// Returns a hash mapping from sequence header to sequence data.
static stHash *readFastaFile(char *filename) {
FILE *fasta = fopen(filename, "r");
if (fasta == NULL) {
st_errnoAbort("Could not open fasta file %s", filename);
}
stHash *headerToData = stHash_construct3(stHash_stringKey,
stHash_stringEqualKey,
free,
free);
struct List *seqs = constructEmptyList(0, NULL);
struct List *seqLengths = constructEmptyList(0, free);
struct List *headers = constructEmptyList(0, free);
fastaRead(fasta, seqs, seqLengths, headers);
for (int64_t i = 0; i < seqs->length; i++) {
char *fullHeader = headers->list[i];
stList *headerTokens = stString_splitByString(fullHeader, " ");
char *usableHeader = stString_copy(stList_get(headerTokens, 0));
stHash_insert(headerToData, usableHeader, seqs->list[i]);
stList_destruct(headerTokens);
}
destructList(seqs);
destructList(seqLengths);
destructList(headers);
return headerToData;
}
int main(int argc, char *argv[]) {
FILE *fileHandle;
struct List *seqs;
struct List *seqLengths;
struct List *seqNames;
int32_t i;
assert(argc == 3);
seqs = constructEmptyList(0, free);
seqLengths = constructEmptyList(0, (void (*)(void *))destructInt);
seqNames = constructEmptyList(0, free);
fileHandle = fopen(argv[1], "r");
fastaRead(fileHandle, seqs, seqLengths, seqNames);
fclose(fileHandle);
fileHandle = fopen(argv[2], "w");
for(i=0; i < seqs->length; i++) {
assert(strlen(seqs->list[i]) == *((int32_t *)seqLengths->list[i]));
fastaWrite(seqs->list[i], seqNames->list[i], fileHandle);
}
fclose(fileHandle);
return 0;
}
int main(int argc, char *argv[]) {
/*
* Arguments/options
*/
char *logLevelString = NULL;
char *mfaFile = NULL;
char *outputFile = NULL;
char *treeFile = NULL;
///////////////////////////////////////////////////////////////////////////
// (0) Parse the inputs handed by genomeCactus.py / setup stuff.
///////////////////////////////////////////////////////////////////////////
while (1) {
static struct option long_options[] = {
{ "logLevel", required_argument, 0, 'a' },
{ "mfaFile", required_argument, 0, 'b' },
{ "outputFile", required_argument, 0, 'd' },
{ "treeFile", optional_argument, 0, 't' },
{ "help", no_argument, 0, 'h' },
{ 0, 0, 0, 0 }
};
int option_index = 0;
int key = getopt_long(argc, argv, "a:b:d:t:h", long_options, &option_index);
if (key == -1) {
break;
}
switch (key) {
case 'a':
logLevelString = stString_copy(optarg);
break;
case 'b':
mfaFile = stString_copy(optarg);
break;
case 'd':
outputFile = stString_copy(optarg);
break;
case 't':
treeFile = stString_copy(optarg);
break;
case 'h':
usage();
return 0;
default:
usage();
return 1;
}
}
///////////////////////////////////////////////////////////////////////////
// (0) Check the inputs.
///////////////////////////////////////////////////////////////////////////
if (argc == 1) {
usage();
exit(1);
}
assert(mfaFile != NULL);
assert(outputFile != NULL);
//////////////////////////////////////////////
//Set up logging
//////////////////////////////////////////////
st_setLogLevelFromString(logLevelString);
//////////////////////////////////////////////
//Log (some of) the inputs
//////////////////////////////////////////////
st_logInfo("MFA file name : %s\n", mfaFile);
st_logInfo("Output MAF file : %s\n", outputFile);
st_logInfo("Tree file name: %s\n", treeFile == NULL ? "null" : treeFile);
//////////////////////////////////////////////
//Get the MFA alignment
//////////////////////////////////////////////
//get the alignment
struct List *sequences = constructEmptyList(0, free);
struct List *seqLengths = constructEmptyList(0, (void (*)(void *))destructInt);
struct List *fastaNames = constructEmptyList(0, free);
FILE *fileHandle = fopen(mfaFile, "r");
if (fileHandle == NULL) {
usage();
exit(1);
}
fastaRead(fileHandle, sequences, seqLengths, fastaNames);
fclose(fileHandle);
//////////////////////////////////////////////
//Get the tree alignment
//////////////////////////////////////////////
stTree *tree = NULL;
LeafPtrArray *leafArray = NULL;
int32_t leafCount = 0;
if (treeFile != NULL) {
tree = eTreeX_getTreeFromFile(treeFile);
eTreeX_postOrderTraversal(tree, eTreeX_countLeaves, &leafCount);
leafArray = eTreeX_constructLeafPtrArray(leafCount);
eTreeX_postOrderTraversal(tree, eTreeX_getLeafArray, (void *) leafArray);
}
//////////////////////////////////////////////
//Write the MFA alignment.
//////////////////////////////////////////////
fileHandle = fopen(outputFile, "w");
//write the header.
fprintf(fileHandle, "##maf version=1 scoring=NULL\n");
fprintf(fileHandle, "# converted_from_MFA\n\n");
//write the score line
char *treeString = NULL;
if (treeFile != NULL) {
treeString = stTree_getNewickTreeString(tree);
fprintf(fileHandle, "a score=0 tree=\"%s\"\n", treeString);
}
else {
fprintf(fileHandle, "a score=0\n");
leafCount = sequences->length;
}
//write the alignment
int32_t i, j;
int32_t ii;
const char *label;
for (ii=0; ii<leafCount; ii++) {
if (treeFile != NULL) {
label = stTree_getLabel((stTree *) leafArray->ptrArray[ii]);
/* Do a brute force search to find the appropriate sequence that matches "label" */
for (i=0; i<sequences->length; i++) {
char *fastaHeader = fastaNames->list[i];
char *sequenceName = st_malloc(sizeof(char) *(1 + strlen(fastaHeader)));
sscanf(fastaHeader, "%s", sequenceName); //take the sequence name to be the first word of the sequence.
if (strcmp(label, sequenceName) == 0) {
free(sequenceName);
break;
}
free(sequenceName);
}
}
else {
i = ii;
}
char *sequence = sequences->list[i];
int32_t seqLength = *((int32_t *)seqLengths->list[i]);
assert(seqLength == (int32_t)strlen(sequence));
char *fastaHeader = fastaNames->list[i];
char *sequenceName = st_malloc(sizeof(char) *(1 + strlen(fastaHeader)));
sscanf(fastaHeader, "%s", sequenceName); //take the sequence name to be the first word of the sequence.
int32_t length = 0;
for (j=0; j<(int32_t)strlen(sequence); j++) {
if (sequence[j] != '-') {
length++;
}
}
fprintf(fileHandle, "s\t%s\t%i\t%i\t%s\t%i\t%s\n", sequenceName, 0, length, "+", length, sequence);
free(sequenceName);
}
fclose(fileHandle);
//////////////////////////////////////////////
//Clean up.
//////////////////////////////////////////////
free(mfaFile);
free(outputFile);
free(treeFile);
if (treeFile != NULL) {
stTree_destruct(tree);
free(treeString);
eTreeX_destructLeafPtrArray(leafArray);
}
destructList(sequences);
destructList(seqLengths);
destructList(fastaNames);
return 0;
}
