/* hgCert - hgCert parses cerfification data file and generates an html file and a .tab file */
/* Copyright (C) 2011 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "hCommon.h"
#include "htmshell.h"
void usage()
/* Explain usage and exit. */
{
errAbort(
"hgCert - hgCert parses cerfification data file and generates an html file and a .tab file\n"
"usage: hgCert certificate.txt >certificate.html\n");
}
char *doLine(char *lineType, char *lineIn)
{
char *result;
char line[1000];
strcpy(line, lineIn);
*(line+strlen(line) - 1) = '\0';
result = strstr(line, lineType);
if (result == NULL)
{
return(result);
}
else
{
result = result + strlen(lineType);
return(result);
}
}
char *doLine2(char *lineIn, char *lineType)
{
char *chp;
char line[1000];
strcpy(line, lineIn);
*(line+strlen(line) - 1) = '\0';
chp = strstr(line, ":");
if (chp == NULL) return(strdup("???"));
*chp = '\0';
chp ++;
chp ++;
chp = strdup(chp);
strcpy(lineType, line);
if (strcmp(chp, " ") == 0) chp = strdup(" ");
return(chp);
}
int main(int argc, char *argv[])
{
char *infileName;
FILE *inf, *outf;
char line[1000];
char *content;
char *contact="";
char *join;
char *join1, *join2;
char *spanner,
*variation,
*variationEvidence,
*comment,
*evaluation,
*remark;
char lineType[100];
//int i,j;
if (argc != 2)
{
usage();
}
else
{
infileName = argv[1];
fprintf(stdout, "\n%sNon-standard Join Certificates\n", getCspMetaHeader());
fprintf(stdout, "\n");
fprintf(stdout, "\n");
fprintf(stdout, "\n");
fprintf(stdout, "| Accession 1 | \n");
fprintf(stdout, " Accession 2 | \n");
fprintf(stdout, " Spanner | \n");
fprintf(stdout, " Variation | \n");
fprintf(stdout, " Variation Evidence | \n");
fprintf(stdout, " Comment | \n");
fprintf(stdout, " Evaluation | \n");
fprintf(stdout, " Remark | \n");
fprintf(stdout, " Contact | \n");
fprintf(stdout, " \n");
outf = fopen("cert.tab", "w");
if ((inf = fopen(infileName, "r")) == NULL)
{
fprintf(stderr, "Can't open file %s.\n", infileName);
exit(8);
}
while (fgets(line, 1000, inf) != NULL)
{
content = doLine("CONTACT: ", line);
if (content != NULL)
{
contact = strdup(content);
fgets(line, 1000, inf);
fgets(line, 1000, inf);
}
join = doLine("JOIN: ", line);
if (join != NULL)
{
join1 = join;
join2 = strstr(join, " ");
*join2 = '\0';
join2++;
join1 = strdup(join1);
join2 = strdup(join2);
fgets(line, 1000, inf);
}
else
{
fprintf(stderr, "No JOIN!\n");
exit(1);
}
spanner=variation=variationEvidence=comment=evaluation = remark= strdup(" ");
again:
content = doLine2(line, lineType);
if (strcmp(lineType, "VARIATION") == 0)
{
variation = content;
}
content = doLine2(line, lineType);
if (strcmp(lineType, "SPANNER") == 0)
{
spanner = content;
}
content = doLine2(line, lineType);
if (strcmp(lineType, "VARIATION EVIDENCE") == 0)
{
variationEvidence = content;
}
content = doLine2(line, lineType);
if (strcmp(lineType, "REMARK") == 0)
{
remark = content;
}
content = doLine2(line, lineType);
if (strcmp(lineType, "COMMENT") == 0)
{
comment = content;
}
content = doLine2(line, lineType);
if (strcmp(lineType, "EVALUATION") == 0)
{
evaluation = content;
}
fgets(line, 1000, inf);
if (strlen(line) > 3)
{
goto again;
}
else
{
printf("");
printf("| %s | ", join1);
printf("%s | ", join2);
printf("%s | ", spanner);
printf("%s | ", variation);
printf("%s | ", variationEvidence);
printf("%s | ", comment);
printf("%s | ", evaluation);
printf("%s | ", remark);
printf("%s | ", contact, contact);
printf("
\n");
fprintf(outf, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
join1, join2, spanner, evaluation, variation, variationEvidence,
contact, remark, comment);
}
}
}
/*else
{
fprintf(stderr, "Usage: hgCert certificate.txt >certificate.html\n\n");
return(1);
}
*/
fprintf(stdout, "\n");
fprintf(stdout, "\n");
fclose(outf);
return(0);
}