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/makeDb/outside/hgCGAP/hgCGAP.c src/hg/makeDb/outside/hgCGAP/hgCGAP.c index 1750ce2..de11a7a 100644 --- src/hg/makeDb/outside/hgCGAP/hgCGAP.c +++ src/hg/makeDb/outside/hgCGAP/hgCGAP.c @@ -1,443 +1,443 @@ /* This program parse CGAP data file */ /* Copyright (C) 2009 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. */ #define ALIAS 1 #define BIOCARTA 2 #define CYTOBAND 3 #define GO 4 #define HOMOLOG 5 #define KEGG 6 #define LOCUSID 7 #define MGC_CLONE 8 #define MOTIF 9 #define OMIM 10 #define SEQUENCE 11 #define SNP 12 #define SV_CLONE 13 #define SYMBOL 14 #define TITLE 15 #define UNIGENE 16 #include <stdio.h> #include <stdlib.h> #include <string.h> int done; char line[2000]; FILE *inf; char id[40]; int attr; FILE *fBIOCARTAdesc; FILE *fKEGGdesc; FILE *fALIAS; FILE *fBIOCARTA; FILE *fCYTOBAND; FILE *fGO; FILE *fHOMOLOG; FILE *fKEGG; FILE *fLOCUSID; FILE *fMGC_CLONE; FILE *fMOTIF; FILE *fOMIM; FILE *fSEQUENCE; FILE *fSNP; FILE *fSV_CLONE; FILE *fSYMBOL; FILE *fTITLE; FILE *fUNIGENE; int doALIAS(char *data) { if ((strcmp(data, "NA") != 0) && (strcmp(data, "na") != 0) ) { fprintf(fALIAS, "%s\t%s\n",id, data); } return(0); } int doBIOCARTA(char *data) { char *chp; char *desc; chp = strstr(data, "|"); *chp = '\0'; desc = chp+1; fprintf(fBIOCARTA, "%s\t%s\n",id, data); fprintf(fBIOCARTAdesc, "%s\t%s\n",data, desc); return(0); } int doCYTOBAND(char *data) { fprintf(fCYTOBAND, "%s\t%s\n",id, data); return(0); } int doGO(char *data) { fprintf(fGO, "%s\t%s\n",id, data); return(0); } int doHOMOLOG(char *data) { fprintf(fHOMOLOG, "%s\t%s\n",id, data); return(0); } int doKEGG(char *data) { char *chp; char *desc; chp = strstr(data, "|"); *chp = '\0'; desc = chp+1; fprintf(fKEGG, "%s\t%s\n",id, data); fprintf(fKEGGdesc, "%s\t%s\n",data, desc); return(0); } int doLOCUSID(char *data) { fprintf(fLOCUSID, "%s\t%s\n",id, data); return(0); } int doMGC_CLONE(char *data) { fprintf(fMGC_CLONE, "%s\t%s\n",id, data); return(0); } int doMOTIF(char *data) { fprintf(fMOTIF, "%s\t%s\n",id, data); return(0); } int doOMIM(char *data) { fprintf(fOMIM, "%s\t%s\n",id, data); return(0); } int doSEQUENCE(char *data) { fprintf(fSEQUENCE, "%s\t%s\n",id, data); return(0); } int doSNP(char *data) { fprintf(fSNP, "%s\t%s\n",id, data); return(0); } int doSV_CLONE(char *data) { fprintf(fSV_CLONE, "%s\t%s\n",id, data); return(0); } int doSYMBOL(char *data) { if ((strcmp(data, "NA") != 0) && (strcmp(data, "na") != 0) ) { fprintf(fSYMBOL, "%s\t%s\n",id, data); } return(0); } int doTITLE(char *data) { fprintf(fTITLE, "%s\t%s\n",id, data); return(0); } int doUNIGENE(char *data) { fprintf(fUNIGENE, "%s\t%s\n",id, data); return(0); } int processRecord(char *attrStr, char *data) { if (strcmp(attrStr, "ALIAS") == 0) { attr = ALIAS; goto setDone; } if (strcmp(attrStr, "BIOCARTA") == 0) { attr = BIOCARTA; goto setDone; } if (strcmp(attrStr, "CYTOBAND") == 0) { attr = CYTOBAND; goto setDone; } if (strcmp(attrStr, "GO") == 0) { attr = GO; goto setDone; } if (strcmp(attrStr, "HOMOLOG") == 0) { attr = HOMOLOG; goto setDone; } if (strcmp(attrStr, "KEGG") == 0) { attr = KEGG; goto setDone; } if (strcmp(attrStr, "LOCUSID") == 0) { attr = LOCUSID; goto setDone; } if (strcmp(attrStr, "MGC_CLONE") == 0) { attr = MGC_CLONE; goto setDone; } if (strcmp(attrStr, "MOTIF") == 0) { attr = MOTIF; goto setDone; } if (strcmp(attrStr, "OMIM") == 0) { attr = OMIM; goto setDone; } if (strcmp(attrStr, "SEQUENCE") == 0) { attr = SEQUENCE; goto setDone; } if (strcmp(attrStr, "SNP") == 0) { attr = SNP; goto setDone; } if (strcmp(attrStr, "SV_CLONE") == 0) { attr = SV_CLONE; goto setDone; } if (strcmp(attrStr, "SYMBOL") == 0) { attr = SYMBOL; goto setDone; } if (strcmp(attrStr, "TITLE") == 0) { attr = TITLE; goto setDone; } if (strcmp(attrStr, "UNIGENE") == 0) { attr = UNIGENE; goto setDone; } setDone: switch (attr) { case ALIAS: doALIAS(data); break; case BIOCARTA: doBIOCARTA(data); break; case CYTOBAND: doCYTOBAND(data); break; case GO: doGO(data); break; case HOMOLOG: doHOMOLOG(data); break; case KEGG: doKEGG(data); break; case LOCUSID: doLOCUSID(data); break; case MGC_CLONE: doMGC_CLONE(data); break; case MOTIF: doMOTIF(data); break; case OMIM: doOMIM(data); break; case SEQUENCE: doSEQUENCE(data); break; case SNP: doSNP(data); break; case SV_CLONE: doSV_CLONE(data); break; case SYMBOL: doSYMBOL(data); break; case TITLE: doTITLE(data); break; case UNIGENE: doUNIGENE(data); break; } return(0); } int do1Record() { char *chp; char *attr; char *data; // line shoud be like ">>12345" if (line[0] != '>') { printf("Wrong first line:%s\n", line);fflush(stdout); exit(1); } strcpy(id, line+2); while (fgets(line, sizeof(line), inf) != NULL) { *(line + strlen(line) - 1 ) = '\0'; chp = strstr(line, ":"); if (chp != NULL) { *chp = '\0'; attr = line; data = chp + 2; processRecord(attr, data); } else { if ((line[0] != '>') || (line[1] != '>')) { printf("CGAP ID line not found:\n%s\n", line); break; } else { return(0); } } } done = 1; return(0); } int main(argc, argv) int argc; char **argv; { char **p; char *arg1; if (argc==2) { p=argv; p++; arg1=*p; fALIAS = fopen("cgapALIAS.tab", "w"); fBIOCARTA = fopen("cgapBIOCARTA.tab", "w"); fCYTOBAND = fopen("cgapCYTOBAND.tab", "w"); fGO = fopen("cgapGO.tab", "w"); fHOMOLOG = fopen("cgapHOMOLOG.tab", "w"); fKEGG = fopen("cgapKEGG.tab", "w"); fLOCUSID = fopen("cgapLOCUSID.tab", "w"); fMGC_CLONE = fopen("cgapMGC_CLONE.tab", "w"); fMOTIF = fopen("cgapMOTIF.tab", "w"); fOMIM = fopen("cgapOMIM.tab", "w"); fSEQUENCE = fopen("cgapSEQUENCE.tab", "w"); fSNP = fopen("cgapSNP.tab", "w"); fSV_CLONE = fopen("cgapSV_CLONE.tab", "w"); fSYMBOL = fopen("cgapSYMBOL.tab", "w"); fTITLE = fopen("cgapTITLE.tab", "w"); fUNIGENE = fopen("cgapUNIGENE.tab", "w"); fBIOCARTAdesc = fopen("cgapBIOCARTAdesc.tab", "w"); fKEGGdesc = fopen("cgapKEGGdesc.tab", "w"); if ((inf = fopen(arg1, "r")) == NULL) { fprintf(stderr, "Can't open file %s.\n", arg1); exit(8); } if (fgets(line, sizeof(line), inf) == NULL) fprintf(stderr, "first fgets failed\n"); *(line + strlen(line) - 1) = '\0'; while (!done) { do1Record(); } } fclose(fALIAS); fclose(fBIOCARTA); fclose(fCYTOBAND); fclose(fGO); fclose(fHOMOLOG); fclose(fKEGG); fclose(fLOCUSID); fclose(fMGC_CLONE); fclose(fMOTIF); fclose(fOMIM); fclose(fSEQUENCE); fclose(fSNP); fclose(fSV_CLONE); fclose(fSYMBOL); fclose(fTITLE); fclose(fUNIGENE); fclose(fBIOCARTAdesc); fclose(fKEGGdesc); return(0); }