/**
* The function reallocate memory for a
* @param self the pointer to be reallocated
* @param size size in bytes
* @param file the source code file (__FILE__) or NULL to not print this info
* @param line the source code line (__LINE__) or 0
* @return return a pointer to the reallocated memory
*/
void *reallocate(void *self, size_t size, const char *file, int line){
return checkPointerError(realloc(self,size), "Can't reallocate memory", file, line, -1);
}
int main(int argc, char** argv) {
int next_option, verbose;
const char* const short_options = "vhd:o:s:g:r:";
FILE *s;
char *line = NULL;
size_t len = 0;
ssize_t read = 0;
char **fields = NULL;
size_t fieldsSize = 0;
char **samples = NULL;
int samplesLen = 0;
BtreeNode_t *genes = NULL;
void **genesArray = NULL;
int genesLen = 0;
struct dirent **namelist;
int i, n, l, k;
BtreeRecord_t *rec = NULL;
MGene_l gene;
double cllSum, nbcSum, tmpValue, tmp1Value;
int cllLen, nbcLen;
int cllLenTMP, nbcLenTMP;
FILE *outFile = NULL;
FILE *geneFile = NULL;
FILE *sumFile = NULL;
FILE *repFile = NULL;
char *dir = NULL;
int s1Len;
int s2Len;
program_name = argv[0];
const struct option long_options[] = {
{ "help", 0, NULL, 'h'},
{ "verbose", 0, NULL, 'v'},
{ "output", 1, NULL, 'o'},
{ "dir", 1, NULL, 'd'},
{ "gene", 1, NULL, 'g'},
{ "sum", 1, NULL, 's'},
{ "rep", 1, NULL, 'r'},
{ NULL, 0, NULL, 0} /* Required at end of array. */
};
verbose = 0;
do {
next_option = getopt_long(argc, argv, short_options, long_options, NULL);
switch (next_option) {
case 'h':
print_usage(stdout, 0);
case 'v':
verbose = 1;
break;
case 'd':
dir = strdup(optarg);
break;
case 'o':
outFile = checkPointerError(fopen(optarg, "w"), "Can't open OUTPUT file", __FILE__, __LINE__, -1);
break;
case 'g':
geneFile = checkPointerError(fopen(optarg, "w"), "Can't open GENE file", __FILE__, __LINE__, -1);
break;
case 's':
sumFile = checkPointerError(fopen(optarg, "w"), "Can't open SUM file", __FILE__, __LINE__, -1);
break;
case 'r':
repFile = checkPointerError(fopen(optarg, "w"), "Can't open replicate file", __FILE__, __LINE__, -1);
break;
}
} while (next_option != -1);
if (!dir || !outFile || !sumFile) {
print_usage(stderr, -1);
}
fprintf(geneFile, "GeneId\tTranscriptId\tNBC_Gene_TPM\tNBC_Exon_TPM\tNBC_Intron_TPM\tNBC_Intron_Exon_Ratio\tNBC_LOG2_Intron_Exon_Ratio\tCLL_Gene_TPM\tCLL_Exon_TPM\tCLL_Intron_TPM\tCLL_Intron_Exon_Ratio\tCLL_LOG2_Intron_Exon_Ratio\tHausdorff_distance\tCLL_NBC_Intron_Ratio\tLOG2_CLL_NBC_Intron_Ratio\tCLL_NBC_Exon_Ratio\tLOG2_CLL_NBC_Exon_Ratio\n");
fprintf(outFile, "GeneId\tTranscriptId\tIntron_Exon_Number\tType");
fprintf(repFile, "GeneId\tTranscriptId");
cllLen = nbcLen = samplesLen = 0;
n = scandir(dir, &namelist, 0, alphasort);
if (n < 0)
perror("scandir");
else {
for (i = 0; i < n; i++) {
if (strbcmp(namelist[i]->d_name, ".ent") == 0) {
s = fopen(namelist[i]->d_name, "r");
fseeko(s, 0, SEEK_END);
if (ftello(s) != 0) {
samples = reallocate(samples, sizeof (samples) * (samplesLen + 1), __FILE__, __LINE__);
samples[samplesLen] = strdup(namelist[i]->d_name);
if (strncmp(samples[samplesLen], "CLL", 3) == 0) cllLen++;
if (strncmp(samples[samplesLen], "NBC", 3) == 0) nbcLen++;
samplesLen++;
}
fclose(s);
}
free(namelist[i]);
}
}
free(namelist);
for (i = 0; i < samplesLen; i++) {
s = checkPointerError(fopen(samples[i], "r"), "Can't open sample ENT file", __FILE__, __LINE__, -1);
*(strstr(samples[i], ".ent")) = '\0';
fprintf(outFile, "\t%s\t%s_Reads", samples[i], samples[i]);
fprintf(repFile, "\t%s_Exon\t%s_Exon_Reads\t%s_Intron\t%s_Intron_Reads", samples[i], samples[i], samples[i], samples[i]);
if (verbose) printf("Parsing ENT file: %s\n", samples[i]);
while ((read = getline(&line, &len, s)) != -1) {
if (strncmp(line, "Gene_Id", 7) != 0) {
fieldsSize = splitString(&fields, line, "\t");
if (fieldsSize == 8) {
gene = NewMGene(fields);
rec = BTreeFind(genes, gene, GeneKeyCMP);
if (rec == NULL) {
gene->entities = reallocate(gene->entities, sizeof (MEntity_t) * (gene->entitiesLen + 1), __FILE__, __LINE__);
gene->entities[gene->entitiesLen].length = atoi(fields[5]);
gene->entities[gene->entitiesLen].type = strdup(fields[3]);
gene->NBCIntronExonRatio = allocate(sizeof (double) * nbcLen, __FILE__, __LINE__);
for (k = 0; k < nbcLen; k++) {
gene->NBCIntronExonRatio[k] = NAN;
}
gene->CLLIntronExonRatio = allocate(sizeof (double) * cllLen, __FILE__, __LINE__);
for (k = 0; k < cllLen; k++) {
gene->CLLIntronExonRatio[k] = NAN;
}
gene->repExonTPM = allocate(sizeof (double) * samplesLen, __FILE__, __LINE__);
for (k = 0; k < samplesLen; k++) {
gene->repExonTPM[k] = NAN;
}
gene->repExonCount = allocate(sizeof (int) * samplesLen, __FILE__, __LINE__);
for (k = 0; k < samplesLen; k++) {
gene->repExonCount[k] = NAN;
}
gene->repIntronTPM = allocate(sizeof (double) * samplesLen, __FILE__, __LINE__);
for (k = 0; k < samplesLen; k++) {
gene->repIntronTPM[k] = NAN;
}
gene->repIntronCount = allocate(sizeof (int) * samplesLen, __FILE__, __LINE__);
for (k = 0; k < samplesLen; k++) {
gene->repIntronCount[k] = NAN;
}
gene->entities[gene->entitiesLen].samples = allocate(sizeof (MEntitySample_t) * (samplesLen), __FILE__, __LINE__);
for (k = 0; k < samplesLen; k++) {
gene->entities[gene->entitiesLen].samples[k].sample = samples[k];
gene->entities[gene->entitiesLen].samples[k].count = -1;
gene->entities[gene->entitiesLen].samples[k].TPM = INFINITY;
}
gene->entities[gene->entitiesLen].samples[i].count = atoi(fields[6]);
gene->entities[gene->entitiesLen].samples[i].TPM = strtod(fields[7], NULL);
gene->entitiesLen++;
genes = BtreeInsert(genes, gene, gene, GeneKeyCMP);
} else {
FreeMGene(gene);
gene = rec->value;
l = atoi(fields[4]) - 1;
if (l >= gene->entitiesLen) {
gene->entities = reallocate(gene->entities, sizeof (MEntity_t) * (gene->entitiesLen + 1), __FILE__, __LINE__);
gene->entities[l].length = atoi(fields[5]);
gene->entities[l].type = strdup(fields[3]);
gene->entities[l].samples = allocate(sizeof (MEntitySample_t) * (samplesLen), __FILE__, __LINE__);
for (k = 0; k < samplesLen; k++) {
gene->entities[gene->entitiesLen].samples[k].sample = samples[k];
gene->entities[gene->entitiesLen].samples[k].count = -1;
gene->entities[gene->entitiesLen].samples[k].TPM = INFINITY;
}
gene->entities[l].samples[i].count = atoi(fields[6]);
gene->entities[l].samples[i].TPM = strtod(fields[7], NULL);
gene->entitiesLen++;
} else {
gene->entities[l].samples[i].sample = samples[i];
gene->entities[l].samples[i].count = atoi(fields[6]);
gene->entities[l].samples[i].TPM = strtod(fields[7], NULL);
}
}
} else {
fprintf(stderr, "\n\n%s\n\n", line);
printLog(stderr, "Bad ENT format", __FILE__, __LINE__, -1);
}
freeArrayofPointers((void **) fields, fieldsSize);
}
}
fclose(s);
}
fprintf(outFile, "\tCLL_Mean\tNBC_Mean\tCLL_NBC_Mean_Diff\n");
fprintf(repFile, "\n");
s1Len = s2Len = 0;
for (i = 0; i < samplesLen; i++) {
strcat(samples[i], ".out");
s = checkPointerError(fopen(samples[i], "r"), "Can't open sample OUT file", __FILE__, __LINE__, -1);
*(strstr(samples[i], ".out")) = '\0';
if (verbose) printf("Parsing OUT file: %s\n", samples[i]);
while ((read = getline(&line, &len, s)) != -1) {
if (strncmp(line, "Gene_Id", 7) != 0) {
fieldsSize = splitString(&fields, line, "\t");
if (fieldsSize == 12) {
gene = NewMGene(fields);
rec = BTreeFind(genes, gene, GeneKeyCMP);
if (rec == NULL) {
fprintf(stderr, "\n\n%s\n\n", line);
printLog(stderr, "Wrong GENE name", __FILE__, __LINE__, -1);
}
FreeMGene(gene);
gene = rec->value;
if (gene->length == -1) {
gene->length = atoi(fields[3]);
} else if (gene->length != atoi(fields[3])) {
fprintf(stderr, "\n\n%s\n\n", line);
printLog(stderr, "Wrong GENE length", __FILE__, __LINE__, -1);
}
tmpValue = strtod(fields[5], NULL);
if (!isnan(tmpValue) && !isinf(tmpValue)) {
if (strncmp(samples[i], "CLL", 3) == 0) {
gene->CLLTPM += tmpValue;
gene->CLLTMPCount++;
} else {
gene->NBCTPM += tmpValue;
gene->NBCTMPCount++;
}
}
tmpValue = strtod(fields[7], NULL);
if (!isnan(tmpValue) && !isinf(tmpValue)) {
gene->repExonCount[i] = tmpValue;
}
tmpValue = strtod(fields[8], NULL);
if (!isnan(tmpValue) && !isinf(tmpValue)) {
gene->repExonTPM[i] = tmpValue;
if (strncmp(samples[i], "CLL", 3) == 0) {
gene->CLLTPMExon += tmpValue;
gene->CLLexonCount++;
} else {
gene->NBCTPMExon += tmpValue;
gene->NBCexonCount++;
}
}
tmpValue = strtod(fields[10], NULL);
if (!isnan(tmpValue) && !isinf(tmpValue)) {
gene->repIntronCount[i] = tmpValue;
}
tmp1Value = strtod(fields[11], NULL);
if (!isnan(tmp1Value) && !isinf(tmp1Value)) {
gene->repIntronTPM[i] = tmp1Value;
if (strncmp(samples[i], "CLL", 3) == 0) {
gene->CLLTPMIntron += tmp1Value;
gene->CLLintronCount++;
gene->CLLIntronExonRatio[s1Len] = tmp1Value;
} else {
gene->NBCTPMIntron += tmp1Value;
gene->NBCintronCount++;
gene->NBCIntronExonRatio[s2Len] = tmp1Value;
}
}
} else {
fprintf(stderr, "\n\n%s\n\n", line);
printLog(stderr, "Bad OUT format", __FILE__, __LINE__, -1);
}
freeArrayofPointers((void **) fields, fieldsSize);
}
}
fclose(s);
if (strncmp(samples[i], "CLL", 3) == 0) s1Len++;
else s2Len++;
}
BtreeRecordsToArray(&genesArray, &genesLen, genes);
for (i = 0; i < genesLen; i++) {
nbcSum = ((MGene_l) genesArray[i])->NBCTPMExon / ((MGene_l) genesArray[i])->NBCexonCount;
tmpValue = ((MGene_l) genesArray[i])->NBCTPMIntron / ((MGene_l) genesArray[i])->NBCintronCount;
fprintf(geneFile, "%s\t%s\t%.4f\t%.4f\t%.4f\t%.4f\t%.4f",
((MGene_l) genesArray[i])->geneId,
((MGene_l) genesArray[i])->transcriptId,
((MGene_l) genesArray[i])->NBCTPM / ((MGene_l) genesArray[i])->NBCTMPCount,
nbcSum,
tmpValue,
tmpValue / nbcSum,
log2(tmpValue / nbcSum));
cllSum = ((MGene_l) genesArray[i])->CLLTPMExon / ((MGene_l) genesArray[i])->CLLexonCount;
tmp1Value = ((MGene_l) genesArray[i])->CLLTPMIntron / ((MGene_l) genesArray[i])->CLLintronCount;
fprintf(geneFile, "\t%.4f\t%.4f\t%.4f\t%.4f\t%.4f\t%.4f\t%.4f\t%.4f\t%.4f\t%.4f\n",
((MGene_l) genesArray[i])->CLLTPM / ((MGene_l) genesArray[i])->CLLTMPCount,
cllSum,
tmpValue,
tmpValue / cllSum,
log2(tmpValue / cllSum),
HausdorffDistance(((MGene_l) genesArray[i])->CLLIntronExonRatio, cllLen, ((MGene_l) genesArray[i])->NBCIntronExonRatio, nbcLen),
tmp1Value / tmpValue,
log2(tmp1Value / tmpValue),
cllSum / nbcSum,
log2(cllSum / nbcSum));
for (l = 0; l < ((MGene_l) genesArray[i])->entitiesLen; l++) {
fprintf(outFile, "%s\t%s\t%d", ((MGene_l) genesArray[i])->geneId, ((MGene_l) genesArray[i])->transcriptId, l + 1);
cllSum = nbcSum = 0.0;
cllLenTMP = nbcLenTMP = 0;
for (k = 0; k < samplesLen; k++) {
if (strncmp(samples[k], "CLL", 3) == 0 && ((MGene_l) genesArray[i])->entities[l].samples[k].TPM != INFINITY) {
cllLenTMP++;
cllSum += ((MGene_l) genesArray[i])->entities[l].samples[k].TPM;
}
if (strncmp(samples[k], "NBC", 3) == 0 && ((MGene_l) genesArray[i])->entities[l].samples[k].TPM != INFINITY) {
nbcLenTMP++;
nbcSum += ((MGene_l) genesArray[i])->entities[l].samples[k].TPM;
}
if (k == 0) {
fprintf(outFile, "\t%s", ((MGene_l) genesArray[i])->entities[l].type);
}
fprintf(outFile, "\t%.4f\t%d", ((MGene_l) genesArray[i])->entities[l].samples[k].TPM, ((MGene_l) genesArray[i])->entities[l].samples[k].count);
}
cllSum = cllSum / cllLenTMP;
nbcSum = nbcSum / nbcLenTMP;
fprintf(outFile, "\t%.4f\t%.4f\t", cllSum, nbcSum);
if (fabs(cllSum) <= 0.000001 && fabs(nbcSum) <= 0.000001) {
fprintf(outFile, "nan\n");
} else {
fprintf(outFile, "%.4f\n", cllSum - nbcSum);
}
}
fprintf(repFile, "%s\t%s", ((MGene_l) genesArray[i])->geneId, ((MGene_l) genesArray[i])->transcriptId);
for (k = 0; k < samplesLen; k++) {
fprintf(repFile, "\t%.4f\t%d\t%.4f\t%d", ((MGene_l) genesArray[i])->repExonTPM[k], ((MGene_l) genesArray[i])->repExonCount[k],
((MGene_l) genesArray[i])->repIntronTPM[k], ((MGene_l) genesArray[i])->repIntronCount[k]);
}
fprintf(repFile, "\n");
}
for (k = 0; k < samplesLen; k++) {
cllSum = 0.0;
for (i = 0; i < genesLen; i++) {
for (l = 0; l < ((MGene_l) genesArray[i])->entitiesLen; l++) {
if (((MGene_l) genesArray[i])->entities[l].samples[k].TPM != INFINITY) {
cllSum += ((MGene_l) genesArray[i])->entities[l].samples[k].TPM;
}
}
}
fprintf(sumFile, "%s\t%.4f\n", samples[k], cllSum);
}
if (dir) free(dir);
if (genesArray) free(genesArray);
BTreeFree(genes, FreeMGene, NULL);
freeArrayofPointers((void **) samples, samplesLen);
if (line) free(line);
fclose(outFile);
fclose(geneFile);
fclose(sumFile);
fclose(repFile);
return (EXIT_SUCCESS);
}
/**
* The function allocates memory of size bytes
*
* @param size size in bytes
* @param file the source code file (__FILE__) or NULL to not print this info
* @param line the source code line (__LINE__) or 0
* @return return a pointer to the allocated memory
*/
void *allocate(size_t size, const char *file, int line) {
return checkPointerError(malloc(size), "Can't allocate memory", file, line, -1);
}
int main(int argc, char** argv) {
int i, p;
int next_option, verbose;
const char* const short_options = "vhg:i:o:";
char *outputName, *output = NULL, *input = NULL;
FILE *gtfFile = NULL;
FILE *inFile = NULL;
FILE *outFile = NULL;
FILE *errFile = NULL;
FILE *entFile = NULL;
int max = 3000;
Chromosome_l chr = NULL;
int rFrom, rTo, rLen, total = 0, errors = 0;
time_t now, later;
double seconds;
int extragenic = 0;
bool flag = false;
program_name = argv[0];
const struct option long_options[] = {
{ "help", 0, NULL, 'h'},
{ "verbose", 0, NULL, 'v'},
{ "gtf", 1, NULL, 'g'},
{ "output", 1, NULL, 'o'},
{ "input", 1, NULL, 'i'},
{ NULL, 0, NULL, 0} /* Required at end of array. */
};
verbose = 0;
do {
next_option = getopt_long(argc, argv, short_options, long_options, NULL);
switch (next_option) {
case 'h':
print_usage(stdout, 0);
case 'v':
verbose = 1;
break;
case 'o':
output = strdup(optarg);
break;
case 'i':
if (strlen(optarg) == 1 && optarg[0] == '-'){
inFile = stdin;
}else{
inFile = checkPointerError(fopen(optarg, "r"), "Can't open INPUT file", __FILE__, __LINE__, -1);
}
break;
case 'g':
gtfFile = checkPointerError(fopen(optarg, "r"), "Can't open GTF file", __FILE__, __LINE__, -1);
break;
}
} while (next_option != -1);
if (!gtfFile || !output || ! inFile) {
print_usage(stderr, -1);
}
outputName = allocate(sizeof(char) * (strlen(output) + 10), __FILE__, __LINE__);
sprintf(outputName,"%s.out", output);
outFile = checkPointerError(fopen(outputName, "w"), "Can't open OUT file", __FILE__, __LINE__, -1);
sprintf(outputName,"%s.err", output);
errFile = checkPointerError(fopen(outputName, "w"), "Can't open ERR file", __FILE__, __LINE__, -1);
sprintf(outputName,"%s.ent", output);
entFile = checkPointerError(fopen(outputName, "w"), "Can't open ENT file", __FILE__, __LINE__, -1);
free(outputName);
free(output);
time(&now);
if (verbose) printf("Reading chromosomes from GTF file\n");
Chromosome_f *chrFactory = NewChromosomeFactory(gtfFile);
time(&later);
if (verbose) printf("Chromosomes loaded in %.0f s\n", difftime(later, now));
if (verbose) printf("Parsing SAM file\n");
SAM_f *samFactory = NewSAMFactory();
Reads_f *readsFactory = NewReadsFactory(samFactory, chrFactory, errFile);
readsFactory->processReadFromSAM(readsFactory, inFile, verbose);
if (verbose) printf("Processing GTF structure\n");
chrFactory->calculus(chrFactory);
if (verbose) printf("Printing results\n");
chrFactory->print(chrFactory, outFile, entFile);
FreeSAMFactory(&samFactory);
FreeChromosomeFactory(&chrFactory);
fclose(gtfFile);
fclose(outFile);
fclose(errFile);
fclose(entFile);
return (EXIT_SUCCESS);
}
