detect_collinear_tandem_arrays.cc

#include "detect_collinear_tandem_arrays.h"
#include <getopt.h>
void read_gff(char* path)
{
    if (!ifstream(path))
    {
        cout<<"Cannot read gff_file!"<<endl;
        exit(1);
    }
    ifstream in(path);
    string line, word;
    Gene_feat gf;
    while (!in.eof())
    {
        getline(in,line);
        if (line=="")
            break;
        istringstream test(line);
        getline(test,gf.mol,'\t');
        getline(test,gf.name,'\t');
        getline(test,word,'\t');
        istringstream int_iss(word);
        int_iss>>gf.mid;
        gene_map[gf.name] = gf;
    }
    Gene_feat *gf1;
    map<string, Gene_feat>::iterator it;
    for (it=gene_map.begin(); it!=gene_map.end(); it++)
    {
        gf1 = &(it->second);
        allg.insert(gf1);
    }
    int i=0;
    geneSet::iterator it6;
    for (it6=allg.begin();it6!=allg.end();it6++)
    {
        (*it6)->geneid=i;
        i++;
    }
}

void read_blast(char* path)
{
    ifstream in(path);
    int i;
    int total_num=0;
    string line,word,geneids,gene1,gene2;
    double evalue;
    map<string, double>blast_map;
    map<string, double>::iterator it;
    cout<<"Reading BLAST file and pre-processing"<<endl;
    while (!in.eof())
    {
        getline(in,line);
        if (line=="")
            break;
        istringstream test(line);
        getline(test,gene1,'\t');
        getline(test,gene2,'\t');
        getline(test,word,'\t');
        getline(test,word,'\t');
        getline(test,word,'\t');
        getline(test,word,'\t');
        getline(test,word,'\t');
        getline(test,word,'\t');
        getline(test,word,'\t');
        getline(test,word,'\t');
        getline(test,word,'\t');
        istringstream double_iss(word);
        double_iss>>evalue;
        i=gene1.compare(gene2);
        if (i==0)
        {
            continue;
        }
        else if (i<0)
        {
            geneids=gene1+"&"+gene2;
        }
        else
        {
            geneids=gene2+"&"+gene1;
        }
        it = blast_map.find(geneids);
        if (it==blast_map.end())
        {
            blast_map[geneids]=evalue;
        }
        else
        {
            if (evalue<it->second)
            {
                it->second=evalue;
            }
        }
        total_num++;
    }
    in.close();
    double score;
    Blast_record br;
    map<string, Gene_feat>::iterator it1, it2;
    Gene_feat *gf1, *gf2;
    cout<<"Generating BLAST list"<<endl;
    for (it=blast_map.begin();it!=blast_map.end();it++)
    {
        istringstream test(it->first);
        getline(test,gene1,'&');
        getline(test,gene2,'&');
        it1 = gene_map.find(gene1);
        it2 = gene_map.find(gene2);
        if (it1==gene_map.end() || it2==gene_map.end()) continue;
        gf1 = &(it1->second), gf2 = &(it2->second);
        if (gf1->mol.empty() || gf2->mol.empty()) continue;
//////////////////////////////////////////////////////////////////////////////////
        if (gf1->geneid<gf2->geneid)
        {
            br.gene1=gene1;
            br.gene2=gene2;
            br.mol1=gf1->mol;
            br.mol2=gf2->mol;
            br.id1=gf1->geneid;
            br.id2=gf2->geneid;
        }
        else
        {
            br.gene1=gene2;
            br.gene2=gene1;
            br.mol1=gf2->mol;
            br.mol2=gf1->mol;
            br.id1=gf2->geneid;
            br.id2=gf1->geneid;
        }
//////////////////////////////////////////////////////////////////////////////////
        br.score = it->second;
        match_list.push_back(br);
    }

    int selected_num = match_list.size();
    cout<<selected_num<<" matches imported ("<<total_num-selected_num<<" discarded)"<<endl;
}

void compute_tandem()
{
    cout<<"Detecting tandem arrays..."<<endl;
    int i,j,k;
    tandem_pair temp;
    for (i=0;i<match_list.size();i++)
    {
        if (match_list[i].mol1==match_list[i].mol2&&(match_list[i].id1-match_list[i].id2)==-1)
        {
            temp.gene1=match_list[i].gene1;
            temp.gene2=match_list[i].gene2;
            temp.mol=match_list[i].mol1;
            temp.sp=match_list[i].mol1.substr(0,2);
            temp.id=match_list[i].id1;
            alltandempair.push_back(temp);
        }
    }
    sort(alltandempair.begin(),alltandempair.end());
    tandem_array temp1;
    temp1.gene.push_back(alltandempair[0].gene1);
    temp1.gene.push_back(alltandempair[0].gene2);
    temp1.sp=alltandempair[0].sp;
    temp1.mol=alltandempair[0].mol;
    j=alltandempair[0].id;
    for (i=1;i<alltandempair.size();i++)
    {
        if (alltandempair[i].id==j+1)
        {
            temp1.gene.push_back(alltandempair[i].gene2);
            j++;
        }
        else
        {
            alltandemarray.push_back(temp1);
            temp1.gene.clear();
            temp1.gene.push_back(alltandempair[i].gene1);
            temp1.gene.push_back(alltandempair[i].gene2);
            temp1.sp=alltandempair[i].sp;
            temp1.mol=alltandempair[i].mol;
            j=alltandempair[i].id;
        }
    }
    for (i=0;i<alltandemarray.size();i++)
    {
        for (j=0;j<alltandemarray[i].gene.size();j++)
        {
            tandemgeneid[alltandemarray[i].gene[j]]=i;
        }
    }
}

void read_synteny(char* path)
{
    if (!ifstream(path))
    {
        cout<<"Cannot read collinearity_file!"<<endl;
        exit(1);
    }
    string gene1,gene2;
    ifstream in(path);
    string line, word;
    size_t found;
    tandem_cluster temp;
    map<string,int>::iterator it21,it22;
    while (!in.eof())
    {
        getline(in,line);
        if (line=="")
            continue;
        found=line.find("#");
        if (found!=string::npos)
        {
            continue;
        }
        istringstream test(line);
        getline(test,word,'\t');
        getline(test,gene1,'\t');
        getline(test,gene2,'\t');
        it21=tandemgeneid.find(gene1);
        it22=tandemgeneid.find(gene2);
        if (it21!=tandemgeneid.end()||it22!=tandemgeneid.end())
        {
            temp.anchor1=gene1;
            temp.anchor2=gene2;
            temp.array_id1=-1;
            temp.array_id2=-1;
            if (it21!=tandemgeneid.end())
                temp.array_id1=it21->second;
            if (it22!=tandemgeneid.end())
                temp.array_id2=it22->second;
            alltandemcluster.push_back(temp);
        }
    }
}

void print_file(char* path)
{
    cout<<"Outputting results..."<<endl;
    int i,j;
    ofstream result;
    result.open(path,ios::out);
    result<<"Anchor1\tTandem_array1\tAnchor2\tTandem_array2\n";
    for (i=0;i<alltandemcluster.size();i++)
    {
        result<<alltandemcluster[i].anchor1<<"\t";
        if (alltandemcluster[i].array_id1<0)
        {
            result<<alltandemcluster[i].anchor1<<"\t";
        }
        else
        {
            for (j=0;j<alltandemarray[alltandemcluster[i].array_id1].gene.size()-1;j++)
            {
                result<<alltandemarray[alltandemcluster[i].array_id1].gene[j]<<",";
            }
            result<<alltandemarray[alltandemcluster[i].array_id1].gene[j]<<"\t";
        }
        result<<alltandemcluster[i].anchor2<<"\t";
        if (alltandemcluster[i].array_id2<0)
        {
            result<<alltandemcluster[i].anchor2<<endl;
        }
        else
        {
            for (j=0;j<alltandemarray[alltandemcluster[i].array_id2].gene.size()-1;j++)
            {
                result<<alltandemarray[alltandemcluster[i].array_id2].gene[j]<<",";
            }
            result<<alltandemarray[alltandemcluster[i].array_id2].gene[j]<<endl;
        }
    }
    cout<<"Done!"<<endl;
}

int main(int argc, char *argv[])
{
    if (argc < 9)
    {
        cout<<"Usage: ./detect_collinear_tandem_arrays -g gff_file -b blast_file -c collinearity_file -o output_file"<<endl;
        exit(1);
    }
    char gpath[200], bpath[200], spath[200], opath[200];
    int c,e_g,e_b,e_s,e_o;
    e_g=e_b=e_s=e_o=1;
    while ((c = getopt(argc, argv, "g:b:c:o:")) != -1)
    {
        switch (c)
        {
        case 'g':
            sprintf(gpath,"%s",optarg);
            e_g=0;
            break;
        case 'b':
            sprintf(bpath,"%s",optarg);
            e_b=0;
            break;
        case 'c':
            sprintf(spath,"%s",optarg);
            e_s=0;
            break;
        case 'o':
            sprintf(opath,"%s",optarg);
            e_o=0;
            break;
        case '?':
            if (optopt!='g' || optopt!='b' || optopt!='c' ||optopt!='o')
            {
                cout<<"Usage: ./detect_collinear_tandem_arrays -g gff_file -b blast_file -c collinearity_file -o output_file"<<endl;
            }
            break;
        }
    }
    if (e_g+e_b+e_s+e_o>0)
    {
        cout<<"Usage: ./detect_collinear_tandem_arrays -g gff_file -b blast_file -c collinearity_file -o output_file"<<endl;
        exit(1);
    }
    read_gff(gpath);
    read_blast(bpath);
    compute_tandem();
    read_synteny(spath);
    print_file(opath);
    return 1;
}