struct blackListRange *genbankBlackListParse(char *blackList)
/* parse a black list file into blackListRange data structure */
{
struct lineFile *lf = lineFileMayOpen(blackList, TRUE);
if (lf == NULL)
errAbort("Could not open black list file %s. ", blackList);
struct blackListRange *ranges = NULL;
char *words[2];
while(lineFileRow(lf, words))
{
char *prefix1 = cloneString(words[0]);
genbankDropVer(prefix1, prefix1);
char *number1 = skipToNumeric(prefix1);
int begin = atoi(number1);
*number1 = 0; // null so now prefix1 points to only the prefix
char *prefix2 = cloneString(words[1]);
genbankDropVer(prefix2, prefix2);
char *number2 = skipToNumeric(prefix2);
int end = atoi(number2);
*number2 = 0; // null so now prefix2 points to only the prefix
if (differentString(prefix1, prefix2))
errAbort("blackList file %s has accesions with different prefixes on line %d\n",
lf->fileName, lf->lineIx);
if (begin > end)
errAbort("blackList file %s has end before begin on line %d\n",
lf->fileName, lf->lineIx);
struct blackListRange *range;
AllocVar(range);
range->prefix = prefix1;
range->begin = begin;
range->end = end;
slAddHead(&ranges, range);
}
return ranges;
}
static char *getCcdsRefSeqSummary(struct sqlConnection *conn, struct ccdsInfo *rsCcds)
/* get the refseq summary for a CCDS */
{
struct ccdsInfo *ci;
char accBuf[GENBANK_ACC_BUFSZ];
char *summary = NULL;
for (ci = rsCcds; ci != NULL; ci = ci->next)
{
summary = getRefSeqSummary(conn, genbankDropVer(accBuf, ci->mrnaAcc));
if (summary != NULL)
return summary;
}
return NULL;
}
static char *getCcdsGeneSymbol(struct sqlConnection *conn, struct ccdsInfo *rsCcds)
/* get the gene name for a CCDS */
{
struct ccdsInfo *ci;
char accBuf[GENBANK_ACC_BUFSZ], query[256];
char *geneSym = NULL;
for (ci = rsCcds; ci != NULL; ci = ci->next)
{
sqlSafef(query, sizeof(query), "select name from %s where mrnaAcc='%s'",
refLinkTable, genbankDropVer(accBuf, ci->mrnaAcc));
geneSym = sqlQuickString(conn, query);
if (geneSym != NULL)
return geneSym;
}
return NULL;
}
static char *findRefSeqSummary(struct sqlConnection *conn,
struct geneSimilarities *refSeqs,
char **sumAccv)
/* Given similar refseq genes, find the first one with a RefSeq
* summary and return that summary, or NULL if not found. Also returns
* accv of matched */
{
char buf[GENBANK_ACC_BUFSZ];
struct geneSim *rs;
for (rs = refSeqs->genes; rs != NULL; rs = rs->next)
{
char *sum = getRefSeqSummary(conn, genbankDropVer(buf, rs->gene->name));
if (sum != NULL)
{
*sumAccv = cloneString(rs->gene->name);
return sum;
}
}
*sumAccv = NULL;
return NULL;
}
