Commit d3428e35 authored by Raquel Bromberg's avatar Raquel Bromberg

Bug fixed in code for generating scrambled proteomes

parent a51aac66
......@@ -60,9 +60,9 @@ class org
void setp_discrepancy(double d);
void setp_conserved(int i);
void setp_chosen_column(int i);
void setp_set_pv_size(int i);
// void setp_set_pv_size(int i);
void setp_set_pvv_size(int i);
void setp_set_pv_val(int index, int i1, int i2, int i3, int i4, int i5);
// void setp_set_pv_val(int index, int i1, int i2, int i3, int i4, int i5);
void setp_set_pvv_gnums_val(int index, vector<int> vals);
void setp_set_pvv_gis_val(int index, vector<int> vals);
void setp_set_keeper(int index,int i);
......@@ -93,20 +93,20 @@ class org
void fill_fields(string dir_par);
void generate_tags(bool do_scrambled, bool partial_run);
void generate_scrambled_tags();
// void generate_scrambled_tags();
void clear_tags();
void clear_scr_tags();
void write_out_aa_array(ofstream& outstream);
int mark_keepers(vector<string> keepers);
void write_out_gene(int index);
void clear_proteins();
void increment_ggs(int gene_id,int gnums_size,int vector_size);
// void increment_ggs(int gene_id,int gnums_size,int vector_size);
void increment_ggs(int gene_id,int gnums_size,int vector_size,double d);
void write_out_new_proteome(int index);
void add_file(string s);
void add_discr(int instances, double avg_rep);
double get_discr();
void count_conserved();
void increment_conserved();
void count_filtered_proteomes(vector<int>& v);
void push_back_file_size(int fs);
void add_aa_count(int index, int count);
......@@ -161,11 +161,11 @@ void org::generate_tags(bool do_scrambled, bool partial_run)
p.generate_tags(ordinal,do_scrambled,partial_run);
}
void org::generate_scrambled_tags()
/*void org::generate_scrambled_tags()
{
p.generate_scrambled_tags(ordinal);
}
*/
void org::set_ordinal(int i)
{
ordinal=i;
......@@ -202,10 +202,11 @@ void org::setp_size_real_tags(int i)
p.set_size_real_tags(i);
}
void org::setp_set_pv_val(int index,int i1, int i2, int i3, int i4, int i5)
/*void org::setp_set_pv_val(int index,int i1, int i2, int i3, int i4, int i5)
{
p.set_pv_val(index,i1,i2,i3,i4,i5);
}
*/
void org::setp_set_pvv_gnums_val(int index, vector<int> vals)
{
......@@ -231,10 +232,10 @@ void org::setp_chosen_column(int i)
p.set_chosen_column(i);
}
void org::setp_set_pv_size(int i)
/*void org::setp_set_pv_size(int i)
{
p.set_pv_size(i);
}
}*/
void org::setp_set_pvv_size(int i)
{
......@@ -478,6 +479,7 @@ void org::write_out_aa_array(ofstream& outstream)
if(total_num_aa<=0)
{
cout<<"In org::write_out_aa_array(ofstream&). total_num_aa="<<total_num_aa<<endl;
cout<<"ordinal="<<ordinal<<endl;
exit(1);
}
......@@ -526,10 +528,10 @@ void org::clear_proteins()
p.clear_proteins();
}
void org::increment_ggs(int gene_id,int gnums_size,int vector_size)
/*void org::increment_ggs(int gene_id,int gnums_size,int vector_size)
{
p.increment_ggs(gene_id,gnums_size,vector_size);
}
}*/
void org::increment_ggs(int gene_id,int gnums_size,int vector_size,double d)
{
......@@ -585,9 +587,9 @@ double org::get_discr()
return p.get_discr();
}
void org::count_conserved()
void org::increment_conserved()
{
p.count_conserved();
p.increment_conserved();
}
int org::get_conserved()
......
No preview for this file type
......@@ -63,7 +63,8 @@ int main(int argc, char* argv[])
u.rm_mkdir(path+"/"+bfn,"TAGSscr");
u.rm_mkdir(path+"/"+bfn,"HIST");
u.rm_mkdir(path+"/"+bfn,"SAVEDORGS");
srand(time(NULL));
#pragma omp parallel for
for(int i=0; i<to; i++)
{
......
......@@ -35,7 +35,7 @@ const bool DO_SCRAMBLING = true; //DO_SCRAMBLING: Can be set to false when user
//generating very slightly different results; keeping this random background
//constant can be useful for testing/debugging, etc.
const int NUM_FILES_CUTOFF = 5; //NUM_FILES_CUTOFF: For each directory of .faa files, checks how many there are in total.
const int NUM_FILES_CUTOFF = 10; //NUM_FILES_CUTOFF: For each directory of .faa files, checks how many there are in total.
//If there are more .faa files than this cutoff, the organism is flagged in
//problematic_inputs.txt. This is to facilitate identifying downloads
//which consist of hundreds of .faa files for a single organism.
......@@ -634,6 +634,7 @@ void sttagger::write_out_tags_v2()
organisms.at(0).clear_tags();
outstream.close();
/*
ofstream histstream;
histstream.open( (path+"/"+bfn+"/"+bfn+"_hist.txt").c_str());
if(histstream.fail())
......@@ -645,7 +646,7 @@ void sttagger::write_out_tags_v2()
histstream<<ordinal<<endl<<organisms.at(0).get_total_num_aa()<<endl;
organisms.at(0).write_out_aa_array(outstream);
histstream<<endl;
histstream.close();
histstream.close();*/
}
void sttagger::write_out_scr_tags(int organism)
......
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