readme.txt updated. Examples directory modified. Output statements from...

readme.txt updated. Examples directory modified. Output statements from programs reduced. All programs and files not involved in the core SlopeTree routines removed. Some minor code cleanup.

.gitignore

@@ -9,4 +9,18 @@ mtax
 rapidnj
 sttag
 tmerg
-
+archaea_run_no_filtering.sh
+gc.prt
+script_cm.sh
+script_stmif.sh
+buildconcat.cpp
+genome_mapped.txt
+readme_conflict.txt
+script_do_sttagg.sh
+script_strun.sh
+buildconcat_output_aligned.txt
+merge_hgt_pairs_files.cpp
+script_do_tmerg.sh
+buildconcat_output.txt
+rzs.cpp
+script_filter.sh

Examples/Ex1/FAA/uncultured_Termite_group_1_bacterium_phylotype_Rs_D17_uid59059/NC_020420.faa

+>gi|189485766|ref|YP_001956706.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MWNEIIIELKEKIPTEWLEPIKEESFKDDILTLAVPDTYYAQKYETDYEPLIQNILKAKTGKAVGLQFQI
+VASKLLAEPVIKDEKPKAQLIKKTKFTGNPYFKNPAEFTKFAKETTKKEIEISIGQKVMTSMPTKYGAKD
+VITFSILNNKMFAYPNDKRKNAKVKMDIRFSNDTVKTFDLYRGQLETRGKGYGQLTTTHAKILLAVIHIW
+QEQGCKFADEGQACYVNTTVREIAKKLGYKSFSGADHERLLQKTKDLADLPMVIADRKEAHSFTILYDVS
+THVIEDSEGNDTNRRTISIVFNPFIAKQLYDRKVILRKPQCYKIKNPTAIKFLLCYDKRIIKGFNLKMNI
+SEVANDLEIETNKTSNIITNIKNAFQELNGYELNDSYSLHVELVKEGKEWIVIAERISKEKQQPLKALLA
+>gi|189485767|ref|YP_001956707.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MKKLICFVMLGCFVLTFVSCGKRSAMLQDVASVKIEEVKLENGENKTPPPDDPAPEDPETITKADRRVGI
+IAGMACMAIAFTGLAIYWMCCGSRKPFEFQVPQDEQNEKPDSEIPKLDNEVPEKPLVDANQDKSELNA
+>gi|189485768|ref|YP_001956708.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MKFKKVICVYLTLVLFLTGCENLKSQIRGNQNTDASADQQTGNIIKSDNNGIIEKEETKKLDDKVIGLVV
+GDEKEKTSSKEPELRWQDKAKKYAGDAVHFLYEHKEQVYFVGIAVIYLLWKERLFQQQNHQDQMQWHLAQ
+IQQLQQAQDQIQQMPVQDQIQYLQQLQNHFLQAQFNLQQLNQDPNLIQQFQQVQDQIQNGIGQLQAQVQQ
+QIQPQLAQLQLG
+>gi|189485769|ref|YP_001956709.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MEYKKETDYYENDMRHTADAPKLEKRLRKSLNVFGLILLVLAVYLFGSFLLCSCYRRGVVGGVVADNNAV
+LPDAVTELKSDKKLINGAGLSLSERSVVAEPFRFGVIVPVVNNDG
+>gi|189485770|ref|YP_001956710.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MKFKKALCVYLTIVLFLTGCENLKSRIRGNQNTDASADQQTGNIIKSGNNGIIEKEETKELDGKSFGLDA
+NGNGSSLQGENTEKETPSEEPELMWQDKAKKYAGDAGHFLYEHKGKIAFAVVVVAGVYWFGIRPINGLPA
+QPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPLLPV
+QPLLHVRPEVLQLRQEQALQQYQQQQHEIEELFVPDAVDLFAALGADMTVLDVMLSELRSQITQLYRLQV
+RQLQEQLRLQEPQAQEQLLQRQLQERLILAQERQDLLQLRINNLRRHFRQYQAMPFLQIEYLEYQHRLTQ
+QLLQQAQQQVQQRQEQQLAELAEQAQQVQQRQEQQLAELAEQAQQLAEQEQQQEQQLAELAEKL
+>gi|189485771|ref|YP_001956711.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MRDILMIKIKDKYKLVENIFPINNPFRSSRTVQKALKIINKNFVCNIIVLSLLLCSCGKKQALLNTAITE
+KSEVVSELKSELAKIQKELKEKKEKLIEVQEELEKAIEVQEELEKENWQNLWELYDNRMGFFLLGLLTAD
+LIVLGCICCTMCSCC
+>gi|189485772|ref|YP_001956712.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MEYKKETDYYENDMRHTADAPKLEKRLRKSLNVFGLILLVLAVYLFGSFLLCSCYRRGVVGGVVADNNAV
+LPDAVTELKSDKKLINGAGLSLSERSVVAEPFRFGVIVPVVNNDG
+>gi|189485773|ref|YP_001956713.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MKKIIILLVVFLMFFGCYKKPITNIPVPEEIEEIKIPDVYYFSDMFTACNCFLAISTLFFLATVMFAGYS
+FLGKDFDINDYRRPVELGNRIVPQRGNNI
+>gi|189485774|ref|YP_001956714.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MKKIFAVILMLSVFLSGCHRKVITGISKNENDVPTSTNTPAPEPTSTPMPTSTPAFMDCFPKYKAPSSTP
+APLDADDYYDNWTKCVLLYVDDDGNWVNGKHKHSEAHKRLLLKDL

Examples/Ex1/FAA/uncultured_Termite_group_1_bacterium_phylotype_Rs_D17_uid59059/NC_020421.faa

+>gi|189485776|ref|YP_001956715.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MWNEIITELKEKIPTEWLEPIKEESFKDDILTLAVPDTYYAQKYETDYKPLIQNILKAKTGKAVGLQFQI
+VASKLLAEPVIKDEKPKTQLMKKTKFNGKPYFENPAEFVSIAKAASQVKETDIKNAELTSMPNKYGITNV
+ASFSLLDSKFFTYPNDKRKKTKVEMPVRFSNGVVKVYNLYRGQFAINDNGYGQLTTTHAKIFFAIIHIWQ
+KQNSRYADNKGFYAVVDISMRELAKQLGYQKVSGADYRRLLQRVKELVDFPMILSDGRVAHTFTFLNSAI
+GRTVHQSGKNKLMLRLTLNPFISKQFYERNVILRNPQCYKIKNPTAFKFLLCYDKRVVKGNNLKLNIYEV
+ANDLELNISKLCHGVSVLKVAFRELNGYELNDSYRLYVELVKEEREWIVIAERISKEKQQPLKALLA
+>gi|189485777|ref|YP_001956716.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MKLKKALCVYLTIVLFLTGCENLKSQIRGNQNTVASADQPTGDIIKSDNSGIIEKQKEKESDLKKIENNV
+DNPNGDNGGDNNGDNPNGDNGGDNPNGDNGGDNNGDSSQHKSSSEANGKDLRGWLWDHKGSISGIVLASA
+VVIGAIGFWGGQPNVCAVNYFYVPQAVQENQAQVQVPAVQENQAQVQVPAVQENQAQVQVPAVQENQAQV
+QVPAVQENQAQVQVPAVQENQAQVQVPAVQENQAQVQVPAVQENQAQVQVPAVQENQAQVQVPAVQGNQN
+PNLVYFDIHSGRYIPGNQNPNLVYFDIHSGRYIPIVRGNPNPILVVQGNLYQVQGNESPFPVLLVEENQV
+QVPAVQELPSQQQLQRIQNRLDQLQGQLRNLESHAIFQFQQIQVEAEALQLHNEQYIQLIGSIVDDPLYP
+QLNLQFQQICQILRHSHSLQLYDIGFHIFLMREILDHHLHLTARNLPDVYGPPPRWEALRVQEQLERHNQ
+QLNQLYQQIEGRLVIEQSVLGARPDSQQRQQELREFNELAIQLQEHQRRIEALLKWLI
+>gi|189485778|ref|YP_001956717.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MTAVKFKKIFAVILMLSVFLSGCQRQVITGVSKNENDVSTSTNTPVPEPTPTPTPAPEPTPTPTPVPEPT
+PTPTPVPEPTPTPTPVPEPTPTPTPVPEPTPTPTPVPEPTPAFMDCFPKYEAPLSTPAPLDEDDYYDNRV
+KWALSHVDDDGNWVNGKHSEAPKCLLVDYYNKF

Examples/Ex1/FAA/uncultured_Termite_group_1_bacterium_phylotype_Rs_D17_uid59059/NC_020422.faa

+>gi|189485780|ref|YP_001956718.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MWNEIKTELTEKIPTIWLEPVKEESFKDDILMLNVPNRYYAEKYKTDFKELIQSVIKTKIGKDIGLQCQI
+ELLPEPITKDKKPKTTSKTPLIKETKFNGKPYFESPAELTEISKEISQAKEIDVDNTKLTSMPVKYSIKD
+VVSFSLLNSKMFTYPNDKRKKTKVEINIRFNNGTIKPLDLYRGQLDFNDEGYGQLTTTHAKIFLAITHIW
+QKQGCKFANNSYLAVVDISIRELAKQLGYQKFSGADYKRLLRKTKELADFPMILADMYEAHTFTLLYDVS
+NHKLKKSRNNKNMLRILINPFIAKQLYERKVILRNPQCYKIKNPTAIKFLICYDKRIIKGNNLRLNIFEI
+ANDLEVNINNITSVAENLKNAFQELNGYELNDSYSLHVELIKENKEWIVVADRVLKEKQQSLKVNCRTDI
+ECEA
+>gi|189485781|ref|YP_001956719.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MLSLKDNKKSFFSLMCLFFLVVCGCHSAKEFRDGYITGLADGYALSVNEFKYNAELAKIKDEFDWSKVDF
+KSEMKMYLDENKDIEKKVYDDYVKNGRKV
+>gi|189485782|ref|YP_001956720.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MPTPTPPLTPASPEPASQDKLKKIALFCPPLTQLMFIYGLGLVEGAIQASLPYLFSSPTIISTLSIMFAN
+MPIVGAMWFALFAYRSEVSTLSNVLDWSLPALLVFGEFLYFCGVGAVSPFSHWLWSIDPV

Examples/Ex1/FAA/uncultured_Termite_group_1_bacterium_phylotype_Rs_D17_uid59059/NS_000192.faa

+>gi|189485766|ref|YP_001956706.1| hypothetical protein TGRD_P1-1 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MWNEIIIELKEKIPTEWLEPIKEESFKDDILTLAVPDTYYAQKYETDYEPLIQNILKAKTGKAVGLQFQI
+VASKLLAEPVIKDEKPKAQLIKKTKFTGNPYFKNPAEFTKFAKETTKKEIEISIGQKVMTSMPTKYGAKD
+VITFSILNNKMFAYPNDKRKNAKVKMDIRFSNDTVKTFDLYRGQLETRGKGYGQLTTTHAKILLAVIHIW
+QEQGCKFADEGQACYVNTTVREIAKKLGYKSFSGADHERLLQKTKDLADLPMVIADRKEAHSFTILYDVS
+THVIEDSEGNDTNRRTISIVFNPFIAKQLYDRKVILRKPQCYKIKNPTAIKFLLCYDKRIIKGFNLKMNI
+SEVANDLEIETNKTSNIITNIKNAFQELNGYELNDSYSLHVELVKEGKEWIVIAERISKEKQQPLKALLA
+>gi|189485767|ref|YP_001956707.1| hypothetical protein TGRD_P1-2 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MKKLICFVMLGCFVLTFVSCGKRSAMLQDVASVKIEEVKLENGENKTPPPDDPAPEDPETITKADRRVGI
+IAGMACMAIAFTGLAIYWMCCGSRKPFEFQVPQDEQNEKPDSEIPKLDNEVPEKPLVDANQDKSELNA
+>gi|189485768|ref|YP_001956708.1| hypothetical protein TGRD_P1-3 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MKFKKVICVYLTLVLFLTGCENLKSQIRGNQNTDASADQQTGNIIKSDNNGIIEKEETKKLDDKVIGLVV
+GDEKEKTSSKEPELRWQDKAKKYAGDAVHFLYEHKEQVYFVGIAVIYLLWKERLFQQQNHQDQMQWHLAQ
+IQQLQQAQDQIQQMPVQDQIQYLQQLQNHFLQAQFNLQQLNQDPNLIQQFQQVQDQIQNGIGQLQAQVQQ
+QIQPQLAQLQLG
+>gi|189485769|ref|YP_001956709.1| hypothetical protein TGRD_P1-4 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MEYKKETDYYENDMRHTADAPKLEKRLRKSLNVFGLILLVLAVYLFGSFLLCSCYRRGVVGGVVADNNAV
+LPDAVTELKSDKKLINGAGLSLSERSVVAEPFRFGVIVPVVNNDG
+>gi|189485770|ref|YP_001956710.1| hypothetical protein TGRD_P1-5 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MKFKKALCVYLTIVLFLTGCENLKSRIRGNQNTDASADQQTGNIIKSGNNGIIEKEETKELDGKSFGLDA
+NGNGSSLQGENTEKETPSEEPELMWQDKAKKYAGDAGHFLYEHKGKIAFAVVVVAGVYWFGIRPINGLPA
+QPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPLLPV
+QPLLHVRPEVLQLRQEQALQQYQQQQHEIEELFVPDAVDLFAALGADMTVLDVMLSELRSQITQLYRLQV
+RQLQEQLRLQEPQAQEQLLQRQLQERLILAQERQDLLQLRINNLRRHFRQYQAMPFLQIEYLEYQHRLTQ
+QLLQQAQQQVQQRQEQQLAELAEQAQQVQQRQEQQLAELAEQAQQLAEQEQQQEQQLAELAEKL
+>gi|189485771|ref|YP_001956711.1| hypothetical protein TGRD_P1-6 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MRDILMIKIKDKYKLVENIFPINNPFRSSRTVQKALKIINKNFVCNIIVLSLLLCSCGKKQALLNTAITE
+KSEVVSELKSELAKIQKELKEKKEKLIEVQEELEKAIEVQEELEKENWQNLWELYDNRMGFFLLGLLTAD
+LIVLGCICCTMCSCC
+>gi|189485772|ref|YP_001956712.1| hypothetical protein TGRD_P1-7 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MEYKKETDYYENDMRHTADAPKLEKRLRKSLNVFGLILLVLAVYLFGSFLLCSCYRRGVVGGVVADNNAV
+LPDAVTELKSDKKLINGAGLSLSERSVVAEPFRFGVIVPVVNNDG
+>gi|189485773|ref|YP_001956713.1| hypothetical protein TGRD_P1-8 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MKKIIILLVVFLMFFGCYKKPITNIPVPEEIEEIKIPDVYYFSDMFTACNCFLAISTLFFLATVMFAGYS
+FLGKDFDINDYRRPVELGNRIVPQRGNNI
+>gi|189485774|ref|YP_001956714.1| hypothetical protein TGRD_P1-9 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MKKIFAVILMLSVFLSGCHRKVITGISKNENDVPTSTNTPAPEPTSTPMPTSTPAFMDCFPKYKAPSSTP
+APLDADDYYDNWTKCVLLYVDDDGNWVNGKHKHSEAHKRLLLKDL

Examples/Ex1/FAA/uncultured_Termite_group_1_bacterium_phylotype_Rs_D17_uid59059/NS_000193.faa

+>gi|189485776|ref|YP_001956715.1| hypothetical protein TGRD_P2-1 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MWNEIITELKEKIPTEWLEPIKEESFKDDILTLAVPDTYYAQKYETDYKPLIQNILKAKTGKAVGLQFQI
+VASKLLAEPVIKDEKPKTQLMKKTKFNGKPYFENPAEFVSIAKAASQVKETDIKNAELTSMPNKYGITNV
+ASFSLLDSKFFTYPNDKRKKTKVEMPVRFSNGVVKVYNLYRGQFAINDNGYGQLTTTHAKIFFAIIHIWQ
+KQNSRYADNKGFYAVVDISMRELAKQLGYQKVSGADYRRLLQRVKELVDFPMILSDGRVAHTFTFLNSAI
+GRTVHQSGKNKLMLRLTLNPFISKQFYERNVILRNPQCYKIKNPTAFKFLLCYDKRVVKGNNLKLNIYEV
+ANDLELNISKLCHGVSVLKVAFRELNGYELNDSYRLYVELVKEEREWIVIAERISKEKQQPLKALLA
+>gi|189485777|ref|YP_001956716.1| hypothetical protein TGRD_P2-2 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MKLKKALCVYLTIVLFLTGCENLKSQIRGNQNTVASADQPTGDIIKSDNSGIIEKQKEKESDLKKIENNV
+DNPNGDNGGDNNGDNPNGDNGGDNPNGDNGGDNNGDSSQHKSSSEANGKDLRGWLWDHKGSISGIVLASA
+VVIGAIGFWGGQPNVCAVNYFYVPQAVQENQAQVQVPAVQENQAQVQVPAVQENQAQVQVPAVQENQAQV
+QVPAVQENQAQVQVPAVQENQAQVQVPAVQENQAQVQVPAVQENQAQVQVPAVQENQAQVQVPAVQGNQN
+PNLVYFDIHSGRYIPGNQNPNLVYFDIHSGRYIPIVRGNPNPILVVQGNLYQVQGNESPFPVLLVEENQV
+QVPAVQELPSQQQLQRIQNRLDQLQGQLRNLESHAIFQFQQIQVEAEALQLHNEQYIQLIGSIVDDPLYP
+QLNLQFQQICQILRHSHSLQLYDIGFHIFLMREILDHHLHLTARNLPDVYGPPPRWEALRVQEQLERHNQ
+QLNQLYQQIEGRLVIEQSVLGARPDSQQRQQELREFNELAIQLQEHQRRIEALLKWLI
+>gi|189485778|ref|YP_001956717.1| hypothetical protein TGRD_P2-3 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MTAVKFKKIFAVILMLSVFLSGCQRQVITGVSKNENDVSTSTNTPVPEPTPTPTPAPEPTPTPTPVPEPT
+PTPTPVPEPTPTPTPVPEPTPTPTPVPEPTPTPTPVPEPTPAFMDCFPKYEAPLSTPAPLDEDDYYDNRV
+KWALSHVDDDGNWVNGKHSEAPKCLLVDYYNKF

Examples/Ex1/FAA/uncultured_Termite_group_1_bacterium_phylotype_Rs_D17_uid59059/NS_000194.faa

+>gi|189485780|ref|YP_001956718.1| hypothetical protein TGRD_P3-1 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MWNEIKTELTEKIPTIWLEPVKEESFKDDILMLNVPNRYYAEKYKTDFKELIQSVIKTKIGKDIGLQCQI
+ELLPEPITKDKKPKTTSKTPLIKETKFNGKPYFESPAELTEISKEISQAKEIDVDNTKLTSMPVKYSIKD
+VVSFSLLNSKMFTYPNDKRKKTKVEINIRFNNGTIKPLDLYRGQLDFNDEGYGQLTTTHAKIFLAITHIW
+QKQGCKFANNSYLAVVDISIRELAKQLGYQKFSGADYKRLLRKTKELADFPMILADMYEAHTFTLLYDVS
+NHKLKKSRNNKNMLRILINPFIAKQLYERKVILRNPQCYKIKNPTAIKFLICYDKRIIKGNNLRLNIFEI
+ANDLEVNINNITSVAENLKNAFQELNGYELNDSYSLHVELIKENKEWIVVADRVLKEKQQSLKVNCRTDI
+ECEA
+>gi|189485781|ref|YP_001956719.1| hypothetical protein TGRD_P3-2 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MLSLKDNKKSFFSLMCLFFLVVCGCHSAKEFRDGYITGLADGYALSVNEFKYNAELAKIKDEFDWSKVDF
+KSEMKMYLDENKDIEKKVYDDYVKNGRKV
+>gi|189485782|ref|YP_001956720.1| hypothetical protein TGRD_P3-3 [uncultured Termite group 1 bacterium phylotype Rs-D17]
+MPTPTPPLTPASPEPASQDKLKKIALFCPPLTQLMFIYGLGLVEGAIQASLPYLFSSPTIISTLSIMFAN
+MPIVGAMWFALFAYRSEVSTLSNVLDWSLPALLVFGEFLYFCGVGAVSPFSHWLWSIDPV

archaea_run_no_filtering.sh

-#!/bin/sh
-# $1 = full path to directory containing FAA directory
-# $2 = tag length
-
-./mif $1 $2
-#./sttag -p $1 -s B -f 1
-#./tmerg $1 $2
-#./filt -p $1 -f 10
-#./cm -p $1 -f -1 -o -1
-#./mdist $1
-#./fh $1

buildconcat.cpp

-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <cstdlib>
-#include <omp.h>
-
-#include "util.h"
-
-using namespace std;
-
-const int MATCH_LENGTH=10;
-const int MATCH_CUTOFF=8;
-
-struct cset
-{
-  vector<string> cpv;
-};
-
-int find_max_overlaps(vector<string> cpv, string s);
-
-int main(int argc, char* argv[])
-{
-  if(argc<2)
-    {
-      cout<<"Wrong use of function. ./bc <path to FAA_csv_x_y>"<<endl;
-      exit(1);
-    }
-
-  string path=argv[1];
-  util u;
-
-  vector<cset> cprots;
-  vector<string> directories;
-  directories = u.load_names(path.c_str());
-  for(int i=0; i<directories.size(); i++)
-    {
-      cset cset_temp;
-      ifstream instream;
-      instream.open( (path+"/"+directories.at(i)+"/csv_proteins.faa").c_str());
-      if(instream.fail())
-	{
-	  cout<<"Failed to open instream to csv_proteins.faa"<<endl;
-	  exit(1);
-	}
-      
-      string eater;
-      instream>>eater;
-      while(!instream.eof())
-	{
-	  if(eater[0]=='>')
-	    {
-	      char buffer[1000];
-	      instream.getline(buffer,1000);
-	      string info_line = eater+" "+buffer;
-
-	      instream>>eater; //first part of protein
-
-	      string ps;
-
-	      while(!instream.eof() && eater[0]!='>')
-		{
-		  ps += eater;		  
-		  instream>>eater;
-		}
-
-	      cset_temp.cpv.push_back(ps);		
-	    }
-	}
-      cprots.push_back(cset_temp);
-      instream.close();
-    }
-
-  cout<<"Size of cprots = "<<cprots.size()<<endl;
-
-  vector<string> concatenated;
-  string s1;
-  for(int i=0; i<cprots.at(0).cpv.size(); i++)
-    {
-      s1+=cprots.at(0).cpv.at(i);
-    }
-  cout<<s1<<endl;
-
-#pragma omp parallel for
-  for(int i=1; i<cprots.size(); i++)
-    {
-      string s2;
-      for(int j=0; j<cprots.at(0).cpv.size(); j++)
-	{
-	  int index = find_max_overlaps(cprots.at(i).cpv,cprots.at(0).cpv.at(j));
-	  s2+=cprots.at(i).cpv.at(index);
-	}
-#pragma omp critical
-      concatenated.push_back(s2);
-      cout<<"done with i="<<i<<"/"<<cprots.size()<<endl;
-    }
-
-  ofstream outstream;
-  outstream.open("buildconcat_output.txt");
-
-  for(int i=0; i<concatenated.size(); i++)
-    {
-      cout<<">gi| "<<directories.at(i)<<endl<<concatenated.at(i)<<endl;
-      outstream<<">gi| "<<directories.at(i)<<endl<<concatenated.at(i)<<endl;
-    }
-
-  outstream.close();
-  return 0;
-}
-
-int find_max_overlaps(vector<string> cpv, string s)
-{
-  vector<int> mv;
-  for(int i=0; i<cpv.size(); i++)
-    {
-      mv.push_back(0);
-    }
-
-  for(int i=0; i<cpv.size(); i++)
-    {
-      for(int j=0; j<cpv.at(i).length(); j++)
-	{
-	  string s2=cpv.at(i).substr(j,MATCH_LENGTH);
-	  for(int k=0; k<s.length(); k++)
-	    {
-	      int matches=0;
-	      string s1=s.substr(k,MATCH_LENGTH);
-	      for(int f=0; f<s1.length(); f++)
-		{
-		  if(s1[f]==s2[f])
-		    {
-		      matches++;
-		    }
-		}
-	      if(matches>=MATCH_CUTOFF)
-		{
-		  mv.at(i)++;
-		}
-	    }
-	}
-    }
-
-  int result_index=0;
-  int max=mv.at(0);
-  for(int i=0; i<mv.size(); i++)
-    {
-      if(mv.at(i)>max)
-	{
-	  max=mv.at(i);
-	  result_index=i;
-	}
-    }
-
-  return result_index;
-}

dSTm.sh

 #!/bin/sh
 # $1 = full path to directory containing FAA directory
 # $2 = tag length
-# $3 = 'B' for bacteria, 'A' for archaea, 'O' for other
+# $3 = 'B' for bacteria, 'A' for archaea, 'O' (capital o, not zero) for Other
 # $4 = path to directory containing names.dmp and nodes.dmp
 
-./mif $1 $2
+echo "Number of parameters = "$#
+if [ "$#" -ne 4 ]; then
+    echo "Illegal number of parameters"
+    exit
+fi
+
+echo "Input okay. Bash script proceeding..."
+
+./mif $1 -k $2
 ./sttag $1 -f 1 -s $3
 wait
 ./tmerg $1

file_info.h

@@ -6,48 +6,86 @@
 using namespace std;
 
 const int TAGLENGTHCHECKER=20;
+const bool DEBUG_FI=true;
 
 class file_info
 {
  private:
+  bool verbose;
  public:
   file_info();
   ~file_info();
   void read_line();
   void set_file_name(string file_name_par);
-  char get_caa();
-  void delete_pFile();
+  //  char get_caa();
+  //  void delete_pFile();
   string get_current_line();
-  void open(string path);
-  string file_name;
+  //  void open(string path_par);
+  void set_path(string path_par);
+  void open();
+  void set_position();
+  //  string file_name;
+  string path;
   int total_tags;
   int strings_read_in;
   string s;
+  string last_read;
   int gnum;
   int gene_id;
   FILE * pFile;
+  fpos_t position; //so that the files can be closed and then reopened
 };
 
 file_info::file_info()
 {
-  cout<<"In constructor"<<endl;
+  if(DEBUG_FI || verbose)
+    {
+      cout<<"In file_info::file_info()"<<endl;	
+    }
+
+  verbose=false;
 }
 
-void file_info::open(string path)
+file_info::~file_info()
 {
-  cout<<"In open. path = "<<path<<endl;
+  cout<<"Top of file_info destructor."<<endl;
+  //  fclose(pFile);
+  cout<<"Closed the file."<<endl;
+  //delete pFile;
+  cout<<"Bottom of file_info destructor."<<endl;
+}
+
+
+/********************************
+Open a TAGS file, e.g. TAGS0.txt,
+files found in TAGS/ or TAGSscr/.
+Read in the number of k-mers (actually 3-tuples) in the file, which
+is the first value in any tags file.
+Point position to the first sequence in the file.
+Then close the file.
+ *******************************/
+void file_info::set_path(string path_par)
+{
+  path = path_par;
+
+  if(DEBUG_FI || verbose)
+    {
+      cout<<"In file_info::set_path(string)"<<endl;
+      cout<<"path="<<path<<endl;
+    }
+
   pFile = fopen( path.c_str(), "r");
   if(pFile==NULL) 
     {
       perror("Error opening file");
+      exit(1);
     }
   else
     {
       char buffer[200];
-      if(fgets(buffer,200,pFile) != NULL)
+      if(fgets(buffer,200,pFile) != NULL) //Read in the total size of the file (first value in a TAGS*.txt file
 	{
 	  total_tags = atoi(buffer);
-	  cout<<"total_tags = "<<total_tags<<endl;
 	}
       else
 	{
@@ -55,26 +93,74 @@ void file_info::open(string path)
 	  exit(1);
 	}
     }
+
   strings_read_in=0;
+
+  fgetpos(pFile,&position); //point to the first sequence in the file.
+
+  //  read_line();
+
+  if(DEBUG_FI || verbose)
+    {
+      cout<<"total_tags in current TAGS file = "<<total_tags<<endl;
+      cout<<"End of file_info::set_path(string)"<<endl;
+    }
+
+  fclose(pFile);
+}
+
+void file_info::open()
+{
+  if(DEBUG_FI || verbose)
+    {
+      cout<<"In file_info::open(string)"<<endl;
+    }
+
+  pFile = fopen( path.c_str(), "r");
+  if(pFile==NULL) 
+    {
+      perror("Error opening file");
+      exit(1);
+    }
+  else
+    {
+      fsetpos(pFile,&position); //set the position to the last place we read from.
+    }
+
+  //  strings_read_in=0;
+  //  fgetpos(pFile,&position); //point to the first sequence in the file.
   read_line();
-  cout<<"end of open"<<endl;
+
+  if(s==last_read)
+    {
+      strings_read_in--;
+    }
+
+  if(DEBUG_FI || verbose)
+    {
+      cout<<"total_tags in current TAGS file = "<<total_tags<<endl;
+      cout<<"End of file_info::open(string)"<<endl;
+    }  
 }
 
-file_info::~file_info()
+void file_info::set_position()
 {
-  cout<<"Top of file_info destructor."<<endl;
+  fgetpos(pFile,&position);
   fclose(pFile);  
-  cout<<"Closed the file."<<endl;
-  //delete pFile;
-  cout<<"Bottom of file_info destructor."<<endl;
 }
 
+/**************************
+Literally, just read the next line into variable s.
+Strings shorter than TAGLENGTHCHECKER (default=20)
+cause the program to exit.
+***************************/
 void file_info::read_line()
 {
   char buffer[200];  
   if(pFile==NULL) 
     {
-      perror("Error opening file");
+      perror("perror in file_info::read_line(): Error opening file - pFile==NULL");
+      exit(1);
     }
   else
     {
@@ -90,6 +176,8 @@ void file_info::read_line()
       cout<<"Big problem in little read_line"<<endl;
       exit(