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/omimParseAv/omimParseAv.c src/hg/protein/omimParseAv/omimParseAv.c index 76dc970..fb36115 100644 --- src/hg/protein/omimParseAv/omimParseAv.c +++ src/hg/protein/omimParseAv/omimParseAv.c @@ -1,363 +1,363 @@ /* omimParseAv - parse the AV fields of OMIM records */ /* Copyright (C) 2013 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 "hdb.h" #include "options.h" #include "localmem.h" #include "dystring.h" #include "portable.h" #include "obscure.h" boolean avDebug = FALSE; char buffer[80*5000]; char *fieldType; FILE *omimAvPos; char empty[1] = {""}; struct omimSubField /* An OMIM sub field. */ { char *omimId; /* OMIM ID */ char *fieldType; /* field type */ char *subFieldId; /* sub-field ID */ int startPos; /* offset of starting position */ int subFieldLen; /* length of text of the sub-field */ char *text; /* text of the sub-field */ }; char aaCode3[20][4] = { "ALA", "VAL", "LEU", "ILE", "PRO", "PHE", "TRP", "MET", "GLY", "SER", "THR", "CYS", "TYR", "ASN", "GLN", "ASP", "GLU", "LYS", "ARG", "HIS" }; char aaCode1[20][2] = { "A", "V", "L", "I", "P", "F", "W", "M", "G", "S", "T", "C", "Y", "N", "Q", "D", "E", "K", "R", "H" }; void usage() /* Explain usage and exit. */ { errAbort( "omimParseAv - parse the AV fields of OMIM records \n" "usage:\n" " omimParseAv omimDb omimTextFile avSubOutFile avPosOutFile\n" ); } static struct optionSpec options[] = { {NULL, 0}, }; boolean findAaSub(char *lineIn, struct omimSubField *subFd, FILE *avPosFh) /* check the input line to see if it contains a patern of AA substitution (AAAnnAAA) and print out a record if it does. */ { char *words[300]; char inStr[300]; int wcnt; char *chp, *chpa, *chp1, *chp2; char ch; char aa1 = ' '; char aa2 = ' '; int avPos; int aaCnt; int i, j; boolean posValid; boolean result; result = FALSE; /* chop the line into words */ safef(inStr, sizeof(inStr), "%s", lineIn); wcnt = chopString(inStr, " ,", words, 300); /* check each word */ for (j=0; j<wcnt; j++) { aaCnt = 0; chp1 = chp2 = NULL; /* check each AA */ for (i=0; i<20; i++) { chp = words[j]; chpa = strstr(words[j], aaCode3[i]); if (chpa != NULL) { aaCnt++; /* remember first AA */ if (aaCnt == 1) { aa1 = *aaCode1[i]; chp1 = chpa; } /* remember 2nd AA */ if (aaCnt == 2) { aa2 = *aaCode1[i]; chp2 = chpa; } } } /* if the word contains 2 AAs, do further checking */ if (aaCnt == 2) { /* switch chp1 and chp2 if chp1 goes after chp2 */ if (chp1 > chp2) { ch = aa1; chp = chp1; chp1 = chp2; chp2 = chp; aa1 = aa2; aa2 = ch; } /* check if the characters between two AAs are all digits */ chp = chp1 + 3; posValid = TRUE; while (chp < chp2) { if (!isdigit(*chp)) { //fprintf(stderr, //"%s in '%s' is not a valid AA substution string.\n", words[j], lineIn); posValid = FALSE; } chp ++; } ch = *chp2; *chp2 = '\0'; avPos = atoi(chp1+3); *chp2 = ch; if (posValid) { fprintf(avPosFh, "%s\t%s\t%s\t%d\t%c\t%c\n", subFd->omimId, subFd->subFieldId, words[j], avPos, aa1, aa2); fflush(avPosFh); result = TRUE; return(result); } } } return(result); } struct omimSubField *newSubFd(struct lm *lm, char *omimId, char *fieldType) /* allocat and initialize a new omimSubField object */ { struct omimSubField *subFd; lmAllocVar(lm, subFd); subFd->omimId = omimId; subFd->fieldType = fieldType; return(subFd); } void printSubField(struct omimSubField *subFd, FILE *fh2, FILE *avSubFh) /* print out the sub-field data */ { int bytesRead; fseek(fh2, (long)(subFd->startPos), SEEK_SET); if (subFd->subFieldLen >= sizeof(buffer)) { fprintf(stderr, "Subfield %s %s length %d exceeds the size of buffer %d.\n", subFd->omimId, subFd->subFieldId, subFd->subFieldLen, (int)sizeof(buffer)); exit(1); } bytesRead = (long)fread(buffer, (size_t)1, (size_t)(subFd->subFieldLen), fh2); *(buffer + subFd->subFieldLen) = '\0'; fprintf(avSubFh, "%s\t%s\t%s\t%d\t%d\n", subFd->omimId, subFd->fieldType, subFd->subFieldId, subFd->startPos, subFd->subFieldLen); if (avDebug) { printf("%s\t%s--->\n%s<---\n", subFd->omimId, subFd->subFieldId, buffer);fflush(stdout); } } void omimParseAv(char *omimDb, char *omimTxtFileName, FILE *fh2, FILE *avSubFh, FILE *outFh) { struct sqlConnection *conn2, *conn3, *conn4; char query2[256], query3[256]; struct sqlResult *sr2, *sr3; char **row2, **row3; char *omimId, *fieldType; char *startPos, *fieldLength; long bytesRead; char *line; int lineSize; char *chp, *chp2; boolean avPosFound = FALSE; size_t iStart, fieldLen; int subLen = 0; boolean entryProcessed; /* sub-field start and end position */ int subFdStartPos = 0; int subFdEndPos = 0; char *subFieldText; char *subAvNum; struct lm *lm; struct omimSubField *subFd; struct lineFile *lf = lineFileOpen(omimTxtFileName, TRUE); conn2= hAllocConn(); /* loop thru all recordd in the omimField table */ sqlSafef(query2, sizeof query2, "select * from %s.omimField where fieldType='AV'", omimDb); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { omimId = row2[0]; fieldType = row2[1]; startPos = row2[2]; fieldLength = row2[3]; lm = lmInit(8*1024); lmAllocVar(lm, subFd); iStart = (size_t)atoi(startPos); fieldLen = (size_t)atoi(fieldLength); lineFileSeek(lf, iStart, SEEK_SET); entryProcessed = FALSE; subAvNum = NULL; while (!entryProcessed) { if (!lineFileNext(lf, &line, &lineSize)) { fprintf(stderr, "Premature end of file reached.\n"); exit(1); } /* check if the line is the starting of a sub AV entry */ if (*line == '.') { if (subAvNum != NULL) { subFdEndPos = lf->lineStart + lf->bufOffsetInFile - 1; subLen = subFdEndPos - subFdStartPos; subFd->subFieldLen = subLen; printSubField(subFd, fh2, avSubFh); } subAvNum = strdup(line+1); subFd = newSubFd(lm, omimId, fieldType); subFd->subFieldId = subAvNum; subFdStartPos = lf->lineEnd + lf->bufOffsetInFile; subFd->startPos = subFdStartPos; /* reset the boolean flag, once the ".0000xx" sub AV line found */ avPosFound = FALSE; } /* search for the pattern, only if it is not found for a sub entry yet */ if (!avPosFound) { avPosFound = findAaSub(line, subFd, outFh); } if ((lf->lineStart + lf->bufOffsetInFile) >= (iStart + fieldLen - 1)) { entryProcessed = TRUE; subFdEndPos = lf->lineStart + lf->bufOffsetInFile - 1; subLen = subFdEndPos - subFdStartPos; subFd->subFieldLen = subLen; printSubField(subFd, fh2, avSubFh); } } lmCleanup(&lm); row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); hFreeConn(&conn2); } int main(int argc, char *argv[]) /* Process command line. */ { FILE *omimAvSubFh, *omimAvPosFh, *fh2; optionInit(&argc, argv, options); if (argc != 5) usage(); fh2 = mustOpen(argv[2], "r"); omimAvSubFh = mustOpen(argv[3], "w"); omimAvPosFh = mustOpen(argv[4], "w"); omimParseAv(argv[1], argv[2], fh2, omimAvSubFh, omimAvPosFh); fclose(omimAvPosFh); return 0; }