1caf0560fb6ecf569f8a6ebf17d3593612a5d7f6 angie Fri May 22 15:59:17 2015 -0700 hgIntegrator: instead of comma-separated lists of wiggle values that get quite long for large regions, output the average of values in a region. I got a couple requests for this at the Biology of Genomes poster session. refs #14579 diff --git src/lib/annoFormatTab.c src/lib/annoFormatTab.c index d6683ce..dde5d8f 100644 --- src/lib/annoFormatTab.c +++ src/lib/annoFormatTab.c @@ -1,290 +1,290 @@ /* annoFormatTab -- collect fields from all inputs and print them out, tab-separated. */ /* Copyright (C) 2013 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "annoFormatTab.h" #include "annoGratorQuery.h" #include "dystring.h" struct annoFormatTab { struct annoFormatter formatter; // External interface char *fileName; // Output file name, can be "stdout" FILE *f; // Output file handle struct hash *columnVis; // Hash of columns that have been explicitly selected // or deselected by user. boolean needHeader; // TRUE if we should print out the header }; static void makeFullColumnName(char *fullName, size_t size, char *sourceName, char *colName) /* If sourceName is non-empty, make fullName sourceName.colName, otherwise just colName. */ { if (isNotEmpty(sourceName)) safef(fullName, size, "%s.%s", sourceName, colName); else safecpy(fullName, size, colName); } void annoFormatTabSetColumnVis(struct annoFormatter *vSelf, char *sourceName, char *colName, boolean enabled) /* Explicitly include or exclude column in output. sourceName must be the same * as the corresponding annoStreamer source's name. */ { struct annoFormatTab *self = (struct annoFormatTab *)vSelf; if (! self->columnVis) self->columnVis = hashNew(0); char fullName[PATH_LEN]; makeFullColumnName(fullName, sizeof(fullName), sourceName, colName); hashAddInt(self->columnVis, fullName, enabled); } static boolean columnIsIncluded(struct annoFormatTab *self, char *sourceName, char *colName) // Return TRUE if column has not been explicitly deselected. { if (self->columnVis) { char fullName[PATH_LEN]; makeFullColumnName(fullName, sizeof(fullName), sourceName, colName); int vis = hashIntValDefault(self->columnVis, fullName, 1); if (vis == 0) return FALSE; } return TRUE; } static void printHeaderColumns(struct annoFormatTab *self, struct annoStreamer *source, boolean isFirst) /* Print names of included columns from this source. */ { FILE *f = self->f; char *sourceName = source->name; char fullName[PATH_LEN]; if (source->rowType == arWig) { // Fudge in the row's chrom, start, end as output columns even though they're not in autoSql if (isFirst) { makeFullColumnName(fullName, sizeof(fullName), sourceName, "chrom"); fprintf(f, "#%s", fullName); isFirst = FALSE; } makeFullColumnName(fullName, sizeof(fullName), sourceName, "start"); fprintf(f, "\t%s", fullName); makeFullColumnName(fullName, sizeof(fullName), sourceName, "end"); fprintf(f, "\t%s", fullName); } struct asColumn *col; int i; for (col = source->asObj->columnList, i = 0; col != NULL; col = col->next, i++) { if (columnIsIncluded(self, sourceName, col->name)) { if (isFirst) { fputc('#', f); isFirst = FALSE; } else fputc('\t', f); makeFullColumnName(fullName, sizeof(fullName), sourceName, col->name); fputs(fullName, f); } } } static void aftInitialize(struct annoFormatter *vSelf, struct annoStreamer *primary, struct annoStreamer *integrators) /* Print header, regardless of whether we get any data after this. */ { struct annoFormatTab *self = (struct annoFormatTab *)vSelf; if (self->needHeader) { char *primaryHeader = primary->getHeader(primary); if (isNotEmpty(primaryHeader)) fprintf(self->f, "# Header from primary input:\n%s", primaryHeader); printHeaderColumns(self, primary, TRUE); struct annoStreamer *grator; for (grator = integrators; grator != NULL; grator = grator->next) printHeaderColumns(self, grator, FALSE); fputc('\n', self->f); self->needHeader = FALSE; } } static double wigRowAvg(struct annoRow *row) /* Return the average value of floats in row->data. */ { float *vector = row->data; int len = row->end - row->start; double sum = 0.0; int i; for (i = 0; i < len; i++) sum += vector[i]; return sum / (double)len; } static char **wordsFromWigRowAvg(struct annoRow *row) /* Return an array of strings with a single string containing the average of values in row. */ { double avg = wigRowAvg(row); char **words; AllocArray(words, 1); char avgStr[32]; safef(avgStr, sizeof(avgStr), "%lf", avg); words[0] = cloneString(avgStr); return words; } static char **wordsFromWigRowVals(struct annoRow *row) /* Return an array of strings with a single string containing comma-sep per-base wiggle values. */ { float *vector = row->data; int len = row->end - row->start; struct dyString *dy = dyStringNew(10*len); int i; for (i = 0; i < len; i++) dyStringPrintf(dy, "%g,", vector[i]); char **words; AllocArray(words, 1); words[0] = dyStringCannibalize(&dy); return words; } static char **wordsFromRow(struct annoRow *row, struct annoStreamer *source, boolean *retFreeWhenDone) /* If source->rowType is arWords, return its words. Otherwise translate row->data into words. */ { if (row == NULL) return NULL; boolean freeWhenDone = FALSE; char **words = NULL; if (source->rowType == arWords) words = row->data; else if (source->rowType == arWig) { freeWhenDone = TRUE; //#*** config options: avg? more stats? list of values? - boolean doAvg = FALSE; + boolean doAvg = TRUE; if (doAvg) words = wordsFromWigRowAvg(row); else words = wordsFromWigRowVals(row); } else errAbort("annoFormatTab: unrecognized row type %d from source %s", source->rowType, source->name); if (retFreeWhenDone != NULL) *retFreeWhenDone = freeWhenDone; return words; } static void printColumns(struct annoFormatTab *self, struct annoStreamer *streamer, struct annoRow *row, boolean isFirst) /* Print columns in streamer's row (if NULL, print the right number of empty fields). */ { FILE *f = self->f; char *sourceName = streamer->name; boolean freeWhenDone = FALSE; char **words = wordsFromRow(row, streamer, &freeWhenDone); if (streamer->rowType == arWig) { // Fudge in the row's chrom, start, end as output columns even though they're not in autoSql if (isFirst) { if (row != NULL) fputs(row->chrom, f); isFirst = FALSE; } if (row != NULL) fprintf(f, "\t%u\t%u", row->start, row->end); else fputs("\t\t", f); } struct asColumn *col; int i; for (col = streamer->asObj->columnList, i = 0; col != NULL; col = col->next, i++) { if (columnIsIncluded(self, sourceName, col->name)) { if (isFirst) isFirst = FALSE; else fputc('\t', f); if (words != NULL) fputs((words[i] ? words[i] : ""), f); } } if (freeWhenDone) { freeMem(words[0]); freeMem(words); } } static void aftComment(struct annoFormatter *fSelf, char *content) /* Print out a comment line. */ { if (strchr(content, '\n')) errAbort("aftComment: no multi-line input"); struct annoFormatTab *self = (struct annoFormatTab *)fSelf; fprintf(self->f, "# %s\n", content); } static void aftFormatOne(struct annoFormatter *vSelf, struct annoStreamRows *primaryData, struct annoStreamRows *gratorData, int gratorCount) /* Print out tab-separated columns that we have gathered in prior calls to aftCollect, * and start over fresh for the next line of output. */ { struct annoFormatTab *self = (struct annoFormatTab *)vSelf; // Got one row from primary; what's the largest # of rows from any grator? int maxRows = 1; int iG; for (iG = 0; iG < gratorCount; iG++) { int gratorRowCount = slCount(gratorData[iG].rowList); if (gratorRowCount > maxRows) maxRows = gratorRowCount; } // Print out enough rows to make sure that all grator rows are included. int iR; for (iR = 0; iR < maxRows; iR++) { printColumns(self, primaryData->streamer, primaryData->rowList, TRUE); for (iG = 0; iG < gratorCount; iG++) { struct annoRow *gratorRow = slElementFromIx(gratorData[iG].rowList, iR); printColumns(self, gratorData[iG].streamer, gratorRow, FALSE); } fputc('\n', self->f); } } static void aftClose(struct annoFormatter **pVSelf) /* Close file handle, free self. */ { if (pVSelf == NULL) return; struct annoFormatTab *self = *(struct annoFormatTab **)pVSelf; freeMem(self->fileName); carefulClose(&(self->f)); annoFormatterFree(pVSelf); } struct annoFormatter *annoFormatTabNew(char *fileName) /* Return a formatter that will write its tab-separated output to fileName. */ { struct annoFormatTab *aft; AllocVar(aft); struct annoFormatter *formatter = &(aft->formatter); formatter->getOptions = annoFormatterGetOptions; formatter->setOptions = annoFormatterSetOptions; formatter->initialize = aftInitialize; formatter->comment = aftComment; formatter->formatOne = aftFormatOne; formatter->close = aftClose; aft->fileName = cloneString(fileName); aft->f = mustOpen(fileName, "w"); aft->needHeader = TRUE; return (struct annoFormatter *)aft; }