a44421a79fb36cc2036fe116b97ea3bc9590cd0c braney Fri Dec 2 09:34:39 2011 -0800 removed rcsid (#295) diff --git src/hg/hgc/dbRIP.c src/hg/hgc/dbRIP.c index 9f050a4..4539c32 100644 --- src/hg/hgc/dbRIP.c +++ src/hg/hgc/dbRIP.c @@ -1,228 +1,227 @@ /* Handle details pages for dbRIP tracks. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "hgc.h" #include "hui.h" #include "obscure.h" #include "cheapcgi.h" #include "htmshell.h" #include "dbRIP.h" #include "polyGenotype.h" -static char const rcsid[] = "$Id: dbRIP.c,v 1.9 2010/05/11 01:43:28 kent Exp $"; static int sortEthnicGroup(const void *e1, const void *e2) /* used by slSort to sort the polyGenotype in order of ethnic group name */ { const struct polyGenotype *p1 = *((struct polyGenotype**)e1); const struct polyGenotype *p2 = *((struct polyGenotype**)e2); return(strcmp(p1->ethnicGroup, p2->ethnicGroup)); } static void polyTable(char *name) { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; struct polyGenotype *pgList = NULL; sprintf(query, "select * from polyGenotype where name = '%s'", name); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { struct polyGenotype *pg; AllocVar(pg); pg = polyGenotypeLoad(row); slAddHead(&pgList, pg); } sqlFreeResult(&sr); hFreeConn(&conn); if (slCount(pgList) > 0) { struct polyGenotype *pg; int totalPlusPlus = 0; int totalPlusMinus = 0; int totalMinusMinus = 0; int totalSamples = 0; double alleleFrequency = 0.0; double unbiasedHeterozygosity = 0.0; int sampleSize = 0; int plusAlleles = 0; int minusAlleles = 0; slSort(&pgList,sortEthnicGroup); printf("<B>Polymorphism Frequencies and Genotypes:</B><BR>\n"); /* This surrounding table avoids the problem of the border lines of * the second table go missing. Something about the style sheet ... */ printf("<TABLE BGCOLOR=\"#FFFEE8\" CELLPADDING=0><TR><TD>\n"); printf("<TABLE BORDER=2 bgcolor=\"#e4cdf2\">\n"); printf("<TR bgcolor=\"#d2abf2\"><TH align=center>Ethnic Group</TH>"); printf("<TH align=center>Sample Size</TH>"); printf("<TH align=center>Allele Frequency</TH>"); printf("<TH align=center>+/+</TH>"); printf("<TH align=center>+/-</TH>"); printf("<TH align=center>-/-</TH>"); printf("<TH align=center>Unbiased Heterozygosity</TH>"); printf("</TR>\n"); for (pg = pgList; pg != NULL; pg = pg->next) { plusAlleles = (pg->plusPlus << 1) + pg->plusMinus; minusAlleles = (pg->minusMinus << 1) + pg->plusMinus; sampleSize = pg->plusPlus + pg->plusMinus + pg->minusMinus; if ((plusAlleles + minusAlleles) > 0) { alleleFrequency = (double)plusAlleles / (double)(plusAlleles + minusAlleles); } else alleleFrequency = 0.0; printf("<TR><TD align=left>%s</TD>", pg->ethnicGroup); printf("<TD align=center>%d</TD>", sampleSize); printf("<TD align=center>%.3f</TD>", alleleFrequency); printf("<TD align=center>%d</TD>", pg->plusPlus); printf("<TD align=center>%d</TD>", pg->plusMinus); printf("<TD align=center>%d</TD>", pg->minusMinus); /* adjust by 2N/(2N-1) for small sample heterozygosity calculation * http://www.genetics.org/cgi/content/abstract/89/3/583 * Masatoshi Nei (1978) */ if (sampleSize > 0) { unbiasedHeterozygosity=2*alleleFrequency*(1.0 - alleleFrequency); unbiasedHeterozygosity *= (double)(sampleSize << 1) / (double)((sampleSize << 1) - 1); } else unbiasedHeterozygosity=2*alleleFrequency*(1.0 - alleleFrequency); printf("<TD align=center>%.3f</TD>", unbiasedHeterozygosity); printf("</TR>\n"); totalSamples += sampleSize; totalPlusPlus += pg->plusPlus; totalMinusMinus += pg->minusMinus; totalPlusMinus += pg->plusMinus; } plusAlleles = (totalPlusPlus << 1) + totalPlusMinus; minusAlleles = (totalMinusMinus << 1) + totalPlusMinus; if ((plusAlleles + minusAlleles) > 0) { alleleFrequency = (double)plusAlleles / (double)(plusAlleles + minusAlleles); } else { alleleFrequency = 0.0; } printf("<TR><TH align=left>All Samples</TH>"); printf("<TH align=center>%d</TH>", totalSamples); printf("<TH align=center>%.3f</TH>", alleleFrequency); printf("<TH align=center>%d</TH>", totalPlusPlus); printf("<TH align=center>%d</TH>", totalPlusMinus); printf("<TH align=center>%d</TH>", totalMinusMinus); if (totalSamples > 0) { unbiasedHeterozygosity = 2 * alleleFrequency * (1.0 - alleleFrequency); unbiasedHeterozygosity *= (double)(totalSamples << 1)/(double)((totalSamples << 1) - 1); } else unbiasedHeterozygosity = 2 * alleleFrequency * (1.0 - alleleFrequency); printf("<TH align=center>%.3f</TH>", unbiasedHeterozygosity); printf("</TR>\n"); printf("</TABLE>\n"); printf("</TD></TR></TABLE>\n"); } else printf("<B>Polymorphism Frequencies and Genotypes:</B> NA<BR>\n"); } void dbRIP(struct trackDb *tdb, char *item, char *itemForUrl) /* Put up dbRIP track info */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char table[64]; boolean hasBin; struct dbRIP *loadItem; struct dyString *query = newDyString(512); char **row; boolean firstTime = TRUE; int start = cartInt(cart, "o"); int itemCount = 0; genericHeader(tdb, item); hFindSplitTable(database, seqName, tdb->table, table, &hasBin); dyStringPrintf(query, "select * from %s where chrom = '%s' and ", table, seqName); hAddBinToQuery(winStart, winEnd, query); dyStringPrintf(query, "name = '%s' and chromStart = %d", item, start); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); ++itemCount; loadItem = dbRIPLoad(row+hasBin); printf("<B>Database ID:</B> %s<BR>\n", loadItem->name); printf("<B>Original ID:</B> %s<BR>\n", loadItem->originalId); printf("<B>Class:</B> %s<BR>\n", loadItem->polyClass); printf("<B>Family:</B> %s<BR>\n", loadItem->polyFamily); printf("<B>Subfamily:</B> %s<BR>\n", loadItem->polySubfamily); printf("<B>Associated Disease:</B> %s<BR>\n", loadItem->disease); printf("<B>Sequence of L1 insertion and 400bp flanking on each side:</B>"); printf("(<span style='color:blue;'>5' flanking-</span>"); // ' = ' printf("<span style='color:green;'><span style='text-decoration:underline;'>"); printf("TSD1</span>-</span><span style='color:red'>REPEAT SEQUENCE</span>"); printf("<span style='color:green;'>-<span style='text-decoration:underline;'>"); printf("TSD2</span>-</span><span style='color:blue;'>3' flanking</span>)<br>"); // ' = ' printf("(\"<span style='color:green; text-decoration:underline;'>nnnnn</span>\""); printf(" --> unknown TSD; \"<span style='color:red;'>NNNNNNNNNN</span>\" -->"); printf(" unknown Repeat Sequence):<BR>\n<PRE><span style='color:blue;'>%s", loadItem->polySeq); printf("</span></PRE><BR>\n"); printf("<B>Forward Primer:</B> %s<BR>\n", loadItem->forwardPrimer); printf("<B>Reverse Primer:</B> %s<BR>\n", loadItem->reversePrimer); if (loadItem->tm > 0.0) printf("<B>Annealing Temperature:</B> %.1f °C.<BR>\n", loadItem->tm); else printf("<B>Annealing Temperature:</B> NA<BR>\n"); if (loadItem->filledSize > 0) printf("<B>PCR Product Size (Filled):</B> %d bp.<BR>\n", loadItem->filledSize); else printf("<B>PCR Product Size (Filled):</B> NA<BR>\n"); if (loadItem->emptySize > 0) printf("<B>PCR Product Size (Empty):</B> %d bp.<BR>\n", loadItem->emptySize); else printf("<B>PCR Product Size (Empty):</B> NA<BR>\n"); printf("<B>Ascertaining Method:</B> %s<BR>\n", loadItem->ascertainingMethod); printf("<B>Insertion found in reference sequence:</B> %s<BR>\n", startsWith("UCSC",loadItem->polySource) ? "yes" : "no"); printf("<B>Remarks:</B> %s<BR>\n", loadItem->remarks); if (strlen(loadItem->genoRegion) > 0) printf("<B>Gene Context:</B> %s<BR>\n", loadItem->genoRegion); else printf("<B>Gene Context:</B> NA<BR>\n"); polyTable(loadItem->name); printPosOnChrom(loadItem->chrom, loadItem->chromStart, loadItem->chromEnd, loadItem->strand, TRUE, loadItem->name); printf("<HR>\n<B>Reference(s):</B> %s\n<HR>\n", loadItem->reference); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); }