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/protein/omimParseRec/omimParseRec.c src/hg/protein/omimParseRec/omimParseRec.c index b1e559c..439abe3 100644 --- src/hg/protein/omimParseRec/omimParseRec.c +++ src/hg/protein/omimParseRec/omimParseRec.c @@ -1,290 +1,290 @@ /* omimParseRec - parse text of OMIM records by different field types */ /* 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 "linefile.h" #include "hash.h" #include "options.h" #include "localmem.h" #include "dystring.h" #include "portable.h" #include "obscure.h" FILE *fh2; /* 2nd file handle pointing to the OMIM text file */ FILE *recFh; FILE *fieldFh; void usage() /* Explain usage and exit. */ { errAbort( "omimParseRec - parse OMIM records by different field types\n" "usage:\n" " omimParseRec omimText outRecFile outFieldFile\n" ); } static struct optionSpec options[] = { {NULL, 0}, }; struct omimRecord /* An OMIM record. */ { char *id; /* OMIM ID */ char type; /* OMIM type */ char *title; /* OMIM title */ char *geneSymbol; /* gene symbol */ int startPos; int endPos; char *av; char *cd; char *cn; char *cs; char *ed; char *rf; char *sa; char *tx; }; struct omimField /* An OMIM field. */ { char *omimId; /* OMIM ID */ char *type; /* field type */ char *title; /* field title */ int startPos; int endPos; }; struct omimLitRef /* A OMIM literature reference. */ { struct omimLitRef *next; char *title; /* Title of article. */ char *cite; /* Journal/book/patent citation. */ struct slName *authorList; /* Author names in lastName, F.M. format. */ char *rp; /* Somewhat complex 'Reference Position' line. */ struct hashEl *rxList; /* Cross-references. */ struct hashEl *rcList; /* TISSUE=XXX X; STRAIN=YYY; parsed out. */ char *pubMedId; /* pubMed ID, may be NULL. */ char *medlineId; /* Medline ID, may be NULL. */ char *doiId; /* DOI ID, may be NULL. */ }; char buffer[80*10000]; void printField(struct omimField *omimFd, FILE *outf) /* print out field info */ { long bytesRead; fprintf(outf, "%s\t%s\t%d\t%d\n", omimFd->omimId, omimFd->type, omimFd->startPos, omimFd->endPos - omimFd->startPos + 1); fflush(stdout); if (((omimFd->endPos - omimFd->startPos + 1) + 1) >sizeof(buffer)) { fprintf(stderr, "field %s for OMIM record %s needs %d bytes, which exceeded buffer size of %d\n", omimFd->type, omimFd->omimId, (omimFd->endPos - omimFd->startPos + 1) + 1, (int)sizeof(buffer)); exit(1); } fseek(fh2, (long)(omimFd->startPos), SEEK_SET); bytesRead = (long)fread(buffer, (size_t)1, (size_t)(omimFd->endPos - omimFd->startPos + 1), fh2); *(buffer+bytesRead) = '\0'; } struct omimRecord *omimRecordNext(struct lineFile *lf, struct lm *lm, /* Local memory pool for this structure. */ struct dyString *dy, /* Scratch string to use. */ FILE *recFh, FILE *fieldFh) /* Read next record from file and parse it into omimRecord structure * that is allocated in memory. */ { char *line; struct omimRecord *omimr; char *chp; int lineSize; char *fieldType; boolean recDone, fieldDone; char *row[1]; boolean endOfFile = FALSE; boolean endOfRec = FALSE; boolean firstFieldDone = FALSE; struct omimField *omimFd = NULL; recDone = FALSE; /* Parse record number and title lines. */ if (!lineFileRow(lf, row)) return NULL; if (!sameString(row[0], "*RECORD*")) { errAbort("Expecting *RECORD* line %d of %s", lf->lineIx, lf->fileName); } lmAllocVar(lm, omimr); omimr->startPos = lf->lineStart + lf->bufOffsetInFile; if (!lineFileNext(lf, &line, &lineSize)) return NULL; if (!sameString(line, "*FIELD* NO")) errAbort("Expecting *FIELD* NO line %d of %s", lf->lineIx, lf->fileName); if (!lineFileNextReal(lf, &line)) errAbort("%s ends in middle of a record", lf->fileName); omimr->id = lmCloneString(lm, line); if (!lineFileNextReal(lf, &line)) errAbort("%s ends in middle of a record", lf->fileName); if (!sameString(line, "*FIELD* TI")) errAbort("Expecting *FIELD* TI line %d of %s ---%s---", lf->lineIx, lf->fileName, line); if (!lineFileNext(lf, &line, &lineSize)) errAbort("%s ends in middle of a record", lf->fileName); if (!isdigit(*line)) { omimr->type = *line; } else { omimr->type = '\0'; } /* some records may not have gene symbol */ omimr->geneSymbol = ""; chp = strstr(line, ";"); if (chp != NULL) { *chp = '\0'; chp++; if (*chp == ' ') chp++; if (*chp != '\0') omimr->geneSymbol = cloneString(chp); } chp = strstr(line, omimr->id); if (chp == NULL) { errAbort("Expecting TI line for record %s, %d of %s ---%s===", omimr->id, lf->lineIx, lf->fileName, line); } chp = chp + strlen(omimr->id); chp++; omimr->title = lmCloneString(lm, chp); // !!! need to enhance it later to include startPos and length info. fprintf(recFh, "%s\t%c\t%s\t%s\n", omimr->id, omimr->type, omimr->geneSymbol, omimr->title); /* !!! temporarily skip lines before first FIELD after title */ /* further processing TBD */ while (strstr(line, "*FIELD*") == NULL) { lineFileNext(lf, &line, &lineSize); } lineFileReuse(lf); /* process a field */ firstFieldDone = FALSE; fieldDone = FALSE; while (!recDone) { if (!lineFileNext(lf, &line, &lineSize)) { endOfFile = TRUE; } /* "*THEEND*" signals the end of the OMIM text file */ if (sameWord(line, "*THEEND*")) endOfFile = TRUE; if (!endOfFile && (strstr(line, "*RECORD*") != NULL)) { endOfRec = TRUE; } /* handle termination of record here */ if (endOfFile || endOfRec) { lineFileReuse(lf); recDone = TRUE; if (firstFieldDone) { /* extra minus 1 to get rid of empty line at the end */ omimr ->endPos = lf->lineStart + lf->bufOffsetInFile - 1 - 1; omimFd->endPos = lf->lineStart + lf->bufOffsetInFile - 1 - 1; /* End of record or end of line also means end of a field. Print the field info */ printField(omimFd, fieldFh); } break; } chp = strstr(line, "*FIELD*"); if (chp != NULL) { fieldType = chp + strlen("*FIELD* "); if (!firstFieldDone) { lmAllocVar(lm, omimFd); firstFieldDone = TRUE; /* do not print anything at the first "*FIELD*" line */ } else { /* extra minus 1 to get rid of empty line at the end */ omimFd->endPos = lf->lineStart + lf->bufOffsetInFile - 1 - 1; /* print previous field info */ printField(omimFd, fieldFh); } /* fill in current field info */ omimFd->omimId = cloneString(omimr->id); omimFd->type = cloneString(fieldType); omimFd->startPos = lf->lineEnd + lf->bufOffsetInFile; } } if (endOfFile) return NULL; return omimr; } void omimParseRec(char *omimTextFile, FILE *recFh, FILE *fieldFh) /* omimParseRec - parse OMIM flat text file. */ { struct lineFile *lf = lineFileOpen(omimTextFile, TRUE); struct omimRecord *omimr; struct dyString *dy = newDyString(4096); for (;;) { struct lm *lm = lmInit(8*1024); omimr = omimRecordNext(lf, lm, dy, recFh, fieldFh); if (omimr == NULL) break; lmCleanup(&lm); } dyStringFree(&dy); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 4) usage(); fh2 = mustOpen(argv[1], "r"); recFh = mustOpen(argv[2], "w"); fieldFh = mustOpen(argv[3], "w"); omimParseRec(argv[1], recFh, fieldFh); return 0; }