void buildTranscript(int sp, int ep) {
int cur_s, cur_e; // current_start, current_end
string transcript_id = items[sp].getTranscriptID();
string gene_id = items[sp].getGeneID();
string gene_name = "", transcript_name = "";
char strand = items[sp].getStrand();
string seqname = items[sp].getSeqName();
string left = items[sp].getLeft();
vec.clear();
cur_s = cur_e = -1;
for (int i = sp; i <= ep; ++i) {
int start = items[i].getStart();
int end = items[i].getEnd();
general_assert(strand == items[i].getStrand(), "According to the GTF file given, a transcript has exons from different orientations!");
general_assert(seqname == items[i].getSeqName(), "According to the GTF file given, a transcript has exons on multiple chromosomes!");
if (items[i].getGeneName() != "") {
if (gene_name == "") gene_name = items[i].getGeneName();
else general_assert(gene_name == items[i].getGeneName(), "A transcript is associated with multiple gene names!");
}
if (items[i].getTranscriptName() != "") {
if (transcript_name == "") transcript_name = items[i].getTranscriptName();
else general_assert(transcript_name == items[i].getTranscriptName(), "A transcript is associated with multiple transcript names!");
}
if (cur_e + 1 < start) {
if (cur_s > 0) vec.push_back(Interval(cur_s, cur_e));
cur_s = start;
}
cur_e = (cur_e < end ? end : cur_e);
}
if (cur_s > 0) vec.push_back(Interval(cur_s, cur_e));
// if (gene_name != "") gene_id += "_" + gene_name;
// if (transcript_name != "") transcript_id += "_" + transcript_name;
transcripts.add(Transcript(transcript_id, gene_id, seqname, strand, vec, left));
}
bool buildTranscript(int sp, int ep) {
int cur_s, cur_e; // current_start, current_end
vector<Interval> vec;
string transcript_id = items[sp].getTranscriptID();
string gene_id = items[sp].getGeneID();
char strand = items[sp].getStrand();
string seqname = items[sp].getSeqName();
string left = items[sp].getLeft();
vec.clear();
cur_s = cur_e = -1;
for (int i = sp; i <= ep; i++) {
int start = items[i].getStart();
int end = items[i].getEnd();
if (strand != items[i].getStrand()) {
fprintf(stderr, "According to the GTF file given, a transcript has exons from different orientations!\n");
exit(-1);
}
if (seqname != items[i].getSeqName()) {
fprintf(stderr, "According to the GTF file given, a transcript has exons on multiple chromosomes!\n");
exit(-1);
}
if (cur_e + 1 < start) {
if (cur_s > 0) vec.push_back(Interval(cur_s, cur_e));
cur_s = start;
}
cur_e = (cur_e < end ? end : cur_e);
}
if (cur_s > 0) vec.push_back(Interval(cur_s, cur_e));
transcripts.add(Transcript(transcript_id, gene_id, seqname, strand, vec, left));
return true;
}
int main(int argc, char* argv[]) {
if (argc < 5 || ((hasMappingFile = atoi(argv[3])) && argc < 6)) {
printf("Usage: synthesisRef refName quiet hasMappingFile<0,no;1,yes;2,allele-specific> [mappingFile] reference_file_1 [reference_file_2 ...]\n");
exit(-1);
}
verbose = !atoi(argv[2]);
if (hasMappingFile) { loadMappingInfo(hasMappingFile, argv[4]); }
// allele-specific
if (hasMappingFile == 2) { transcripts.setType(2); }
int start = hasMappingFile ? 5 : 4;
ifstream fin;
string line, gseq;
string seqname, gene_id, transcript_id;
vector<Interval> vec;
M = 0;
name2seq.clear();
for (int i = start; i < argc; i++) {
fin.open(argv[i]);
general_assert(fin.is_open(), "Cannot open " + cstrtos(argv[i]) + "! It may not exist.");
unsigned long int line_no = 0; //Keep track of file line number
getline(fin, line);
line_no += 1;
while ((fin) && (line[0] == '>')) {
istringstream strin(line.substr(1));
strin>>seqname;
gseq = "";
while((getline(fin, line)) && (line[0] != '>')) {
line_no += 1;
gseq += line;
}
int len = gseq.length();
assert(len > 0);
for (int j = 0; j < len; j++) gseq[j] = check(gseq[j],line_no);
name2seq[seqname] = gseq;
transcript_id = seqname;
gene_id = seqname;
if (hasMappingFile) {
mi_iter = mi_table.find(seqname);
general_assert(mi_iter != mi_table.end(), "Mapping Info is not correct, cannot find " + seqname + "'s gene_id!");
gene_id = mi_iter->second;
if (hasMappingFile == 2) {
mi_iter2 = mi_table2.find(seqname);
general_assert(mi_iter2 != mi_table2.end(), "Mapping Info is not correct, cannot find allele " + seqname + "'s transcript_id!");
transcript_id = mi_iter2->second;
}
}
vec.clear();
vec.push_back(Interval(1, len));
transcripts.add(Transcript(transcript_id, gene_id, seqname, '+', vec, ""));
++M;
if (verbose && M % 1000000 == 0) { printf("%d sequences are processed!\n", M); }
}
fin.close();
}
if (M < 1) {
fprintf(stderr, "Number of transcripts in the reference is less than 1!\n");
exit(-1);
}
assert(M == transcripts.getM());
transcripts.sort();
writeResults(hasMappingFile, argv[1]);
return 0;
}
