38df39129282c979360585e60168d2a5b22fcf7c fanhsu Fri Apr 29 15:33:58 2011 -0700 Added RNA picture plotted by VARNA for EvoFold. diff --git src/hg/hgc/rnaFoldClick.c src/hg/hgc/rnaFoldClick.c index 504eae0..5bf87f5 100644 --- src/hg/hgc/rnaFoldClick.c +++ src/hg/hgc/rnaFoldClick.c @@ -1,369 +1,401 @@ /* Handle details pages for rna fold (evofold) tracks. */ #include "common.h" #include "jksql.h" #include "hgMaf.h" #include "maf.h" #include "cart.h" #include "hgc.h" #include "hCommon.h" #include "hgColors.h" #include "obscure.h" #include "customTrack.h" #include "htmshell.h" #include "rnautil.h" #include "rnaSecStr.h" #include "memalloc.h" static char const rcsid[] = "$Id: rnaFoldClick.c,v 1.9 2010/05/11 01:43:29 kent Exp $"; /* Taken from hgc.c (should probably be in hgc.h)*/ #define RED 0xFF0000 #define GREEN 0x00FF00 #define BLUE 0x0000FF #define BLACK 0x000000 #define CYAN 0x00FFFF #define GRAY 0xcccccc #define LTGRAY 0x999999 #define ORANGE 0xDD6600 #define MAGENTA 0xFF00FF #define LTPURPLE 0x9966CC #define SCORE_SHADES_COUNT 10 void printRfamUrl(char *itemName) /* Print a link to the Rfam entry corresponding to the item. */ { char *query = cloneString(itemName); char *end = strchr(query, '.'); if (!end) return; else *end = 0; printf("

%s

", itemName); freeMem(query); } void doubleArray2binArray(double *scores, int size, double minScore, double maxScore, int *binArray, int binCount) /* Will assign a bin to each score in 'scores' and store it in 'binArray' */ { int i; for (i = 0; i < size; i++) binArray[i] = assignBin(scores[i], minScore, maxScore, binCount); } void htmlColorPrintString(FILE *f, char *s, int *colorFormat, int *colors, int L) /* Prints s to f wrapping characters in html tags for coloring * according to colorFormat and colors. colorFormat must be of same * length as s. Each position of colorFormat defines which of the * colors to use. Use 0 for default color. If L is non-NULL it * defines a mximum length to print.*/ { int i; if (!L || (L && strlen(s)", colors[0]); /* default color */ for (i = 0; i < L; i++) { if (colorFormat[i] == 0) fprintf(f, "%c", s[i]); else fprintf(f, "%c", colors[ colorFormat[i] ], s[i]); } fprintf(f, ""); } void mafAndFoldHeader(FILE *f) /* Print header for maf and fold the section*/ { fprintf(f, "

Multiple alignment and RNA secondary structure annotation

"); } void mkPosString(char *s, int size) /* Make a string-ruler with a decimal every tenth position */ { int i, d; for (i = 0, d = 0; i < size; i++) if (i%10 == 0) { s[i] = '0' + d; d++; if (d == 10) d = 0; } else s[i] = ' '; s[size] = '\0'; } char *mkScoreString(double *scores, int L, char *referenceText) /* allocate string of score symbols, adjust for gaps in reference sequene */ { char *s = (char *) needMem(L+1); char *scoreString = NULL; int i, n; for (i=0;i 9) errAbort( "Score not between 0 and 1\n" ); s[i] = '0' + n; } s[L] = 0; scoreString = gapAdjustFold(s, referenceText); freeMem(s); return scoreString; } int *mkScoreColorFormat(double *scores, int L, char *referenceText) /* allocate string of score colors (gray shades), adjust for gaps in reference sequene */ { int *v = NULL; int *scoreColorFormat = NULL; v = (int *) needMem(L *sizeof(int) ); doubleArray2binArray(scores, L, 0.0, 1.0, v, SCORE_SHADES_COUNT); scoreColorFormat = gapIntArrayAdjust(v, referenceText); freeMem(v); return scoreColorFormat; } void defineMafSubstColors(int **p2mafColors) /* Defines the colors used for maf coloring. Must corrspsond to the * markCompensatoryMutations function.*/ { int *mafColors; AllocArray(*p2mafColors, 8); mafColors = *p2mafColors; mafColors[0] = LTGRAY; /* not pairing */ mafColors[1] = LTPURPLE; /* not pairing, substitution */ mafColors[2] = BLACK; /* compatible with pairing */ mafColors[3] = BLUE; /* compatible with pairing, single substitution */ mafColors[4] = GREEN; /* compensatory change */ mafColors[5] = RED; /* not compatible with fold, single subs */ mafColors[6] = ORANGE; /* not compatible with fold, double subs */ mafColors[7] = MAGENTA; /* not compatible with fold, involves indel */ } void htmlPrintMafAndFold(FILE *f, struct mafAli *maf, char *fold, double *scores, int lineSize) /* HTML pretty print maf and fold to f. If scores is non-null then * scores are indicated below alignemnt.*/ { struct mafComp *mc; int i, N, lineStart, lineEnd; int *pairList = NULL; int *mafColors = NULL; int **mafColorFormats = NULL; int *scoreColorFormat = NULL; int scoreColors[] = {0x999999,0x888888,0x777777,0x666666,0x555555,0x444444,0x333333,0x222222,0x111111,0x000000}; char *scoreString = 0; char *pairSymbols; char *posString, *adjPosString; char *adjFold; char foldTag[] = "SS anno"; char scoresTag[] = "score "; char positionTag[] = "offset"; char pairSymbolsTag[]= "pair symbol"; char *referenceText = maf->components->text; /* first sequence in the alignment */ int srcChars = max( strlen(foldTag), strlen(pairSymbolsTag)); int refLength = strlen(referenceText); int foldLength = strlen(fold); /* Adjust fold to gap structure in referenceText */ adjFold = gapAdjustFold(fold, referenceText); /* make arrays for color formatting */ N = slCount(maf->components); AllocArray(mafColorFormats, N); for (i = 0; i < N; i++) AllocArray(mafColorFormats[i], refLength); fold2pairingList(adjFold, refLength, &pairList); for (mc = maf->components, i = 0; mc != NULL; mc = mc->next, i++) markCompensatoryMutations(mc->text, referenceText, pairList, mafColorFormats[i]); defineMafSubstColors(&mafColors); /* Make pos string */ posString = needMem(foldLength + 1); mkPosString(posString, foldLength); adjPosString = gapAdjustFold(posString, referenceText); /* Make a symbol string indicating pairing partner */ pairSymbols = (char *) needMem(refLength + 1); mkPairPartnerSymbols(pairList, pairSymbols, refLength); /* Make the score string and its colorFormat */ if (scores) { scoreString = mkScoreString(scores, foldLength, referenceText); scoreColorFormat = mkScoreColorFormat(scores, foldLength, referenceText); } /* Find max. length of source (species) field. */ for (mc = maf->components; mc != NULL; mc = mc->next) { int len = strlen(mc->src); if (srcChars < len) srcChars = len; } /* Pretty print maf and fold */ fprintf(f, "
");
 for (lineStart = 0; lineStart < maf->textSize; lineStart = lineEnd)
     {
     int size;
     lineEnd = lineStart + lineSize;
     if (lineEnd >= maf->textSize)
         lineEnd = maf->textSize;
     size = lineEnd - lineStart;
     fprintf(f, "%-*s %.*s\n", srcChars, positionTag, lineSize, adjPosString + lineStart);
     for (mc = maf->components, i = 0; mc != NULL; mc = mc->next, i++)
         {
 	fprintf(f, "%-*s ", srcChars, mc->src);
 	htmlColorPrintString(f, mc->text + lineStart, mafColorFormats[i] + lineStart, mafColors, lineSize);
 	fprintf(f, "\n");
 	}
     fprintf(f, "%-*s %.*s\n", srcChars, foldTag, lineSize, adjFold + lineStart);
     fprintf(f, "%-*s %.*s\n", srcChars, pairSymbolsTag, lineSize, pairSymbols + lineStart);
     if (scores)
 	{
 	fprintf(f, "%-*s ", srcChars, scoresTag);
 	htmlColorPrintString(f, scoreString + lineStart, scoreColorFormat + lineStart, scoreColors, lineSize);
 	fprintf(f, "\n");
 	}
     fprintf(f, "\n");
     }
 fprintf(f, "
"); /* clean up*/ freeMem(posString); freeMem(adjPosString); freeMem(adjFold); freeMem(pairSymbols); if (scores) { freeMem(scoreString); freeMem(scoreColorFormat); } for (i = 0; i < N; i++) freeMem(mafColorFormats[i]); freeMem(mafColorFormats); } void mafAndFoldLegend(FILE *f) /* Print legend for the maf and fold section */ { char *s = "0123456789"; int colorFormat[] = {0,1,2,3,4,5,6,7,8,9}; int colors[] = {0x999999,0x888888,0x777777,0x666666,0x555555,0x444444,0x333333,0x222222,0x111111,0x000000}; fprintf(f, "

Color legend

"); fprintf(f, ""); fprintf(f, "", LTGRAY); fprintf(f, "", LTPURPLE); fprintf(f, "", BLACK); fprintf(f, "", BLUE); fprintf(f, "", GREEN); fprintf(f, "", RED); fprintf(f, "", ORANGE); fprintf(f, "", MAGENTA); fprintf(f, "
GRAY: Not part of annotated pair, no substitution.
LT. PURPLE: Not part of annotated pair, substitution.
BLACK: Compatible with annotated pair, no substitutions.
BLUE: Compatible with annotated pair, single substitution.
GREEN: Compatible with annotated pair, double substitution.
RED: Not compatible with annotated pair, single substitution.
ORANGE: Not compatible with annotated pair, double substitution.
MAGENTA: Not compatible with annotated pair, involves gap.
"); /* Score legend */ fprintf(f, "
SCORE: min "); htmlColorPrintString(f, s, colorFormat, colors, 0); fprintf(f, " max"); } struct mafAli *mafFromRnaSecStrItem(char *mafTrack, struct rnaSecStr *item) { struct mafAli *maf; maf = hgMafFrag(database, mafTrack, item->chrom, item->chromStart, item->chromEnd, item->strand[0], NULL, NULL); return maf; } void mafSortBySpeciesOrder(struct mafAli *maf, char *speciesOrder) /* Sort maf components by species. Excised from mafClick.c. */ { int speciesCt; char *species[256]; struct mafComp **newOrder, *mcThis; int i; int mcCount; mcCount = 0; speciesCt = chopLine(cloneString(speciesOrder), species); newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *)); newOrder[mcCount++] = maf->components; for (i = 0; i < speciesCt; i++) { if ((mcThis = mafMayFindCompSpecies(maf, species[i], '.')) == NULL) continue; newOrder[mcCount++] = mcThis; } maf->components = NULL; for (i = 0; i < mcCount; i++) { newOrder[i]->next = 0; slAddHead(&maf->components, newOrder[i]); } slReverse(&maf->components); } +void htmlPrintSecStrDrawing(FILE *f, struct rnaSecStr *item) +{ +char fileName[512]; +struct dnaSeq *seq; +seq = hChromSeq(database, item->chrom, item->chromStart, item->chromEnd); +touppers(seq->dna); +if (item->strand[0] == '-') + reverseComplement(seq->dna, seq->size); +memSwapChar(seq->dna, seq->size, 'T', 'U'); + +safef(fileName, sizeof(fileName), "/gbdb/%s/evoFold/%s/%s.png", + database, item->chrom, item->name); +if (fileExists(fileName)) + { + fprintf(f, "

RNA secondary structure drawing

"); + fprintf(f,""); + + // Could consider to serve up all EvoFold .png files from our public server in the future + // fprintf(f,"\"ERROR:
", + fprintf(f,"\"ERROR:
", + database, item->chrom, item->name); + fprintf(f,""); + } + +freeMem(seq); +} + void doRnaSecStr(struct trackDb *tdb, char *itemName) /* Handle click on rnaSecStr type elements. */ { char *table = tdb->table; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; struct rnaSecStr *item; char extraWhere[256]; char **row; int rowOffset = 0; char *mafTrack = trackDbRequiredSetting(tdb, "mafTrack"); int start = cartInt(cart, "o"); struct mafAli *maf; char option[128]; char *speciesOrder = NULL; /* print header */ genericHeader(tdb, itemName); /* printRfamUrl(itemName); */ genericBedClick(conn, tdb, itemName, start, 6); htmlHorizontalLine(); /* get the rnaSecStr and maf from db */ sprintf(extraWhere, "chromStart = %d and name = '%s'", start, itemName); sr = hExtendedChromQuery(conn, table, seqName, extraWhere, FALSE, NULL, &rowOffset); row = sqlNextRow(sr); item = rnaSecStrLoad(row + rowOffset); maf = mafFromRnaSecStrItem(mafTrack, item); /* order maf by species */ safef(option, sizeof(option), "%s.speciesOrder", tdb->track); speciesOrder = cartUsualString(cart, option, NULL); if (speciesOrder == NULL) speciesOrder = trackDbSetting(tdb, "speciesOrder"); if (speciesOrder) mafSortBySpeciesOrder(maf, speciesOrder); mafAndFoldHeader(stdout); htmlPrintMafAndFold(stdout, maf, item->secStr, item->conf, 100); mafAndFoldLegend(stdout); + +/* Draw structure */ +htmlHorizontalLine(); +htmlPrintSecStrDrawing(stdout, item); + /* track specific html */ printTrackHtml(tdb); /* clean up */ mafAliFree(&maf); rnaSecStrFree(&item); sqlFreeResult(&sr); hFreeConn(&conn); }