void spTest(char *database, char *someAcc)
/* spTest - Test out sp library.. */
{
struct sqlConnection *conn = sqlConnect(database);
char *acc, *id, *binomial, *common;
struct slName *geneList, *gene, *accList, *n, *list;
struct slName *nameList, *name, *keyList, *key, *typeList, *type;
struct spFeature *featList, *feat;
struct spCitation *citeList, *cite;
char *ret = NULL;
int taxon;
int classId = 0, typeId = 0, refId = 0;
printf("input: %s\n", someAcc);
acc = spLookupPrimaryAcc(conn, someAcc);
printf("primary accession: %s\n", acc);
id = spAccToId(conn, acc);
printf("SwissProt id: %s\n", id);
printf("acc from id: %s\n", spIdToAcc(conn, id));
ret = spOrganelle(conn, acc);
printf("organelle: %s\n", (ret == NULL) ? "(null)" : ret);
printf("isCurated: %d\n", spIsCurated(conn, acc));
printf("aaSize: %d\n", spAaSize(conn,acc));
printf("molWeight: %d\n", spMolWeight(conn,acc));
printf("createDate: %s\n", spCreateDate(conn,acc));
printf("seqDate: %s\n", spSeqDate(conn,acc));
printf("annDate: %s\n", spAnnDate(conn,acc));
printf("description: %s\n", spDescription(conn, acc));
taxon = spTaxon(conn, acc);
printf("taxon: %d\n", taxon);
binomial = spTaxonToBinomial(conn, taxon);
printf("first scientific name: %s\n", binomial);
common = spTaxonToCommon(conn, taxon);
printf("first common name: %s\n", common);
printf("taxon from sci: %d\n", spBinomialToTaxon(conn, binomial));
printf("taxon from common: %d\n", spCommonToTaxon(conn, common));
printf("all scientific names:");
nameList = spBinomialNames(conn, acc);
for (name = nameList; name != NULL; name = name->next)
printf(" %s,", name->name);
printf("\n");
printf("gene(s):");
geneList = spGenes(conn,acc);
for (gene=geneList; gene != NULL; gene = gene->next)
printf(" %s,", gene->name);
printf("\n");
for (gene=geneList; gene != NULL; gene = gene->next)
{
accList = spGeneToAccs(conn, gene->name, 0);
printf(" any %s:", gene->name);
for (n = accList; n != NULL; n = n->next)
printf(" %s,", n->name);
printf("\n");
slFreeList(&accList);
printf(" %s %s:", common, gene->name);
accList = spGeneToAccs(conn, gene->name, taxon);
for (n = accList; n != NULL; n = n->next)
printf(" %s,", n->name);
printf("\n");
slFreeList(&accList);
}
slFreeList(&geneList);
printf("keyword(s):");
keyList = spKeywords(conn, acc);
for (key = keyList; key != NULL; key = key->next)
printf(" %s,", key->name);
printf("\n");
for (key = keyList; key != NULL; key = key->next)
{
accList = spKeywordSearch(conn, key->name, taxon);
printPartialList(common, key->name, accList, 4);
slFreeList(&accList);
break; /* This is a little slow, once is enough. */
}
for (key = keyList; key != NULL; key = key->next)
{
accList = spKeywordSearch(conn, key->name, 0);
printPartialList("all", key->name, accList, 4);
slFreeList(&accList);
break; /* This is a little slow, once is enough. */
}
slFreeList(&keyList);
printf("All comments:\n");
list = slComments(conn, acc, NULL);
for (n = list; n != NULL; n = n->next)
printf(" %s\n", n->name);
slFreeList(&list);
typeList = slCommentTypes(conn);
for (type = typeList; type != NULL; type = type->next)
{
list = slComments(conn, acc, type->name);
if (list != NULL)
{
printf("%s comments:\n", type->name);
for (n = list; n != NULL; n = n->next)
printf(" %s\n", n->name);
slFreeList(&list);
}
}
slFreeList(&typeList);
list = spEmblAccs(conn, acc);
printf("GenBank/EMBL:");
for (n = list; n != NULL; n = n->next)
printf(" %s,", n->name);
printf("\n");
if (list != NULL)
printf("acc from %s: %s\n",
list->name, spAccFromEmbl(conn, list->name));
slFreeList(&list);
list = spPdbAccs(conn, acc);
printf("PDB:");
for (n = list; n != NULL; n = n->next)
printf(" %s,", n->name);
printf("\n");
featList = spFeatures(conn, acc, 0, 0);
printf("All features:\n");
for (feat = featList; feat != NULL; feat = feat->next)
{
printFeat(conn, feat);
classId = feat->featureClass;
typeId = feat->featureType;
}
slFreeList(&featList);
if (classId != 0 && typeId != 0)
{
printf("%s class features:\n", spFeatureClassName(conn, classId));
featList = spFeatures(conn, acc, classId, 0);
for (feat = featList; feat != NULL; feat = feat->next)
printFeat(conn, feat);
slFreeList(&featList);
printf("%s type features:\n", spFeatureTypeName(conn, typeId));
featList = spFeatures(conn, acc, 0, typeId);
for (feat = featList; feat != NULL; feat = feat->next)
printFeat(conn, feat);
slFreeList(&featList);
printf("same class & type features:\n");
featList = spFeatures(conn, acc, classId, typeId);
for (feat = featList; feat != NULL; feat = feat->next)
printFeat(conn, feat);
slFreeList(&featList);
printf("class loop: %d->%s->%d\n", classId,
spFeatureClassName(conn, classId),
spFeatureClassId(conn, spFeatureClassName(conn, classId)));
printf("type loop: %d->%s->%d\n", typeId,
spFeatureTypeName(conn, typeId),
spFeatureTypeId(conn, spFeatureTypeName(conn, typeId)));
}
citeList = spCitations(conn, acc);
for (cite = citeList; cite != NULL; cite = cite->next)
{
refId = cite->reference;
printf("title: %s\n", spRefTitle(conn, refId));
printf("authors:");
list = spRefAuthors(conn, refId);
for (n = list; n != NULL; n = n->next)
printf(" %s, ", n->name);
printf("\n");
slFreeList(&list);
printf("location: %s\n", spRefCite(conn, refId));
printf("pubMed: %s\n", spRefPubMed(conn, refId));
}
if (refId != 0)
{
printf("other accs associated with last reference:\n\t");
list = spRefToAccs(conn, refId);
printPartialList("", "", list, 6);
slFreeList(&list);
}
sqlDisconnect(&conn);
}
void makeActiveImagePB(char *psOutput, char *psOutput2)
/* Make image and image map. */
{
char *mapName = "map";
int pixWidth, pixHeight;
char *answer;
char cond_str[255];
struct sqlConnection *conn;
struct sqlConnection *connCentral;
char query[256];
struct sqlResult *sr;
char **row;
int iypos;
char *blatGbDb;
char *sciName, *commonName;
char *spDisplayId;
char *oldDisplayId;
conn = sqlConnect(UNIPROT_DB_NAME);
hPrintf("<br><font size=4>Protein ");
hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" TARGET=_blank><B>%s</B></A>\n",
proteinID, proteinID);
spDisplayId = spAccToId(conn, spFindAcc(conn, proteinID));
if (strstr(spDisplayId, spFindAcc(conn, proteinID)) == NULL)
{
hPrintf(" (aka %s", spDisplayId);
/* show once if the new and old displayId are the same */
oldDisplayId = oldSpDisplayId(spDisplayId);
if (oldDisplayId != NULL)
{
if (!sameWord(spDisplayId, oldDisplayId))
{
hPrintf(" or %s", oldSpDisplayId(spDisplayId));
}
}
hPrintf(")\n");
}
hPrintf(" %s\n", description);
hPrintf("</font><br>");
hPrintf("Organism: ");
/* get scientific and Genbank common name of this organism */
sciName = NULL;
commonName = NULL;
sqlSafefFrag(cond_str, sizeof(cond_str),"accession='%s'", proteinID);
answer = sqlGetField(PROTEOME_DB_NAME, "spXref3", "division", cond_str);
if (answer != NULL)
{
sqlSafefFrag(cond_str, sizeof(cond_str), "id=%s and nameType='scientific name'", answer);
sciName = sqlGetField(PROTEOME_DB_NAME, "taxonNames", "name", cond_str);
sqlSafefFrag(cond_str, sizeof(cond_str), "id=%s and nameType='genbank common name'", answer);
commonName = sqlGetField(PROTEOME_DB_NAME, "taxonNames", "name", cond_str);
}
if (sciName != NULL)
{
hPrintf("%s", sciName);
}
if (commonName != NULL)
{
hPrintf(" (%s)", commonName);
}
hPrintf("<br>");
protSeq = getAA(proteinID);
if (protSeq == NULL)
{
hUserAbort("%s is not a current valid entry in UniProtKB\n", proteinID);
}
protSeqLen = strlen(protSeq);
fflush(stdout);
iypos = 15;
doTracks(proteinID, mrnaID, protSeq, &iypos, psOutput);
if (!hTableExists(database, "pbStamp")) goto histDone;
pbScale = 3;
pixWidth = 765;
insideWidth = pixWidth-gfxBorder;
pixHeight = 350;
if (psOutput2)
{
vg2 = vgOpenPostScript(pixWidth, pixHeight, psOutput2);
}
else
{
trashDirFile(&gifTn2, "pbt", "pbt", ".png");
vg2 = vgOpenPng(pixWidth, pixHeight, gifTn2.forCgi, FALSE);
}
g_vg = vg2;
pbRed = vgFindColorIx(vg2, 0xf9, 0x51, 0x59);
pbBlue = vgFindColorIx(g_vg, 0x00, 0x00, 0xd0);
normalColor = pbBlue;
abnormalColor = pbRed;
bkgColor = vgFindColorIx(vg2, 255, 254, 232);
vgBox(vg2, 0, 0, insideWidth, pixHeight, bkgColor);
/* Start up client side map. */
mapName=cloneString("pbStamps");
hPrintf("\n<MAP Name=%s>\n", mapName);
vgSetClip(vg2, 0, gfxBorder, insideWidth, pixHeight - 2*gfxBorder);
iypos = 15;
/* Draw stamps. */
doStamps(proteinID, mrnaID, protSeq, vg2, &iypos);
/* Finish map. */
hPrintf("</MAP>\n");
/* Save out picture and tell html file about it. */
vgClose(&vg2);
hPrintf("<P>");
hPrintf("\n<IMG SRC=\"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s><BR>",
gifTn2.forCgi, pixWidth, pixHeight, mapName);
if (proteinInSupportedGenome)
{
hPrintf("\n<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#histograms\" TARGET=_blank>");
}
else
{
hPrintf("\n<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#histograms\" TARGET=_blank>");
}
hPrintf("Explanation of Protein Property Histograms</A><BR>");
hPrintf("<P>");
histDone:
hPrintf("<P>");
fflush(stdout);
/* See if a UCSC Genome Browser exist for this organism. If so, display BLAT link. */
connCentral = hConnectCentral();
sqlSafef(query, sizeof(query),
"select defaultDb.name from dbDb, defaultDb where dbDb.scientificName='%s' and dbDb.name=defaultDb.name",
sciName);
sr = sqlGetResult(connCentral, query);
row = sqlNextRow(sr);
if (row != NULL)
{
blatGbDb = strdup(row[0]);
}
else
{
blatGbDb = NULL;
}
sqlFreeResult(&sr);
hDisconnectCentral(&connCentral);
if (proteinInSupportedGenome || (blatGbDb != NULL))
{
hPrintf("\n<B>UCSC Links:</B><BR>\n ");
hPrintf("<UL>\n");
/* Show GB links only if the protein belongs to a supported genome */
if (proteinInSupportedGenome)
{
doGenomeBrowserLink(proteinID, mrnaID, hgsidStr);
doGeneDetailsLink(proteinID, mrnaID, hgsidStr);
}
/* Show Gene Sorter link only if it is valid for this genome */
if (hgNearOk(database))
{
doGeneSorterLink(protDisplayID, mrnaID, hgsidStr);
}
/* Show BLAT link if we have UCSC Genome Browser for it */
if (blatGbDb != NULL)
{
doBlatLink(blatGbDb, sciName, commonName, protSeq);
}
hPrintf("</UL><P>");
}
/* This section shows various types of domains */
conn = sqlConnect(UNIPROT_DB_NAME);
domainsPrint(conn, proteinID);
hPrintf("<P>");
/* Do Pathway section only if the protein belongs to a supported genome */
if (proteinInSupportedGenome);
{
doPathwayLinks(proteinID, mrnaID);
}
printFASTA(proteinID, protSeq);
}
void makeActiveImagePB(char *psOutput, char *psOutput2)
/* Make image and image map. */
{
char *mapName = "map";
int pixWidth, pixHeight;
struct sqlConnection *conn;
char query[256];
struct sqlResult *sr;
char **row;
int iypos;
char *spDisplayId;
char *oldDisplayId;
conn = sqlConnect(UNIPROT_DB_NAME);
printf("<BR>");
hPrintf("<BR><font size=4><B>Protein: ");
hPrintf("%s</B>", proteinID);
/* Please note the hiv database name is hard wired here.*/
safef(query, sizeof(query),
"select subjId from hivVax003Vax004.gsIdXref where aaSeqId = '%s'", proteinID);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
{
printf("<BR>");
hPrintf("<font size=4><B>Subject: ");
hPrintf("<A HREF=\"../cgi-bin/gsidSubj?hgs_subj=%s&submit=Go!\">", row[0]);
hPrintf("%s</A></B><BR>", row[0]);
}
sqlFreeResult(&sr);
spDisplayId = spAccToId(conn, spFindAcc(conn, proteinID));
if (strstr(spDisplayId, spFindAcc(conn, proteinID)) == NULL)
{
hPrintf(" (aka %s", spDisplayId);
/* show once if the new and old displayId are the same */
oldDisplayId = oldSpDisplayId(spDisplayId);
if (oldDisplayId != NULL)
{
if (!sameWord(spDisplayId, oldDisplayId))
{
hPrintf(" or %s", oldSpDisplayId(spDisplayId));
}
}
hPrintf(")\n");
}
hPrintf("</font><br>");
protSeq = getAA(proteinID);
if (protSeq == NULL)
{
errAbort("%s is not a current valid entry in UniProt(SWISS-PROT/TrEMBL)\n", proteinID);
}
protSeqLen = strlen(protSeq);
fflush(stdout);
iypos = 15;
doTracks(proteinID, mrnaID, protSeq, &iypos, psOutput);
if (!hTableExists(database, "pbStamp")) goto histDone;
pbScale = 3;
pixWidth = 520;
insideWidth = pixWidth-gfxBorder;
pixHeight = 350;
if (psOutput2)
{
vg2 = vgOpenPostScript(pixWidth, pixHeight, psOutput2);
}
else
{
trashDirFile(&gifTn2, "pbt", "pbt", ".gif");
vg2 = vgOpenGif(pixWidth, pixHeight, gifTn2.forCgi, FALSE);
}
g_vg = vg2;
pbRed = vgFindColorIx(vg2, 0xf9, 0x51, 0x59);
pbBlue = vgFindColorIx(g_vg, 0x00, 0x00, 0xd0);
normalColor = pbBlue;
abnormalColor = pbRed;
bkgColor = vgFindColorIx(vg2, 255, 254, 232);
vgBox(vg2, 0, 0, insideWidth, pixHeight, bkgColor);
/* Start up client side map. */
mapName=cloneString("pbStamps");
hPrintf("\n<MAP Name=%s>\n", mapName);
vgSetClip(vg2, 0, gfxBorder, insideWidth, pixHeight - 2*gfxBorder);
iypos = 15;
/* Draw stamps. */
doStamps(proteinID, mrnaID, protSeq, vg2, &iypos);
/* Finish map. */
hPrintf("</MAP>\n");
/* Save out picture and tell html file about it. */
vgClose(&vg2);
hPrintf("<P>");
hPrintf("\n<IMG SRC=\"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s><BR>",
gifTn2.forCgi, pixWidth, pixHeight, mapName);
if (proteinInSupportedGenome)
{
hPrintf("\n<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#histograms\" TARGET=_blank>");
}
else
{
hPrintf("\n<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbGsid/pbTracksHelp.shtml#histograms\" TARGET=_blank>");
}
hPrintf("Explanation of Protein Property Histograms</A><BR>");
hPrintf("<P>");
histDone:
hPrintf("<P>");
fflush(stdout);
printFASTA(proteinID, protSeq);
}
