4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/snp/pbToAlleleCounts/pbToAlleleCounts.c src/hg/snp/pbToAlleleCounts/pbToAlleleCounts.c index 67d206f..862874a 100644 --- src/hg/snp/pbToAlleleCounts/pbToAlleleCounts.c +++ src/hg/snp/pbToAlleleCounts/pbToAlleleCounts.c @@ -1,245 +1,245 @@ /* pbToAlleleCounts.c -- reformat Seattel SNP data from prettybase format to bed with alleles and counts */ /* Copyright (C) 2011 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "errAbort.h" #include "linefile.h" #include "obscure.h" #include "dystring.h" #include "cheapcgi.h" #include "dnaseq.h" #include "hdb.h" #include "memalloc.h" #include "hash.h" #include "jksql.h" #include "dystring.h" #include "options.h" #include "sqlNum.h" static int ssnpId=0; boolean strictSnp=FALSE; boolean strictBiallelic=FALSE; static struct optionSpec optionSpecs[] = /* command line option specifications */ { {"strictBiallelic", OPTION_BOOLEAN}, {"strictSnp", OPTION_BOOLEAN}, {NULL, 0} }; void usage() /* Explain usage and exit. */ { errAbort("pbToAlleleCounts -- reformat Seattle SNP data from prettybase format to bed with alleles and counts\n" "Usage: pbToAlleleCounts prettybaseFile strandFile bedFile\n" "Options: strictSnp - ignore loci with non-SNP mutations\n" " strictBiallelic - ignore loci with more than two alleles \n"); } struct alleleInfo /* */ { struct alleleInfo *next; char *allele; int count; }; struct locus /* */ { struct locus *next; char *chrom; int chromStart; int chromEnd; char *name; /* unique locus id */ char *strand; char *hugoId; int sampleSize; int alleleCount; boolean strictSnp; struct alleleInfo *alleles; }; struct strand { struct strand *next; char *name; char *strand; }; void convertToUppercase(char *ptr) /* convert and entire string to uppercase */ { for( ; *ptr !='\0'; ptr++) *ptr=toupper(*ptr); } void printAlleles(FILE *f, struct alleleInfo *ai) /* print alleles and counts for this locus */ { struct alleleInfo *i = NULL; for (i=ai; i!=NULL; i=i->next) fprintf(f,"\t%s\t%d", i->allele, i->count); fprintf(f,"\n"); } void printLocus(FILE *f, struct locus *l) /* print positional information for this locus */ { if (strictSnp&&!l->strictSnp) return; if (strictBiallelic&&l->alleleCount!=2) return; fprintf(f,"%s\t%d\t%d\t%s\t0\t%s\t%d\t%d", l->chrom, l->chromStart, l->chromEnd, l->name, l->strand, l->sampleSize, l->alleleCount); printAlleles(f, l->alleles); } void printLoci(char *output, struct locus *head) /* print all information for this locus */ { FILE *f = mustOpen(output, "w"); struct locus *l = NULL; for (l=head; l!=NULL; l=l->next) printLocus(f, l); } struct hash *readStrand(char *strandFile) /* read the strands from a file */ { struct hash *strandHash = newHash(16); struct lineFile *lf = lineFileOpen(strandFile, TRUE); /* input file */ char *row[2]; /* number of fields in input file */ while (lineFileRow(lf, row)) /* process one snp at a time */ { struct strand *strand; AllocVar(strand); strand->name = cloneString(row[0]); strand->strand = cloneString(row[1]); hashAddSaveName(strandHash, strand->name, strand, &strand->name); } return strandHash; } struct locus *readSs(char *pbFile, char *strandFile) /* determine which allele matches assembly and store in details file */ { struct hash *strandHash = readStrand(strandFile); struct strand *strand = NULL; struct hash *missingHugoIdHash = newHash(16); struct hashCookie hashPtr; char *missingName; struct locus *l = NULL, *lPtr = NULL; struct alleleInfo *aPtr = NULL; struct lineFile *lf = lineFileOpen(pbFile, TRUE); /* input file */ char *row[4], *row2[3]; /* number of fields in input file */ char *pbName; char chrom[32]; int chromStart; int chromEnd; char name[32]; char *allele; while (lineFileRow(lf, row)) /* process one snp at a time */ { struct alleleInfo *ai1 = NULL, *ai2 = NULL, *aiPtr; struct locus *m = NULL; chopString(row[0], "-", row2, 3); chromStart = sqlUnsigned(row2[0]); chromEnd = chromStart+1; safef(chrom, sizeof(chrom), "chr%s", row2[2]); if(l==NULL||l->chrom==NULL||l->chromStart!=chromStart||!(sameString(l->chrom,chrom))) { AllocVar(m); safef(name, sizeof(name), "%s_%d", row2[1], ++ssnpId); m->chrom = cloneString(chrom); m->chromStart = chromStart; m->chromEnd = chromEnd; m->name = cloneString(name); m->hugoId = cloneString(row2[1]); m->strictSnp = TRUE; slAddHead(&l, m); } allele=cloneString(row[2]); convertToUppercase(allele); if ( sameString(allele,"A") || sameString(allele,"C") || sameString(allele,"G") || sameString(allele,"T") ) { for (aiPtr=l->alleles; aiPtr!=NULL; aiPtr=aiPtr->next) if (sameString(aiPtr->allele, allele)) break; if (aiPtr==NULL) { AllocVar(ai1); ai1->allele=cloneString(allele); slAddHead(&(l->alleles), ai1); l->alleleCount++; aiPtr=l->alleles; } aiPtr->count++; l->sampleSize++; } allele=cloneString(row[3]); convertToUppercase(allele); if ( sameString(allele,"A") || sameString(allele,"C") || sameString(allele,"G") || sameString(allele,"T") ) { for (aiPtr=l->alleles; aiPtr!=NULL; aiPtr=aiPtr->next) if (sameString(aiPtr->allele, allele)) break; if (aiPtr==NULL) { AllocVar(ai2); ai2->allele=cloneString(allele); slAddHead(&(l->alleles), ai2); l->alleleCount++; aiPtr=l->alleles; } aiPtr->count++; l->sampleSize++; } } slReverse(&l); for(lPtr=l; lPtr!=NULL; lPtr=lPtr->next) { strand = hashFindVal(strandHash, lPtr->hugoId); if (strand == NULL) { hashStore(missingHugoIdHash, lPtr->hugoId); slRemoveEl(l, lPtr); continue; } lPtr->strand = cloneString(strand->strand); } freeHash(&strandHash); hashPtr = hashFirst(missingHugoIdHash); while ( (missingName=hashNextName(&hashPtr)) != NULL ) printf("HUGO ID was not found in strand.txt (usually from proteome.hgncXref): %s\n", missingName); freeHash(&missingHugoIdHash); return l; } int main(int argc, char *argv[]) /* error check, process command line input, and call getSnpDetails */ { struct locus *l = NULL; optionInit(&argc, argv, optionSpecs); strictSnp = optionExists("strictSnp"); strictBiallelic = optionExists("strictBiallelic"); if (argc != 4) usage(); l = readSs(argv[1], argv[2]); printLoci(argv[3], l); return 0; }