void findContigsWithClones(char *cloneFile, char *ooDir, char *snoopIn)
/* findContigsWithClones - find contigs that contain clones. */
{
struct slName *el;
cloneList = readAllLines(cloneFile);
for (el = cloneList; el != NULL; el = el->next)
chopSuffix(el->name);
snoopFileName = snoopIn;
ooToAllContigs(ooDir, doContig);
}
void reverseLineOrder(char *input, char *output)
/* reverseLineOrder - Write out a file with first line last and last line first.. */
{
struct slName *el, *list = readAllLines(input);
slReverse(&list);
FILE *f = mustOpen(output, "w");
for (el = list; el != NULL; el = el->next)
{
fprintf(f, "%s\n", el->name);
}
carefulClose(&f);
}
void regBedStats(char *fileOfFiles, char *output)
/* regBedStats - Go through bed files and calculate a bunch of statistics on them. */
{
struct slName *in, *inList = readAllLines(fileOfFiles);
FILE *f = mustOpen(output, "w");
int colCount = max(chromColIx, startColIx);
colCount = max(colCount, endColIx);
colCount = max(colCount, scoreColIx);
colCount += 1;
for (in = inList; in != NULL; in = in->next)
{
bedFileStats(in->name, colCount, f);
}
carefulClose(&f);
}
void rowsToCols(char *in, char *out)
/* rowsToCols - Convert rows to columns and vice versa in a text file.. */
{
struct slName *lineList = readAllLines(in);
struct tabRow *row, *rowList;
FILE *f;
int i, origCols;
char *s;
if (fs != NULL)
rowList = tabRowByChar(lineList, fs[0], in, varCol);
else if (fixed)
rowList = tabRowByFixedGuess(lineList, in);
else if (offsets)
{
struct slName *nameList = commaSepToSlNames(offsets), *name;
struct slInt *offList=NULL, *off;
for (name = nameList; name != NULL; name = name->next)
{
off = slIntNew(atoi(name->name));
slAddTail(&offList, off);
}
rowList = tabRowByFixedOffsets(lineList, offList, in);
}
else
rowList = tabRowByWhite(lineList, in, varCol);
origCols = tabRowMaxColCount(rowList);
f = mustOpen(out, "w");
for (i=0; i<origCols; ++i)
{
for (row = rowList; row != NULL; row = row->next)
{
if (i < row->colCount)
s = row->columns[i];
else
s = "";
fprintf(f, "%s", s);
if (row->next == NULL)
fprintf(f, "\n");
else
fprintf(f, "\t");
}
}
carefulClose(&f);
}
void distributeRgbRainbow(char *inList, char *inPairs, char *outTab)
/* distributeRgbRainbow - Associate colors with items on a list where distance between colors
* is proportional to distance between items. */
{
/* Read in inputs */
struct slName *item, *itemList = readAllLines(inList);
verbose(1, "%d items in %s\n", slCount(itemList), inList);
struct pairDistance *pairList= pairDistanceReadAll(inPairs);
verbose(1, "%d pairs in %s\n", slCount(pairList), inPairs);
struct hash *pairHash = pairDistanceHashList(pairList);
/* Open output, and just finish early if it should be empty */
FILE *f = mustOpen(outTab, "w");
if (itemList == NULL)
return;
/* Cope with invert option. */
if (optionExists("invert"))
pairDistanceInvert(pairList);
/* Add up total distance between all items */
double totalDistance = 0.0;
for (item = itemList; item != NULL; item = item->next)
{
struct slName *nextItem = item->next;
if (nextItem == NULL)
break;
totalDistance += pairDistanceHashLookup(pairHash, item->name, nextItem->name);
}
double colorRange = gEnd - gStart;
outputItem(f, itemList->name, gStart);
double soFar = 0.0;
for (item = itemList; item != NULL; item = item->next)
{
struct slName *nextItem = item->next;
if (nextItem == NULL)
break;
double distance = pairDistanceHashLookup(pairHash, item->name, nextItem->name);
soFar += distance;
outputItem(f, nextItem->name, gStart + (soFar/totalDistance * colorRange));
}
carefulClose(&f);
}
void regClusterMakeTableOfTables(char *type, char *input, char *output)
/* regClusterMakeTableOfTables - Make up a table of tables for regCluster program. */
{
FILE *f = mustOpen(output, "w");
struct slName *in, *inList = readAllLines(input);
/* Generally we'll have a bunch of file names that all start and/or end with the same
* thing. This loop will isolate out the bits that vary, and then call a type-specific
* routine to output the metadata columns from the middle parts. */
int commonPrefix = commonPrefixSize(inList);
int commonSuffix = commonSuffixSize(inList);
uglyf("regClusterMakeTableOfTables(type=%s, input=%s, output=%s)\n", type, input, output);
int scoreIx = scoreColIx - 1;
for (in = inList; in != NULL; in = in->next)
{
verbose(2, "Processing %s\n", in->name);
fprintf(f, "%s\t0\t1\t2\t%d\t", in->name, scoreIx);
fprintf(f, "%g", calcNormScoreFactor(in->name, scoreIx));
char *s = in->name;
int len = strlen(s);
char *midString = cloneStringZ(s+commonPrefix, len - commonPrefix - commonSuffix);
if (sameString(type, "uw01"))
uw01MetaOut(f, midString);
else if (sameString(type, "uw02"))
uw02MetaOut(f, midString);
else if (sameString(type, "ans01"))
ans01MetaOut(f, midString);
else if (sameString(type, "ans02"))
ans02MetaOut(f, midString);
else if (sameString(type, "enh01"))
enh01MetaOut(f, midString);
else if (sameString(type, "awgDnase01"))
awgDnase01MetaOut(f, midString);
else
errAbort("Unknown type '%s' in first command line parameter.", type);
freez(&midString);
fprintf(f, "\n");
}
carefulClose(&f);
}
void makeConfigFromFileList(char *input, char *output)
/* makeConfigFromFileList - Create config file for hgBedsToBedExps from list of files.. */
{
FILE *f = mustOpen(output, "w");
struct slName *in, *inList = readAllLines(input);
int commonPrefix = commonPrefixSize(inList);
int commonSuffix = commonSuffixSize(inList);
for (in = inList; in != NULL; in = in->next)
{
char *s = in->name;
int len = strlen(s);
char *midString = cloneStringZ(s+commonPrefix, len - commonPrefix - commonSuffix);
char *factor, *cell;
camelParseTwo(midString, &cell, &factor);
fprintf(f, "%s\t%s\t", factor, cell);
fprintf(f, "%s\t", cellAbbreviation(cell));
fprintf(f, "file\t%d\t", scoreCol-1);
fprintf(f, "%g\t", calcNormScoreFactor(in->name, scoreCol-1));
fprintf(f, "%s\n", in->name);
}
carefulClose(&f);
}
