6; break;
case 'K': case 'k': /* the ketos */
whatint=7; break;
case 'M': case 'm': /* the aminoids */
whatint=8; break;
case 'S': case 's':
whatint=9; break;
case 'W': case 'w':
whatint=10; break;
case 'B': case 'b':
whatint=11; break;
case 'D': case 'd':
whatint=12; break;
case 'H': case 'h':
whatint=13; break;
case 'V': case 'v':
whatint=14; break;
case 'N': case 'n':
whatint=15; break;
case '-':
whatint=16; break;
default:
whatint=17; /* unknown this means your fasta file is naff. */
}
}
if( (whatint == 2) || (whatint == 3) ) {
sqisz[sqidx].sy[0]++;
sqisz[sqidx].ambano[1]++;
} else if (whatint < 5) {
sqisz[sqidx].sy[1]++;
sqisz[sqidx].ambano[1]++;
} else
sqisz[sqidx].ambano[0]++;
}
fclose(fin);
/* postprocessing on the final sequence */
if(sqisz[sqidx].sylen > mxsylen)
mxsylen = sqisz[sqidx].sylen;
if(sqisz[sqidx].sylen < mnsylen)
mnsylen = sqisz[sqidx].sylen;
if(sqisz[sqidx].ambano[0] > mxamb)
mxamb = sqisz[sqidx].ambano[0];
if(sqisz[sqidx].ambano[0] < mnamb)
mnamb = sqisz[sqidx].ambano[0];
/* the last sequence */
CONDREALLOC(ididx0, sqisz[sqidx].ibf, GBUF, sqisz[sqidx].id, char);
sqisz[sqidx].id[ididx0]='\0';
CONDREALLOC(sqisz[sqidx].sylen, sqisz[sqidx].sbf, GBUF, sqisz[sqidx].sq, char);
sqisz[sqidx].sq[sqisz[sqidx].sylen]='\0';
sqisz[sqidx].idz=1+ididx0;
sqisz[sqidx].sqz=1+sqisz[sqidx].sylen;
numsq=sqidx+1, numano=0;
for(i=0;i<numsq;++i) {
if(sqisz[i].ambano[1])
numano++;
}
// return 0;
for(i=numsq;i<gbuf;++i) {
free(sqisz[i].id);
free(sqisz[i].sq);
}
sqisz=realloc(sqisz, numsq*sizeof(i_s));
/* check for uniform sequence size, necessary for alignments */
oneln=f2uniquelens(sqisz, numsq);
int snpcou=0;
for(k=0;k<oneln;++k)
if(sqisz[0].sq[k]!=sqisz[1].sq[k]) // vital: the two sequences may have scored a SNP against the reference, but do they score one against each other?
snpcou++;
printf("File %s: numseq=%u, F2 uniform seq size at %d. SNP Count: %i\n", argv[1], numsq, oneln, snpcou);
for(i=0;i<numsq;++i) {
free(sqisz[i].id);
free(sqisz[i].sq);
}
free(sqisz);
return 0;
}