42f147365cff4903feadc57b95dd6fe94e2d8d4b hiram Mon Jul 21 13:29:35 2014 -0700 completed the joinedRmsk click handling refs #9741 diff --git src/hg/hgc/joinedRmskClick.c src/hg/hgc/joinedRmskClick.c index 8355772..cfae48d 100644 --- src/hg/hgc/joinedRmskClick.c +++ src/hg/hgc/joinedRmskClick.c @@ -1,410 +1,410 @@ /* joinedRmskClick - Click handler for joinedRmskTrack. This is based * loosely on the original rmsk click handler inside * of hgc.c. * * Written by Robert Hubley 12/2012 */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "hgc.h" #include "rmskOut2.h" #include "rmskAlign.h" #include "rmskJoined.h" #include "hCommon.h" void printAlignment (struct rmskAlign *ra) /* * Print RepeatMasker alignment data stored in RM's cAlign format. * The format is basically a lightly compressed diff format where * the query and subject are merged into one squence line. The * runs of exact matching sequences are interrupted by either * single base substitutions annotated as queryBase "/" subjectBase, * insertions in the subject annotated as "+ACTAT+", or deletions * in the query annotated as "-ACTTTG-". */ { int alignLength = 80; char querySeq[alignLength + 1]; char diffSeq[alignLength + 1]; char subjSeq[alignLength + 1]; int inSub = 0; int inDel = 0; int inIns = 0; int aIdx = 0; int sIdx = 0; int qCnt = 0; int sCnt = 0; int qStart = ra->genoStart; int sStart = ra->repStart; if (ra->strand[0] == '-') sStart = ra->repEnd; int maxNameLen = (strlen (ra->genoName) > strlen (ra->repName) ? strlen (ra->genoName) : strlen (ra->repName)); while (ra->alignment[aIdx] != '\0') { if (ra->alignment[aIdx] == '/') inSub = 1; else if (ra->alignment[aIdx] == '-') inDel ^= 1; else if (ra->alignment[aIdx] == '+') inIns ^= 1; else { if (inSub) { subjSeq[sIdx - 1] = ra->alignment[aIdx]; if ((querySeq[sIdx - 1] == 'C' && subjSeq[sIdx - 1] == 'T') || (querySeq[sIdx - 1] == 'T' && subjSeq[sIdx - 1] == 'C') || (querySeq[sIdx - 1] == 'A' && subjSeq[sIdx - 1] == 'G') || (querySeq[sIdx - 1] == 'G' && subjSeq[sIdx - 1] == 'A')) diffSeq[sIdx - 1] = 'i'; else if ((index ("BDHVRYKMSWNX", querySeq[sIdx - 1]) != NULL) || (index ("BDHVRYKMSWNX", subjSeq[sIdx - 1]) != NULL)) diffSeq[sIdx - 1] = '?'; else diffSeq[sIdx - 1] = 'v'; inSub = 0; } else if (inDel) { querySeq[sIdx] = ra->alignment[aIdx]; subjSeq[sIdx] = '-'; diffSeq[sIdx] = '-'; qCnt++; sIdx++; } else if (inIns) { querySeq[sIdx] = '-'; subjSeq[sIdx] = ra->alignment[aIdx]; diffSeq[sIdx] = '-'; sCnt++; sIdx++; } else { diffSeq[sIdx] = ' '; querySeq[sIdx] = ra->alignment[aIdx]; subjSeq[sIdx] = ra->alignment[aIdx]; sCnt++; qCnt++; sIdx++; } if (sIdx == alignLength) { querySeq[sIdx] = '\0'; diffSeq[sIdx] = '\0'; subjSeq[sIdx] = '\0'; printf ("%*s %10d %s %d\n", maxNameLen, ra->genoName, qStart, querySeq, (qStart + qCnt - 1)); printf ("%*s %s\n", maxNameLen, " ", diffSeq); if (ra->strand[0] == '+') printf ("%*s %10d %s %d\n", maxNameLen, ra->repName, sStart, subjSeq, (sStart + sCnt - 1)); else printf ("%*s %10d %s %d\n", maxNameLen, ra->repName, sStart, subjSeq, (sStart - sCnt + 1)); printf ("\n"); qStart += qCnt; if (ra->strand[0] == '+') sStart += sCnt; else sStart -= sCnt; qCnt = 0; sCnt = 0; sIdx = 0; } } aIdx++; } if (sIdx) { querySeq[sIdx] = '\0'; diffSeq[sIdx] = '\0'; subjSeq[sIdx] = '\0'; printf ("%*s %10d %s %d\n", maxNameLen, ra->genoName, qStart, querySeq, (qStart + qCnt - 1)); printf ("%*s %s\n", maxNameLen, " ", diffSeq); if (ra->strand[0] == '+') printf ("%*s %10d %s %d\n", maxNameLen, ra->repName, sStart, subjSeq, (sStart + sCnt - 1)); else printf ("%*s %10d %s %d\n", maxNameLen, ra->repName, sStart, subjSeq, (sStart - sCnt + 1)); ; } } void printOutTableHeader (char strand) /* Print the appropriate HTML table header * given the strand of the element. */ { const char *hd1_style = "style=\"background-color:#C2C9E0; font-size:14px; padding:4px 14px;\""; const char *hd1span_style = "style=\"background-color:#6678B1; font-size:14px; padding:4px 14px;\""; const char *hd2_style = "style=\"background-color:#C2C9E0; font-size:14px; padding:4px 14px; " "border-bottom: 2px solid #6678B1;\""; printf (" <thead>\n"); printf (" <tr>\n"); printf (" <th %s>bit/sw</th>\n", hd1_style); printf (" <th %s>perc</th>\n", hd1_style); printf (" <th %s>perc</th>\n", hd1_style); printf (" <th %s>perc</th>\n", hd1_style); printf (" <th colspan=\"4\" %s>query</th>\n", hd1span_style); printf (" <th %s></th>\n", hd1_style); printf (" <th colspan=\"5\" %s>matching repeat</th>\n", hd1span_style); printf (" <th %s></th>\n", hd1_style); printf (" </tr>\n"); printf (" <tr>\n"); printf (" <th %s>score</th>\n", hd2_style); printf (" <th %s>div.</th>\n", hd2_style); printf (" <th %s>del.</th>\n", hd2_style); printf (" <th %s>ins.</th>\n", hd2_style); printf (" <th %s>sequence</th>\n", hd2_style); printf (" <th %s>begin</th>\n", hd2_style); printf (" <th %s>end</th>\n", hd2_style); printf (" <th %s>remaining</th>\n", hd2_style); printf (" <th %s>orient.</th>\n", hd2_style); printf (" <th %s>name</th>\n", hd2_style); printf (" <th %s>class/family</th>\n", hd2_style); if (strand == 'C') { printf (" <th %s>remaining</th>\n", hd2_style); printf (" <th %s>end</th>\n", hd2_style); printf (" <th %s>begin</th>\n", hd2_style); } else { printf (" <th %s>begin</th>\n", hd2_style); printf (" <th %s>end</th>\n", hd2_style); printf (" <th %s>remaining</th>\n", hd2_style); } printf (" <th %s>id</th>\n", hd2_style); printf (" </tr>\n"); printf (" </thead>\n"); } void doJRepeat (struct trackDb *tdb, char *repeat) /* Main entry point */ { const char *data_style = "style=\"padding:0px 6px;\""; char *table = (tdb ? tdb->table : tdb->track); char outTable[64]; char alignTable[64]; /* Currently using a fixed table name design * with support for two datasets ( baseline and current ). * The baseline dataset is the run which all the other * tracks are based upon. The current can be any more * recent run of RepeatMasker. */ if (startsWith ("rmskJoinedCurrent", table)) { strcpy (alignTable, "rmskAlignCurrent"); strcpy (outTable, "rmskOutCurrent"); } else if (startsWith ("rmskJoinedBaseline", table)) { strcpy (alignTable, "rmskAlignBaseline"); strcpy (outTable, "rmskOutBaseline"); } cartWebStart (cart, database, "%s", tdb->longLabel); int offset = cartInt (cart, "o"); if (offset >= 0) { struct sqlConnection *conn2 = hAllocConn (database); struct sqlResult *sr2; char **row; char query[256]; char qTable[64]; boolean hasBin; int start = cartInt (cart, "o"); if (hTableExists (database, table)) { hFindSplitTable (database, seqName, table, qTable, &hasBin); - safef (query, sizeof (query), + sqlSafef (query, sizeof (query), "select * from %s where chrom = '%s' and alignStart >= %d" " and id = %s", qTable, seqName, start, repeat); sr2 = sqlGetResult (conn2, query); if ((row = sqlNextRow (sr2)) != NULL) { - struct rmskJoined *rmJoin = rmskJoinedLoad (row); + struct rmskJoined *rmJoin = rmskJoinedLoad (row + hasBin); char class[32]; class[0] = '\0'; char family[32]; family[0] = '\0'; char *poundPtr = index (rmJoin->name, '#'); if (poundPtr) { // Terminate name string properly safecpy (class, sizeof (class), poundPtr + 1); *poundPtr = '\0'; char *slashPtr = index (class, '/'); if (slashPtr) { // Terminate class string properly safecpy (family, sizeof (family), slashPtr + 1); *slashPtr = '\0'; } } printf ("<b>Repeat:</b> %s<br>\n", rmJoin->name); printf ("<b>Class:</b> %s<br>\n", class); printf ("<b>Family:</b> %s<br>\n", family); printf ("<b>Orientation:</b> %s<br>\n", rmJoin->strand); printf ("<b>Joined Element Genomic Range:</b> %s:%d-%d<br>\n", rmJoin->chrom, rmJoin->alignStart, rmJoin->alignEnd); printf ("<br><br>\n"); } sqlFreeResult (&sr2); } /* * Locate *.out annotation for this element */ if (hTableExists (database, outTable)) { int isFirst = 0; struct rmskOut2 *ro; hFindSplitTable (database, seqName, outTable, qTable, &hasBin); - safef (query, sizeof (query), + sqlSafef (query, sizeof (query), "select * from %s where genoName = '%s' and genoStart >= %d" " and id = %s", qTable, seqName, start, repeat); sr2 = sqlGetResult (conn2, query); printf ("<h4>RepeatMasker Annotation:</h4>\n"); printf ("The RepeatMasker annotation line(s) for this element. " "If the element is fragmented the output will contain one " "line per joined fragment.<p>\n"); printf ("<table cellspacing=\"0\">\n"); while ((row = sqlNextRow (sr2)) != NULL) { ro = rmskOut2Load (row + hasBin); if (!isFirst++) printOutTableHeader (ro->strand[0]); printf (" <tr>\n"); printf (" <td %s>%d</td>\n", data_style, ro->swScore); printf (" <td %s>%3.1f</td>\n", data_style, (double) ro->milliDiv * (double) 0.01); printf (" <td %s>%3.1f</td>\n", data_style, (double) ro->milliDel * (double) 0.01); printf (" <td %s>%3.1f</td>\n", data_style, (double) ro->milliIns * (double) 0.01); printf (" <td %s>%s</td>\n", data_style, ro->genoName); printf (" <td %s>%d</td>\n", data_style, ro->genoStart); printf (" <td %s>%d</td>\n", data_style, ro->genoEnd); printf (" </A>"); printf (" <td %s>(%d)</td>\n", data_style, ro->genoLeft); printf (" <td %s>%s</td>\n", data_style, ro->strand); printf (" <td %s>%s</td>\n", data_style, ro->repName); printf (" <td %s>%s/%s</td>\n", data_style, ro->repClass, ro->repFamily); printf (" <td %s>%d</td>\n", data_style, ro->repStart); printf (" <td %s>%d</td>\n", data_style, ro->repEnd); printf (" <td %s>(%d)</td>\n", data_style, ro->repLeft); printf (" <td %s>%d</td>\n", data_style, ro->id); printf (" <td>\n"); printf ("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">Browser</A>", hgTracksPathAndSettings (), database, seqName, ro->genoStart + 1, ro->genoEnd); char *tbl = cgiUsualString ("table", cgiString ("g")); printf (" - <A HREF=\"%s&o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&" "strand=%s&table=%s\">" "DNA</A>\n", hgcPathAndSettings (), ro->genoStart, (ro->repName != NULL ? cgiEncode (ro->repName) : ""), seqName, ro->genoStart, ro->genoEnd, cgiEncode (ro->strand), tbl); printf (" </td>\n"); printf (" </tr>\n"); } sqlFreeResult (&sr2); printf ("</table>\n"); } printf ("<br><br>\n"); /* * Locate *.align data for this element */ if (hTableExists (database, alignTable)) { struct rmskAlign *ro; hFindSplitTable (database, seqName, alignTable, qTable, &hasBin); - safef (query, sizeof (query), + sqlSafef (query, sizeof (query), "select * from %s where genoName = '%s' and genoStart >= %d" " and id = %s", qTable, seqName, start, repeat); sr2 = sqlGetResult (conn2, query); printf ("<h4>RepeatMasker Alignments:</h4>\n"); printf ("The raw alignment data used by RepeatMasker to generate " "the final annotation call for this element. NOTE: The " "aligned sequence names and consensus positions may differ " "from the final annotation.<p>\n"); printf ("<table>\n"); while ((row = sqlNextRow (sr2)) != NULL) { ro = rmskAlignLoad (row + hasBin); printf (" <tr>\n"); printf (" <td>%d</td>\n", ro->swScore); printf (" <td>%3.2f</td>\n", (double) ro->milliDiv * (double) 0.01); printf (" <td>%3.2f</td>\n", (double) ro->milliDel * (double) 0.01); printf (" <td>%3.2f</td>\n", (double) ro->milliIns * (double) 0.01); printf (" <td>%s</td>\n", ro->genoName); printf (" <td>%d</td>\n", ro->genoStart); printf (" <td>%d</td>\n", ro->genoEnd); printf (" <td>(%d)</td>\n", ro->genoLeft); printf (" <td>%s</td>\n", ro->strand); printf (" <td>%s</td>\n", ro->repName); printf (" <td>%s/%s</td>\n", ro->repClass, ro->repFamily); if (ro->strand[0] == '-') { printf (" <td>(%d)</td>\n", ro->repLeft); printf (" <td>%d</td>\n", ro->repEnd); printf (" <td>%d</td>\n", ro->repStart); } else { printf (" <td>%d</td>\n", ro->repStart); printf (" <td>%d</td>\n", ro->repEnd); printf (" <td>(%d)</td>\n", ro->repLeft); } printf (" <td>%d</td>\n", ro->id); printf (" </tr><tr><td colspan=\"15\"><pre>\n"); printAlignment (ro); printf (" </pre><td></tr>\n"); } sqlFreeResult (&sr2); printf ("</table>\n"); } hFreeConn (&conn2); } printTrackHtml (tdb); }