a44421a79fb36cc2036fe116b97ea3bc9590cd0c braney Fri Dec 2 09:34:39 2011 -0800 removed rcsid (#295) diff --git src/utils/findMotif/findMotif.c src/utils/findMotif/findMotif.c index 5ef2cec..444494f 100644 --- src/utils/findMotif/findMotif.c +++ src/utils/findMotif/findMotif.c @@ -1,313 +1,312 @@ /* findMotif - find specified motif in nib files. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "dnautil.h" #include "dnaseq.h" #include "dnaLoad.h" #include "portable.h" #include "memalloc.h" #include "obscure.h" -static char const rcsid[] = "$Id: findMotif.c,v 1.13 2009/07/07 17:58:56 hiram Exp $"; char *chr = (char *)NULL; /* process the one chromosome listed */ char *motif = (char *)NULL; /* specified motif string */ unsigned motifLen = 0; /* length of motif */ unsigned long long motifVal; /* motif converted to a number */ unsigned long long complementVal; /* - strand complement */ boolean bedOutput = TRUE; /* output bed file (default) */ boolean wigOutput = FALSE; /* output wiggle format instead of bed file */ char *strand = (char *)NULL; boolean doPlusStrand = TRUE; /* output bed file instead of wiggle */ boolean doMinusStrand = TRUE; /* output bed file instead of wiggle */ void usage() /* Explain usage and exit. */ { errAbort( "findMotif - find specified motif in sequence\n" "usage:\n" " findMotif [options] -motif=<acgt...> sequence\n" "where:\n" " sequence is a .fa , .nib or .2bit file or a file which is a list of sequence files.\n" "options:\n" " -motif=<acgt...> - search for this specified motif (case ignored, [acgt] only)\n" " -chr=<chrN> - process only this one chrN from the sequence\n" " -strand=<+|-> - limit to only one strand. Default is both.\n" " -bedOutput - output bed format (this is the default)\n" " -wigOutput - output wiggle data format instead of bed file\n" " -verbose=N - set information level [1-4]\n" " NOTE: motif must be longer than 4 characters, less than 17\n" " -verbose=4 - will display gaps as bed file data lines to stderr" ); } static struct optionSpec options[] = { {"chr", OPTION_STRING}, {"strand", OPTION_STRING}, {"motif", OPTION_STRING}, {"bedOutput", OPTION_BOOLEAN}, {"wigOutput", OPTION_BOOLEAN}, {NULL, 0}, }; static void scanSeq(struct dnaSeq *seq) { int i, val; FILE *nf = NULL; DNA *dna; unsigned long long mask; unsigned long long chromPosition = 0; register unsigned long long incomingVal = 0; unsigned long long incomingLength = 0; unsigned long long posFound = 0; unsigned long long negFound = 0; unsigned long long posPreviousPosition = 0; unsigned long long negPreviousPosition = 0; register unsigned long long posNeedle = motifVal; register unsigned long long negNeedle = complementVal; unsigned long long enterGap = 1; boolean inGap = FALSE; unsigned long long gapCount = 0; mask = 3; for (i=1; i < motifLen; ++i ) mask = (mask << 2) | 3; verbose(2, "#\tsequence: %s size: %d, motifMask: %#llx\n", seq->name, seq->size, mask); verbose(2, "#\tmotif numerical value: %llu (%#llx)\n", posNeedle, posNeedle); /* Need "chrom" */ dna = seq->dna; for (i=0; i < seq->size; ++i) { ++chromPosition; val = ntVal[(int)dna[i]]; switch (val) { case T_BASE_VAL: case C_BASE_VAL: case A_BASE_VAL: case G_BASE_VAL: incomingVal = mask & ((incomingVal << 2) | val); if (! incomingLength) { if (inGap && (((long long int)chromPosition - (long long int)enterGap) > 0)) { ++gapCount; verbose(3, "#\treturn from gap at %llu, gap length: %llu\n", chromPosition, chromPosition - enterGap); verbose(4, "#GAP %s\t%llu\t%llu\t%llu\t%llu\t%s\n", seq->name, enterGap-1, chromPosition-1, gapCount, chromPosition - enterGap, "+"); /* assume no more gaps, this is safe to a chrom size * of 1 Tb */ enterGap = (unsigned long long)BIGNUM << 10; } } inGap = FALSE; ++incomingLength; if (doPlusStrand && (incomingLength >= motifLen) && (incomingVal == posNeedle)) { ++posFound; if (wigOutput) printf("%llu 1 %#llx == %#llx\n", chromPosition-motifLen+1, incomingVal&mask,posNeedle); else printf("%s\t%llu\t%llu\t%llu\t%d\t%s\n", seq->name, chromPosition-motifLen, chromPosition, posFound+negFound, 1000, "+"); if ((posPreviousPosition + motifLen) > chromPosition) verbose(2, "#\toverlapping + at: %s:%llu-%llu\n", seq->name, posPreviousPosition, chromPosition); posPreviousPosition = chromPosition; } if (doMinusStrand && (incomingLength >= motifLen) && (incomingVal == negNeedle)) { ++negFound; if (wigOutput) printf("%llu -1 %#llx == %#llx\n", chromPosition-motifLen+1, incomingVal&mask,negNeedle); else printf("%s\t%llu\t%llu\t%llu\t%d\t%s\n", seq->name, chromPosition-motifLen, chromPosition, posFound+negFound, 1000, "-"); if ((negPreviousPosition + motifLen) > chromPosition) verbose(2, "#\toverlapping - at: %s:%llu-%llu\n", seq->name, negPreviousPosition, chromPosition); negPreviousPosition = chromPosition; } break; default: if (incomingLength) { verbose(3, "#\tenter gap at %llu\n", chromPosition); enterGap = chromPosition; } inGap = TRUE; incomingVal = 0; incomingLength = 0; break; } } if (inGap && (((long long int)chromPosition - (long long int)enterGap) > 0)) { ++gapCount; verbose(3, "#\treturn from gap at %llu, gap length: %llu\n", chromPosition+1, chromPosition - enterGap + 1); verbose(4, "#GAP %s\t%llu\t%llu\t%llu\t%llu\t%s\n", seq->name, enterGap-1, chromPosition, gapCount, chromPosition - enterGap + 1, "+"); } verbose(2, "#\tfound: %llu times + strand, %llu times - strand\n", posFound, negFound ); verbose(2, "#\t%% of chromosome: %g %% + strand %g %% - strand\n", (double)(posFound*motifLen)/(double)chromPosition, (double)(negFound*motifLen)/(double)chromPosition); carefulClose(&nf); } static void findMotif(char *input) /* findMotif - find specified motif in sequence file. */ { struct dnaLoad *dl = dnaLoadOpen(input); struct dnaSeq *seq; while ((seq = dnaLoadNext(dl)) != NULL) { verbose(2, "#\tprocessing: %s\n", seq->name); scanSeq(seq); } } int main(int argc, char *argv[]) /* Process command line. */ { int i; char *cp; unsigned long long reversed; size_t maxAlloc; char asciiAlloc[32]; optionInit(&argc, argv, options); if (argc < 2) usage(); maxAlloc = 2100000000 * (((sizeof(size_t)/4)*(sizeof(size_t)/4)*(sizeof(size_t)/4))); sprintLongWithCommas(asciiAlloc, (long long) maxAlloc); verbose(4, "#\tmaxAlloc: %s\n", asciiAlloc); setMaxAlloc(maxAlloc); /* produces: size_t is 4 == 2100000000 ~= 2^31 = 2Gb * size_t is 8 = 16800000000 ~= 2^34 = 16 Gb */ dnaUtilOpen(); motif = optionVal("motif", NULL); chr = optionVal("chr", NULL); strand = optionVal("strand", NULL); bedOutput = optionExists("bedOutput"); wigOutput = optionExists("wigOutput"); if (wigOutput) bedOutput = FALSE; else bedOutput = TRUE; if (chr) verbose(2, "#\tprocessing chr: %s\n", chr); if (strand) verbose(2, "#\tprocessing strand: '%s'\n", strand); if (motif) verbose(2, "#\tsearching for motif: %s\n", motif); else { warn("ERROR: -motif string empty, please specify a motif\n"); usage(); } verbose(2, "#\ttype output: %s\n", wigOutput ? "wiggle data" : "bed format"); verbose(2, "#\tspecified sequence: %s\n", argv[1]); verbose(2, "#\tsizeof(motifVal): %d\n", (int)sizeof(motifVal)); if (strand) { if (! (sameString(strand,"+") | sameString(strand,"-"))) { warn("ERROR: -strand specified ('%s') is not + or - ?\n", strand); usage(); } /* They are both on by default, turn off the one not specified */ if (sameString(strand,"-")) doPlusStrand = FALSE; if (sameString(strand,"+")) doMinusStrand = FALSE; } motifLen = strlen(motif); /* at two bits per character, size limit of motif is * number of bits in motifVal / 2 */ if (motifLen > (4*sizeof(motifVal))/2 ) { warn("ERROR: motif string too long, limit %d\n", (4*(int)sizeof(motifVal))/2 ); usage(); } cp = motif; motifVal = 0; complementVal = 0; for (i = 0; i < motifLen; ++i) { switch (*cp) { case 'a': case 'A': motifVal = (motifVal << 2) | A_BASE_VAL; complementVal = (complementVal << 2) | T_BASE_VAL; break; case 'c': case 'C': motifVal = (motifVal << 2) | C_BASE_VAL; complementVal = (complementVal << 2) | G_BASE_VAL; break; case 'g': case 'G': motifVal = (motifVal << 2) | G_BASE_VAL; complementVal = (complementVal << 2) | C_BASE_VAL; break; case 't': case 'T': motifVal = (motifVal << 2) | T_BASE_VAL; complementVal = (complementVal << 2) | A_BASE_VAL; break; default: warn( "ERROR: character in motif: '%c' is not one of ACGT\n", *cp); usage(); } ++cp; } reversed = 0; for (i = 0; i < motifLen; ++i) { int base; base = complementVal & 3; reversed = (reversed << 2) | base; complementVal >>= 2; } complementVal = reversed; verbose(2, "#\tmotif numerical value: %llu (%#llx)\n", motifVal, motifVal); verbose(2, "#\tcomplement numerical value: %llu (%#llx)\n", complementVal, complementVal); if (motifLen < 5) { warn("ERROR: motif string must be more than 4 characters\n"); usage(); } findMotif(argv[1]); return 0; }