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#include "GraphOutput.h"
const string GraphOutput::json_nodes_file_suffix = ".json_nodes";
const string GraphOutput::json_edges_file_suffix = ".json_edges";
const string GraphOutput::json_starters_file_suffix = ".json_starters";
const string GraphOutput::json_file_suffix = ".json";
/************************************************************************************************************************/
/* init function initialize the files need to construct graph file or sequences file */
/* */
/************************************************************************************************************************/
void GraphOutput::init(bool erase){
json_nodes_file_name=(prefix+json_nodes_file_suffix);
json_edges_file_name=(prefix+json_edges_file_suffix);
json_starters_file_name=(prefix+json_starters_file_suffix);
json_file_name=(prefix+json_file_suffix);
nodes_file = fopen(json_nodes_file_name.c_str(),erase?"w":"a");
edges_file = fopen(json_edges_file_name.c_str(),erase?"w":"a");
starters_file = fopen(json_starters_file_name.c_str(),erase?"w":"a");
graph_file = fopen(json_file_name.c_str(),erase?"w":"a");
}
/************************************************************************************************************************/
/* printf GraphOutput and initialize files (files are not erasing) */
/* */
/************************************************************************************************************************/
GraphOutput::GraphOutput(string prefix, id_els first_id_els) : prefix(prefix), first_id_els(first_id_els)
{ // PIERRE: need something different than 0 for the first node
init(true);
}
/*************************************************************************************************************************/
/* Initialize first elements and files (files are erasing) */
/* */
/************************************************************************************************************************/
GraphOutput::GraphOutput(string prefix) : prefix(prefix)
{
first_id_els.node=0;
first_id_els.edge=0;
init(true);
}
/************************************************************************************************************************/
/* write graph file or sequence file */
/* */
/************************************************************************************************************************/
void GraphOutput::close()
{
fclose(nodes_file);
fclose(edges_file);
fclose(starters_file);
ifstream nodes(json_nodes_file_name.c_str(), ios::in);
ifstream edges(json_edges_file_name.c_str(), ios::in);
ifstream starters(json_starters_file_name.c_str(), ios::in);
if(!edges || !nodes || !starters){fprintf(stderr,"Cannot open file %s, %s or %s exit\n", json_edges_file_suffix.c_str(), json_nodes_file_suffix.c_str(), json_starters_file_suffix.c_str()); exit(1);}
string line;
fprintf(graph_file,"{\n"); // overall json {
bool first=true;
while(getline(starters,line)){
if(!first) fprintf(graph_file,",\n"); // separates starters
first = false;
fprintf(graph_file,"%s\n", line.c_str());
fprintf(graph_file,"\"extremGraphs\":[\n"); // we print this line only if we had at least one
int i =0;
//fprintf(graph_file," %s \n"line.c_str());
bool first_data_xtrem_graph=true;
while(getline(nodes,line) && strstr((const char*)line.c_str(), "startNewStarter")==NULL){ //test if is the end of the nodes file and if it's a new starter written
if(!first_data_xtrem_graph) fprintf(graph_file,",\n"); // separates data_xtrem_graph
first_data_xtrem_graph = false;
fprintf(graph_file,"{\"data\":{\"id\":\"k%d\", %s \n\"nodes\":[",i,line.c_str()); // prints data for the starter
// prints the first node (that necessarly exists)
getline(nodes,line);
fprintf(graph_file,"\n\t%s",line.c_str()); // prints the first node without comma before
//for each node of each extension
while(getline(nodes,line)){
//test if there are at the end of the array of node for this extension
if (strstr((const char*)line.c_str(), "endOfKmer")==NULL){ // test of end if it's an other kmer
fprintf(graph_file,",\n\t%s",line.c_str());// prints the other nodes
}
else{ // prints the edges of nodes of this extension
fprintf(graph_file,"\n],\n"); // end of nodes
fprintf(graph_file,"\"edges\": ["); // starts of edges
getline(edges,line);
if (strstr((const char*)line.c_str(), "endOfKmer")==NULL){// test of end if it's an other kmer
fprintf(graph_file,"\n\t%s",line.c_str()); // prints the first edge without comma before
}
else{ // there was NO edge
break;
//getline(edges,line);
}
// We already read one edge, lets continue (starting with a ',')
//for each edges of each extension
while(getline(edges,line)) {
if (strstr((const char*)line.c_str(), "endOfKmer")==NULL){// test of end if it's an other kmer
fprintf(graph_file,",\n\t%s",line.c_str()); // print other edges
}
else{
break;
}
}
break;
}
} // end all edges
if( ! first_data_xtrem_graph) // we read at least one xtrem graph data
fprintf(graph_file,"\n]\n}}"); // END: ] edges, } data, } xtrem graph
i++;
} // end all xtrem graphs of one starter
fprintf(graph_file,"]"); // end all xtrem graphs of this starter
// end at least one starter
fprintf(graph_file,"\n}}"); // end of a starter
} // end all starters
fprintf(graph_file,"\n}"); // end of the json
nodes.close(); remove(json_nodes_file_name.c_str());
edges.close(); remove(json_edges_file_name.c_str());
starters.close();remove(json_starters_file_name.c_str());
fclose(graph_file);
}
/************************************************************************************************************************/
/* print head for a starter */
/* */
/************************************************************************************************************************/
void GraphOutput::print_starter_head(int index, char* sequence)
{
fprintf(starters_file,"\"Starter_%d\":{\"data\":{\"id\":\"S%d\", \"sequence\":\"%s\", \"length\":%ld,\n", index,index, sequence, strlen(sequence));
}
/************************************************************************************************************************/
/* recalculate length for a node (more efficient than capture length in fasta file (in string) */
/* and convert it in integer) */
/* */
/************************************************************************************************************************/
long GraphOutput::sequence_length(string line)
{
string seq_char;
int err,match,start, end;
regex_t preg;
long seq_len=0;
size_t nmatch, size;
const char *str_regex ="([A-Z]+)"; //regex capture sequences characters
const char *line_c =NULL;
line_c = line.c_str();
err = regcomp (&preg, str_regex, REG_EXTENDED);
if (err == 0)//security for error string snapshot and if regex match
{
nmatch = 0;
nmatch = preg.re_nsub;
regmatch_t *pmatch=NULL;
pmatch = (regmatch_t*) malloc (sizeof (*pmatch) * nmatch);
if (pmatch)
{
match = regexec (&preg, line_c, nmatch, pmatch, 0);
regfree (&preg);
if (match == 0)
{
char *seq_char =NULL;
start = pmatch[0].rm_so;
end = pmatch[0].rm_eo;
size = end - start;
seq_len = sizeof(line_c[start])*(size);
}
}
}
else
{
fprintf (stderr, "LOW MEMORY !\n");
exit (EXIT_FAILURE);
}
return seq_len;
}
/************************************************************************************************************************/
/* output a single node to a file */
/* */
/************************************************************************************************************************/
//TODO: comment with xgmml format
void GraphOutput::print_node(long index, char *ascii_node) // output a single node to a file
{
fprintf(nodes_file," { \"data\": { \"id\":\"n%ld\", \"sequence\":\"%s\", \"length\":%ld}}\n",index,ascii_node, strlen(ascii_node));
}
/************************************************************************************************************************/
/* write mark for end of nodes list */
/* */
/************************************************************************************************************************/
void GraphOutput::print_starter_end() // output a single node to a file
{
fprintf(nodes_file,"startNewStarter\n");
}
/************************************************************************************************************************/
/* output a single edges to a file */
/* */
/************************************************************************************************************************/
//TODO: comment with xgmml format
void GraphOutput::print_edge(long index, long id, long id2, string label,string comment)
{
fprintf(edges_file,"{ \"data\":{ \"id\": \"e%ld\", \"source\": \"n%ld\",\"target\": \"n%ld\",\"direction\": \"%s\"%s}}\n",index, id,id2,label.c_str(), comment.c_str());
}
/************************************************************************************************************************/
/* load nodes extremities */
/* */
/************************************************************************************************************************/
void GraphOutput::load_nodes_extremities(string linear_seqs_name)
{
kmer_links.clear(); // PIERRE: reset previous stored kmer links
Bank *Nodes = new Bank((char *)linear_seqs_name.c_str());
long nb_nodes = first_id_els.node; //PIERRE;
char * rseq;
int readlen;
sizeKmer--; // nodes extremities overlap by (k-1)-mers, so let's extract (k-1)-mers
while (Nodes->get_next_seq(&rseq,&readlen))
{
kmer_type left_kmer, right_kmer, left_kmer_fw, left_kmer_rc, right_kmer_fw, right_kmer_rc;
left_kmer = extractKmerFromRead(rseq,0,&left_kmer_fw,&left_kmer_rc, false);
right_kmer = extractKmerFromRead(rseq,readlen-sizeKmer,&right_kmer_fw,&right_kmer_rc, false);
Strand left_strand = (left_kmer == left_kmer_fw)?FW:RC;
Strand right_strand = (right_kmer == right_kmer_fw)?FW:RC;
kmer_links[left_kmer].insert(node_strand(nb_nodes, left_strand, LEFT));
kmer_links[right_kmer].insert(node_strand(nb_nodes, right_strand, RIGHT));
nb_nodes++;
}
Nodes->close();
delete Nodes;
sizeKmer++; // make sure to restore k
}
/************************************************************************************************************************/
/* construct node file and edge file for graph file */
/* */
/************************************************************************************************************************/
id_els GraphOutput::construct_graph(string linear_seqs_name, const string direction) // PIERRE: i need to know the last nb_nodes
{
Bank *Nodes = new Bank((char *)linear_seqs_name.c_str());
id_els nb_els = first_id_els; //Alexan: stucture for print id elements in graph output
char * rseq;
int readlen;
bool end = true;
Nodes->rewind_all();
string kmerSequence = linear_seqs_name;
kmerSequence.erase(0, 13);
strtok( (char*) kmerSequence.c_str(), "_");
// char* direction =strtok( NULL, "_");
fprintf(nodes_file, "\"sequence\":\"%s\", \"direction\":\"%s\", \"type\":\"%s\",\n ", kmerSequence.c_str(),direction.c_str(), original?"original":"degenerated");
sizeKmer--; // nodes extremities overlap by (k-1)-mers, so let's extract (k-1)-mers
// for each node, output all the out-edges (in-edges will correspond to out-edges of neighbors)
/* int nb_seq =0;
string s;
while (getline(file, s))
nb_seq++;*/
while(Nodes->get_next_seq(&rseq,&readlen)){
end = false;
kmer_type left_kmer, right_kmer, left_kmer_fw, left_kmer_rc, right_kmer_fw, right_kmer_rc;
set<node_strand>::iterator it;
left_kmer = extractKmerFromRead(rseq,0,&left_kmer_fw,&left_kmer_rc, false);
right_kmer = extractKmerFromRead(rseq,readlen-sizeKmer,&right_kmer_fw,&right_kmer_rc, false);
Strand left_strand = (left_kmer == left_kmer_fw)?FW:RC;
Strand right_strand = (right_kmer == right_kmer_fw)?FW:RC;
// left edges (are revcomp extensions)
for (it = kmer_links[left_kmer].begin(); it != kmer_links[left_kmer].end(); it++)
{
long cur_node = it->node;
Strand cur_strand = it->strand;
LeftOrRight cur_left_or_right = it->left_or_right;
if (cur_node == nb_els.node) // prevent self loops on same kmer
if (readlen == sizeKmer)
continue;
string label = "R";
if (cur_left_or_right == LEFT)
{
if (cur_strand != left_strand)
label+=(string)"F";
else
continue;
}
else
{
if (cur_strand == left_strand)
label+=(string)"R";
else
continue;
}
print_edge(nb_els.edge, nb_els.node,cur_node,label,"");
nb_els.edge++;
}
// right edges
for (it = kmer_links[right_kmer].begin(); it != kmer_links[right_kmer].end(); it++)
{
long cur_node = it->node;
Strand cur_strand = it->strand;
LeftOrRight cur_left_or_right = it->left_or_right;
if (cur_node == nb_els.node) // prevent self loops on same kmer
if (readlen == sizeKmer)
continue;
string label = "F";
if (cur_left_or_right == LEFT)
{
if (cur_strand == right_strand)
label+=(string)"F";
else
continue;
}
else
{
if (cur_strand != right_strand)
label+=(string)"R";
else
continue;
}
print_edge(nb_els.edge, nb_els.node,cur_node,label,"");
nb_els.edge++; //ALEXAN
}
print_node(nb_els.node, rseq);
nb_els.node++;
end = true ;
}
if(end){
fprintf(edges_file, "endOfKmer\n");
fprintf(nodes_file, "endOfKmer\n");
};
sizeKmer++; // make sure to restore k
Nodes->close();
delete Nodes;
return nb_els; // PIERRE
}
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