char *cartDbMakeRandomKey(int numBits)
/* Generate base64 encoding of a random key of at least size numBits returning string to be freed when done */
{
int numBytes = (numBits + 7) / 8; // round up to nearest whole byte.
numBytes = ((numBytes+2)/3)*3; // round up to the nearest multiple of 3 to avoid equals-char padding in base64 output
FILE *f = mustOpen("/dev/urandom", "r"); // open random system device for read-only access.
char *binaryString = needMem(numBytes);
mustRead(f, binaryString, numBytes);
carefulClose(&f);
char * result = base64Encode(binaryString, numBytes); // converts 3 binary bytes into 4 printable characters
int len = strlen(result);
memSwapChar(result, len, '+', 'A'); // replace + and / with characters that are URL-friendly.
memSwapChar(result, len, '/', 'a');
freeMem(binaryString);
return result;
}
int main(int argc, char *argv[])
{
char *database;
char *outFn;
struct dnaSeq *seq;
struct sqlConnection *conn2;
char query2[256];
struct sqlResult *sr2;
char **row2;
if (argc != 4) usage();
database = argv[1];
conn2= hAllocConn(database);
outFn = argv[2];
outf = mustOpen(outFn, "w");
tgtChrom = argv[3];
sqlSafef(query2, sizeof query2, "select secStr, name, chrom, chromStart, chromEnd, strand from evofold where chrom='%s'", tgtChrom);
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
while (row2 != NULL)
{
secStr = row2[0];
id = row2[1];
chrom = row2[2];
chromStart = atoi(row2[3]);
chromEnd = atoi(row2[4]);
strand = *row2[5];
seq = hChromSeq(database, chrom, chromStart, chromEnd);
touppers(seq->dna);
if (strand == '-')
reverseComplement(seq->dna, seq->size);
memSwapChar(seq->dna, seq->size, 'T', 'U');
safef(javaCmd, sizeof(javaCmd),
"java -cp VARNAv3-7.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN %s -structureDBN '%s' -o evoFold/%s/%s.png",
seq->dna, secStr, chrom, id);
fprintf(outf, "%s\n", javaCmd);
row2 = sqlNextRow(sr2);
}
sqlFreeResult(&sr2);
fclose(outf);
hFreeConn(&conn2);
return(0);
}
void searchOneMaskTrim(struct dnaSeq *seq, boolean isProt,
struct genoFind *gf, FILE *outFile,
struct hash *maskHash,
long long *retTotalSize, int *retCount)
/* Search a single sequence against a single genoFind index. */
{
boolean maskQuery = (qMask != NULL);
boolean lcMask = (qMask != NULL && sameWord(qMask, "lower"));
Bits *qMaskBits = maskQuerySeq(seq, isProt, maskQuery, lcMask);
struct dnaSeq trimmedSeq;
ZeroVar(&trimmedSeq);
trimSeq(seq, &trimmedSeq);
if (qType == gftRna || qType == gftRnaX)
memSwapChar(trimmedSeq.dna, trimmedSeq.size, 'u', 't');
searchOne(&trimmedSeq, gf, outFile, isProt, maskHash, qMaskBits);
*retTotalSize += seq->size;
*retCount += 1;
bitFree(&qMaskBits);
}
void expId()
/* Print id */
{
struct encodeExp *exps = NULL;
int count;
struct slPair *varPairs = NULL;
/* transform var:val to var=val. Can't use var=val on command-line as it conflicts with standard options processing */
if (expVars == NULL)
varPairs = NULL;
else
{
memSwapChar(expVars, strlen(expVars), ':', '=');
varPairs = slPairListFromString(expVars,FALSE); // don't expect quoted EDVs which should always be simple tokens.
}
exps = encodeExpGetFromTable(organism, lab, dataType, cellType, varPairs, table);
count = slCount(exps);
verbose(2, "Results: %d\n", count);
if (count == 0)
errAbort("Experiment not found in table %s", table);
if (count > 1)
errAbort("Found more than 1 match for experiment");
printf("%d\n", exps->ix);
}
