void musAliAt(char *database, char *chrom, char *humanFa, char *mouseFa)
/* musAliAt - Produce .fa files where mouse alignments hit on chr22. */
{
char query[256], **row;
struct sqlResult *sr;
struct sqlConnection *conn;
struct dnaSeq *musSeq, *homoSeq;
struct psl *psl;
struct hash *musHash = newHash(10);
FILE *musOut = mustOpen(mouseFa, "w");
hSetDb(database);
conn = hAllocConn();
sqlSafef(query, sizeof query, "select * from blatMouse where tName = '%s'", chrom);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
psl = pslLoad(row);
if ((musSeq = hashFindVal(musHash, psl->qName)) == NULL)
{
musSeq = hExtSeq(psl->qName);
hashAdd(musHash, psl->qName, NULL);
faWriteNext(musOut, musSeq->name, musSeq->dna, musSeq->size);
freeDnaSeq(&musSeq);
}
pslFree(&psl);
}
}
void retroShowCdnaAli(char *mappedId)
/* Show alignment for accession, mostly ripped off from htcCdnaAli */
{
char *track = cartString(cart, "aliTable");
struct trackDb *tdb = hashMustFindVal(trackHash, track);
char *table = cartString(cart, "table");
int start = cartInt(cart, "o");
struct sqlConnection *conn = hAllocConn(database);
struct sqlConnection *defDbConn = NULL;
struct mappingInfo *mi = mappingInfoNew(conn, table, mappedId);
struct genbankCds cds = getCds(conn, mi);
struct psl *psl;
struct dnaSeq *rnaSeq = NULL;
char *spec = trackDbRequiredSetting(tdb, BASE_COLOR_USE_SEQUENCE);
char *specCopy = cloneString(spec);
char *words[3];
int nwords = chopByWhite(specCopy, words, ArraySize(words));
char acc[512];
/* Print start of HTML. */
writeFramesetType();
puts("<HTML>");
printf("<HEAD>\n<TITLE>%s vs Genomic [%s]</TITLE>\n</HEAD>\n\n", mi->seqId, track);
/* Look up alignment and sequence in database. Always get sequence
* from defaultDb */
psl = loadAlign(conn, mi, start);
if (startsWith("August",mi->geneSet))
safef(acc, sizeof(acc), "aug-%s.T1",mi->seqId);
else
safef(acc, sizeof(acc), "%s",mi->seqId);
// value is: extFile seqTbl extFileTbl
if ((nwords != (int)ArraySize(words)) || !sameString(words[0], "extFile"))
errAbort("invalid %s track setting: %s ", BASE_COLOR_USE_SEQUENCE, spec);
char *seqTable = words[1];
char *extTable = words[2];
rnaSeq = hDnaSeqGet(database, acc, seqTable, extTable);
if (rnaSeq == NULL)
{
char *acc = mi->seqId;
rnaSeq = hExtSeq(database, acc);
if (rnaSeq == NULL)
errAbort("can't get mRNA sequence from %s prefix %s for %s from %s mappedId %s",
database, mi->geneSet, acc, track, mappedId);
}
sqlDisconnect(&defDbConn);
showSomeAlignment(psl, rnaSeq, gftDna, 0, rnaSeq->size, NULL, cds.start, cds.end);
pslFree(&psl);
dnaSeqFree(&rnaSeq);
mappingInfoFree(&mi);
hFreeConn(&conn);
}
