Skip to content

GitLab

Commit f7316f49 authored by David Trudgian's avatar David Trudgian
Browse files

Initial bug fixes and optimizations so working on BioHPC

parent 38ed0730
Hide whitespace changes
Inline Side-by-side
amino_acids.h
View file @ f7316f49
......@@ -13,12 +13,16 @@ class amino_acids
amino_acids();
char get_aa(int i);
int get_aa(char c);
static const string valid_aas;
};
const string amino_acids::valid_aas ="ACDEFGHIKLMNPQRSTVWY";
amino_acids::amino_acids()
{
}
char amino_acids::get_aa(int i)
{
if(i==0)
......
filter.h
View file @ f7316f49
......@@ -80,7 +80,6 @@ class filter
void read_in_files();
void open_tag_files();
void read_in_tags(vector<string>& tags, char current_amino_acid, int& num_refs);
void quicksort(vector<string>& tags, int left, int right);
bool compare_tags(string s1, string s2);
void form_clusters(vector<string>& tags);//, string s);
void view_clusters2(vector<cluster2>& clusters2,vector<string>& tags);
......
makefile
View file @ f7316f49
CPPFLAGS=-O3
all: mif sttag tmerg filt fmerg cm mdist fh dbc mtax
mif: mif.cpp directory_reader.h
g++ mif.cpp -o mif
g++ $(CPPFLAGS) mif.cpp -o mif
sttag: sttag.cpp sttagger.h
g++ sttag.cpp -o sttag
sttag: sttag.cpp sttagger.h org.h util.h amino_acids.h
g++ $(CPPFLAGS) sttag.cpp -fopenmp -o sttag
tmerg: tmerg.cpp tmerg.h
g++ tmerg.cpp -o tmerg
g++ $(CPPFLAGS) tmerg.cpp -o tmerg
filt: filter.cpp filter.h
g++ filter.cpp -o filt
g++ $(CPPFLAGS) filter.cpp -o filt
fmerg: fmerg.cpp util.h
g++ fmerg.cpp -o fmerg
g++ $(CPPFLAGS) fmerg.cpp -o fmerg
cm: cm.cpp util.h
g++ cm.cpp -fopenmp -o cm
# g++ cm.cpp -o cm
g++ $(CPPFLAGS) cm.cpp -fopenmp -o cm
# g++ $(CPPFLAGS) cm.cpp -o cm
dbc: dbc.cpp
g++ dbc.cpp -fopenmp -o dbc
g++ $(CPPFLAGS) dbc.cpp -fopenmp -o dbc
mdist: mdist.cpp mdist.h
g++ mdist.cpp -fopenmp -o mdist
# g++ mdist.cpp -o mdist
g++ $(CPPFLAGS) mdist.cpp -fopenmp -o mdist
# g++ $(CPPFLAGS) mdist.cpp -o mdist
fh: fix_hgt.cpp mdist.h mctr.h
g++ fix_hgt.cpp -fopenmp -o fh
# g++ fix_hgt.cpp -o fh
g++ $(CPPFLAGS) fix_hgt.cpp -fopenmp -o fh
# g++ $(CPPFLAGS) fix_hgt.cpp -o fh
mtax: mtax.cpp
g++ mtax.cpp -o mtax
g++ $(CPPFLAGS) mtax.cpp -o mtax
clean:
\rm mif
......
mctr.h
View file @ f7316f49
......@@ -6,6 +6,7 @@
#include <iostream>
#include <fstream>
#include <vector>
#include <algorithm>
#include <map>
#include <sstream>
#include <math.h>
......@@ -41,7 +42,6 @@ struct krow
};
//int find_top_string(vector<file_aa_pair> v);
void sort_problem_tags(vector<string>& tags, int left, int right);
class mctr
{
......@@ -2831,7 +2831,10 @@ void mctr::setup_it1(ifstream& infostream)
get_problem_tags(files1,"0");
get_problem_tags(files2,"1");
sort_problem_tags(problem_tags,0,problem_tags.size()-1);
std::sort(problem_tags.begin(), problem_tags.end());
if(MCTR_DEBUG)
{
......@@ -2935,7 +2938,7 @@ void mctr::setup_it2(ifstream& infostream)
get_problem_tags(files2,"1",hgt_genes1);
//cout<<"problem_tags at 0 = "<<problem_tags.at(0)<<endl;
//cout<<"size of problem_tags = "<<problem_tags.size()<<endl;
sort_problem_tags(problem_tags,0,problem_tags.size()-1);
std::sort(problem_tags.begin(), problem_tags.end());
//cout<<"problem_tags at 0 = "<<problem_tags.at(0)<<endl;
/* for(int i=0; i<10; i++)
{
......@@ -3523,38 +3526,7 @@ bool mctr::check_composition(string s)
return true;
}
void sort_problem_tags(vector<string>& tags, int left, int right)
{
int i=left;
int j=right;
string pivot=tags.at((left+right)/2);
while(i<=j)
{
while(pivot>tags.at(i))
{
i++;
}
while(pivot<tags.at(j))
{
j--;
}
if(i<=j)
{
string temp = tags.at(i);
tags.at(i) = tags.at(j);
tags.at(j) = temp;
i++;
j--;
}
};
if(left<j)
sort_problem_tags(tags,left,j);
if(i<right)
sort_problem_tags(tags,i,right);
}
int mctr::get_sos_cutoff()
{
......
mdist.h
View file @ f7316f49
......@@ -1825,6 +1825,8 @@ void mdist::read_in_orgs()
ifstream instream;
string orgfile = path+"/"+bfn+"/"+bfn+"_saved_orgs.txt";
u.open_ifile(instream,orgfile,"orgfile");
cout << orgfile << endl;
string eat;
int ord;
......@@ -1840,6 +1842,8 @@ void mdist::read_in_orgs()
//Set the ordinal.
new_org.set_ordinal(ord);
cout << "Organism: " << ord << endl;
//Set the path.
instream>>eat>>s;
new_org.set_path(s);
......@@ -1857,13 +1861,17 @@ void mdist::read_in_orgs()
instream>>eat>>i;
new_org.set_tag_length(i);
//Set bool conserved.
bool b;
instream>>eat>>b;
instream>>eat>>b;
new_org.set_conserved(b);
//Set the files.
instream>>eat>>i;
cout << "numfiles: " << i << endl;
for(int q=0; q<i; q++)
{
instream>>s;
......@@ -1871,7 +1879,10 @@ void mdist::read_in_orgs()
}
//Set the file sizes.
instream>>eat>>i;
instream>>eat>>i;
cout << "numfilesizes: " << i << endl;
for(int q=0; q<i; q++)
{
int fs;
......@@ -1879,8 +1890,13 @@ void mdist::read_in_orgs()
new_org.push_back_file_size(fs);
}
//Set the amino acid counts.
instream>>eat>>i;
cout << "numaacounts: " << i << endl;
for(int q=0; q<i; q++)
{
int aacount;
......@@ -1895,7 +1911,10 @@ void mdist::read_in_orgs()
double d;
instream>>eat>>d; //"discrepancy <double>"
new_org.setp_discrepancy(d);
cout << "discrepancy: " << d << endl;
instream>>eat>>i; //"conserved <int>"
new_org.setp_conserved(i);
......@@ -1906,13 +1925,22 @@ void mdist::read_in_orgs()
new_org.set_ref(b);
instream>>eat>>i; //"proteins.size() <integer which should be 0>"
cout << "proteins.size: " << i << endl;
instream>>eat>>i; //"total_num_proteins <integer which should be greater than 0>"
new_org.set_total_num_proteins(i);
cout << "total_num_proteins: " << i << endl;
new_org.set_total_num_proteins(i);
instream>>eat>>i; //"pv.size() <integer which should not be 0>"
new_org.setp_set_pv_size(i);
for(int q=0; q<i; q++)
cout << "ppv_size: " << i << endl;
for(int q=0; q<i; q++)
{
int keep;
instream>>eat>>keep;
......@@ -1922,10 +1950,15 @@ void mdist::read_in_orgs()
int fs; //filtering_steps
instream>>eat>>fs;
cout << "filtering_steps: " << fs << endl;
int pvv_size;
instream>>eat>>pvv_size; //"pvv.size() <integer which should match the size above>"
new_org.setp_set_pvv_size(pvv_size);
cout << "pvvsize: " << pvv_size << endl;
for(int q=0; q<pvv_size; q++)
{
instream>>eat>>i; //keeper
......@@ -1943,6 +1976,9 @@ void mdist::read_in_orgs()
}
instream>>eat>>i; //"sosv.size() <int like 401>"
cout << "sosv_size: " << pvv_size << endl;
new_org.setp_set_sosv_size(i);
vector<int> sosv_vals;
......
mif.cpp
View file @ f7316f49
......@@ -7,6 +7,7 @@ Identifies redundancy in the input (i.e. exact same proteome present in both ref
#include <iostream>
#include <fstream>
#include <vector>
#include <algorithm>
#include <cstdlib>
#include <getopt.h>
......@@ -127,8 +128,8 @@ int main(int argc, char* argv[])
logstream<<"Number of directories in FAA/ : directories.size() = "<<directories.size()<<endl;
logstream<<"Number of directories in FAA_ref/ : directoreis_ref.size() = "<<directories_ref.size()<<endl;
sort_directories(directories);
sort_directories(directories_ref);
std::sort(directories.begin(), directories.end());
std::sort(directories_ref.begin(), directories_ref.end());
if(MIF_DEBUG || verbose)
......@@ -234,19 +235,4 @@ int main(int argc, char* argv[])
repstream.close();
}
//Alphabetically sort the directories.
void sort_directories(vector<string>& directories)
{
for(int i=0; i<directories.size(); i++)
{
for(int j=i+1; j<directories.size(); j++)
{
if(directories.at(i)>directories.at(j))
{
string temp = directories.at(i);
directories.at(i) = directories.at(j);
directories.at(j) = temp;
}
}
}
}
org.h
View file @ f7316f49
......@@ -133,6 +133,11 @@ org::org()
array.push_back(0);
}
total_num_proteins=0;
// DCT - Wasn't initialized. Causes error later in mdist reading org file.
conserved = false;
}
org::~org()
......
proteome_v2.h
View file @ f7316f49
......@@ -4,9 +4,11 @@
#include <iostream>
#include <fstream>
#include <vector>
#include <algorithm>
#include <set>
#include <cstdlib>
#include <sstream>
#include <iomanip>
#include <cmath>
#include "protein.h"
......@@ -19,6 +21,7 @@ const double KEEPERS_CUTOFF=0.6;
const bool SUMOFSQUARES=true;
const double CONSERVATION_CUTOFF=1.3;
const bool PROTEOME_DEBUG=false;
const int MAXORDDIGITS=5;
using namespace std;
......@@ -71,7 +74,6 @@ class proteome_v2
void populate_proteins(string file);
void populate_kmers();
void quicksort(vector<string>& tv, int left, int right);
bool is_valid(string s);
amino_acids aas;
double get_ratio(int pindex);
......@@ -156,9 +158,15 @@ proteome_v2::proteome_v2()
// {
// sosv.push_back(0);
// }
discrepancy=0;
conserved=0;
filtering_steps=10.0; //Default.
// DCT - Wasn't initialized. Causes error later in mdist reading org file.
chosen_column = 0;
ref = false;
}
int proteome_v2::get_tags_size()
......@@ -242,6 +250,7 @@ void proteome_v2::set_sosv_size(int i)
{
cout<<"proteome_v2::set_sosv_size(int)"<<endl;
cout<<"i = "<<i<<endl;
cout<<"Current sosv.size: " << sosv.size() << endl;
cout<<"Error condition"<<endl;
exit(1);
}
......@@ -353,30 +362,32 @@ void proteome_v2::set_pvv_gnums_val(int index,vector<int> vals)
void proteome_v2::generate_tags(int ordinal,bool do_scrambled)
{
stringstream ss1;
ss1<<ordinal;
string so=ss1.str();
while(so.length()<MAXORDDIGITS)
{
so='0'+so;
}
stringstream sso;
sso << setfill('0') << setw(MAXORDDIGITS) << ordinal;
string so = sso.str();
for(int i=0; i<proteins.size(); i++)
{
stringstream ss;
ss<<i;
string is = ss.str();
for(int j=0; j<proteins.at(i).get_sequence().length(); j++)
{
string s = proteins.at(i).get_sequence().substr(j,tag_length);
if(is_valid(s))
{
while(s.length()<tag_length)
{
s+="^";
}
stringstream ss;
ss<<i;
string is = ss.str();
if(s.length() < tag_length){
s.append(tag_length - s.length(), '^');
}
s += " "+so+" "+is;
tags.push_back(s);
}
}
......@@ -386,6 +397,7 @@ void proteome_v2::generate_tags(int ordinal,bool do_scrambled)
ostemp.keeper=false;
ostemp.deleter=false;
ostemp.internal_repeats=0;
pv.push_back(ostemp);
osv ostemp2;
......@@ -399,6 +411,7 @@ void proteome_v2::generate_tags(int ordinal,bool do_scrambled)
ostemp2.gnums.push_back(0);
ostemp2.gis.push_back(0);
}
pvv.push_back(ostemp2);
if(do_scrambled)
......@@ -409,14 +422,14 @@ void proteome_v2::generate_tags(int ordinal,bool do_scrambled)
string s = scrambled.substr(j,tag_length);
if(is_valid(s))
{
while(s.length()<tag_length)
{
s+="^";
}
if(s.length() < tag_length){
s.append(tag_length - s.length(), '^');
}
stringstream ss;
ss<<i;
string is = ss.str();
s += " "+so+" "+is;
tags_scr.push_back(s);
}
}
......@@ -443,11 +456,13 @@ void proteome_v2::generate_tags(int ordinal,bool do_scrambled)
}
}
quicksort(tags,0,tags.size()-1);
std::sort(tags.begin(), tags.end());
if(do_scrambled)
{
quicksort(tags_scr,0,tags_scr.size()-1);
std:sort(tags_scr.begin(), tags_scr.end());
}
else
{
......@@ -604,6 +619,11 @@ void proteome_v2::generate_scrambled_tags(int ordinal)
for(int i=0; i<proteins.size(); i++)
{
stringstream ss;
ss<<i;
string is = ss.str();
string q = proteins.at(i).get_sequence();
scramble_v2(q);
......@@ -612,13 +632,10 @@ void proteome_v2::generate_scrambled_tags(int ordinal)
string s = q.substr(j,tag_length);
if(is_valid(s))
{
while(s.length()<tag_length)
{
s+="^";
}
stringstream ss;
ss<<i;
string is = ss.str();
if(s.length() < tag_length){
s.append(tag_length - s.length() ,'^');
}
s += " "+so+" "+is;
//cout<<"s = "<<s<<endl;
tags.push_back(s);
......@@ -630,7 +647,7 @@ void proteome_v2::generate_scrambled_tags(int ordinal)
cout<<"Size of size_real_tags = "<<size_real_tags<<endl;
exit(1);
cout<<"Sorting tags: "<<endl;
quicksort(tags,0,tags.size()-1);
std::sort(tags.begin(), tags.end());
cout<<"Done sorting. First elements = "<<tags.at(0)<<endl<<tags.at(1)<<endl<<tags.at(2)<<endl;
}
......@@ -657,12 +674,12 @@ vector<string> proteome_v2::get_scr_tags()
/*
void proteome_v2::read_proteins(string infile)
{
populate_proteins(infile);
populate_proteins(infile);
for(int i=0; i<proteins.size(); i++)
{
proteins.at(i).set_id(i);
}
populate_kmers();
cout<<"size of kmers = "<<kmers.size()<<endl;
}
......@@ -681,12 +698,12 @@ void proteome_v2::add_protein(string info_line, string aaseq)
void proteome_v2::mark_gene(string s, int hit_genome_id)
{
cout<<"In mark_gene s="<<s<<" hit_genome_id="<<hit_genome_id<<endl;
int bottom=0;
int top=kmers.size();
int middle=top/2;
int former_middle=-1;
bool found=false;
while(!found && former_middle!=middle)
{
......@@ -704,7 +721,7 @@ void proteome_v2::add_protein(string info_line, string aaseq)
}
else if(kmers.at(middle).s==s)
{
found=true;
found=true;
proteins.at(kmers.at(middle).source_protein_index).add_hit(hit_genome_id);
cout<<"protein info: "<<proteins.at(kmers.at(middle).source_protein_index).get_genome_hits_size()<<endl;
cout<<"The code is making it in here. kmer = "<<s<<endl;
......@@ -1564,38 +1581,7 @@ void proteome_v2::write_out_gene(int index)
}
}
void proteome_v2::quicksort(vector<string>& tv,int left, int right)
{
int i=left;
int j=right;
string pivot=tv.at((left+right)/2);
while(i<=j)
{
while(pivot>tv.at(i))
{
i++;
}
while(pivot<tv.at(j))
{
j--;
}
if(i<=j)
{
string temp = tv.at(i);
tv.at(i) = tv.at(j);
tv.at(j) = temp;
i++;
j--;
}
};
if(left<j)
quicksort(tv,left,j);
if(i<right)
quicksort(tv,i,right);
}
/*string proteome_v2::scramble(string s)
{
......@@ -1627,13 +1613,10 @@ void proteome_v2::quicksort(vector<string>& tv,int left, int right)
bool proteome_v2::is_valid(string s)
{
for(int i=0; i<s.length(); i++)
{
int index=aas.get_aa(s[i]);
if(index<0 || index>19)
{
return false;
}
std::size_t found = s.find_first_not_of(aas.valid_aas);
if(found != std::string::npos ){
return false;
}
if(SUMOFSQUARES)
......@@ -1647,20 +1630,12 @@ bool proteome_v2::is_valid(string s)
bool proteome_v2::check_composition(string s)
{
vector<int> array;
//int array[20];
for(int i=0; i<20; i++)
{
//array[i]=0;
array.push_back(0);
}
for(int i=0; i<s.length(); i++)
for(int i=0; i<20; i++)
{
int index=aas.get_aa(s[i]);
if(index>=0 && index<20)
{
array[index]++;
}
char aa = aas.get_aa(i);
int aa_count = std::count(s.begin(),s.end(),aa);
array.push_back( aa_count );
}
int result=0;
......
sttagger.h
View file @ f7316f49
......@@ -18,6 +18,7 @@ Class reads in proteins from FAA files specified in info file generated by make_
#include <cmath>
#include <omp.h>
#include "org.h"
#include "util.h"
......@@ -40,7 +41,7 @@ const int NUM_FILES_CUTOFF = 5; //NUM_FILES_CUTOFF: For each directory of .faa
//problematic_inputs.txt. This is to facilitate identifying bad downloads