long_age_align.cpp

/****************************************************************************
 *
 *     LongAGE -- Ultra-long Alignment with Gap Excision
 *     Copyright (C)  Alexej Abyzov
 *                
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the Creative Commons license
 * (Attribution-NonCommerical).
 * See terms at http://creativecommons.org/licenses/by-nc/2.5/legalcode
 *
 * Author: Alexej Abyzov
 */

#include <cstring>
#include <cstdlib>
#include <string.h>
#include <stdlib.h>
#include <inttypes.h>
#include <limits.h>
#include <string>
#include <iostream>
#include <sstream>
#include <fstream>
#include <iomanip>
#ifdef LONG_AGE_TIME
#include <sys/time.h>
#endif
using namespace std;

//--- LONG AGE includes ---
#include "LongAGEaligner.h"
#include "Sequence.h"
#include "Scorer.h"

bool parseValue(string &str,short &val)
{
  if (str == "-") return false;

  int n = str.length(),i = 0;
  string s("");
  if (str[i] == '-') s += str[i++];
  while (i < n && isdigit(str[i])) s += str[i++];
  if (i != n)   return false;
  val = strtol(s.c_str(),NULL,10);
  return true;
}

bool parseStartEnd(string &str,int &start,int &end)
{
  if (str == "-") return false;

  int n = str.length(),i = 0;
  string s(""),e("");
  while (i < n && isdigit(str[i])) s += str[i++];
  if (i == n)          return false;
  if (str[i++] != '-') return false;
  while (i < n && isdigit(str[i])) e += str[i++];
  if (i != n)          return false;
  
  int sv = -1,ev = -1;
  if (s.length() > 0) sv = strtol(s.c_str(),NULL,10);
  if (e.length() > 0) ev = strtol(e.c_str(),NULL,10);
  if (sv == 0 || ev == 0)          return false;
  if (sv > 0 && ev > 0 && ev < sv) return false;
  start = sv;
  end   = ev;
  return true;
}

int parseArgs(string line,string *args,int max_args)
{
  int ret = 0, i = 0;
  while (i < line.length()) {
    args[ret] = "";
    while (i < line.length() && line.at(i) == ' ') i++; // Skipping spaces
    while (i < line.length() && line.at(i) != ' ')
      args[ret] += line.at(i++);
    if (args[ret].length() > 0) ret++;
  }

  return ret;
}

int main(int argc,char *argv[])
{
  const static short DEFAULT_MATCH      =   1;
  const static short DEFAULT_MISMATCH   =  -3;
  const static short DEFAULT_GAP_OPEN   =  -7;
  const static short DEFAULT_GAP_EXTEND =  -1;

  int flag = 0;
  stringstream sout;

  string exe = argv[0];
  exe = exe.substr(exe.rfind('/') + 1);
  string usage = "Usage:\n\t";
  usage += exe; usage += "\n";
  sout.str("");sout<<DEFAULT_MATCH;
  usage += "\t\t[-version] [-allpos]\n";
  usage += "\t\t[-indel|-tdup|-inv|-invl|-invr]\n";
  usage += "\t\t[-match=value:"; usage += sout.str(); usage += "]";
  sout.str("");sout<<DEFAULT_MISMATCH;
  usage += " [-mismatch=value:"; usage += sout.str(); usage += "]\n";
  sout.str("");sout<<DEFAULT_GAP_OPEN;
  usage += "\t\t[-go=value:";    usage += sout.str(); usage += "]";
  sout.str("");sout<<DEFAULT_GAP_EXTEND;
  usage += " [-ge=value:";       usage += sout.str(); usage += "]\n";
  usage += "\t\t[-both] [-revcom1] [-revcom2]\n";
  usage += "\t\t[-coor1=start-end] [-coor2=start-end]";
  usage += " file1.fa file2.fa";
  string age_version = "LongAGE ";
#ifdef LONG_AGE_VERSION
  age_version += LONG_AGE_VERSION;
#else
  age_version += "v???";
#endif
  age_version += "\n";

  cin.seekg(0,ios::end);
  int cin_length = cin.tellg();
  cin.seekg(0,ios::beg);

  if (argc == 2) {
    string tmp(argv[1]);
    if (tmp == "-version") {
      cout<<age_version<<endl;
      return 0;
    }
  }

  if (argc < 3 && cin_length <= 0) {
    cerr<<usage<<endl;
    return 0;
  }

  const static int MAX_ARGS = 1024;
  string args[MAX_ARGS],line;
  int    n_args = 0;

  if (argc > 1) // If we have input arguments
    for (int i = 1;i < argc;i++) {
      args[n_args] = argv[i];
      line += " ";
      line += args[n_args++];
      if (n_args == MAX_ARGS) {
	cerr<<"Too many input arguments. Skipping!"<<endl;
	break;
      }
    }
  else while (cin_length > 0) { // Taking lines from redirection
      getline(cin,line);
      cin_length -= line.length() + 1;
      if (line.length() > 0) {
	n_args = parseArgs(line,args,MAX_ARGS);
	break;
      }
    }

  string    old_file1(""),   old_file2("");
  Sequence *old_seq1 = NULL,*old_seq2 = NULL;

  while (n_args > 0) {
    short match      = DEFAULT_MATCH;
    short mismatch   = DEFAULT_MISMATCH;
    short gap_open   = DEFAULT_GAP_OPEN;
    short gap_extend = DEFAULT_GAP_EXTEND;
    string file1(""),file2("");
    int start1 = -1,end1 = -1;
    int start2 = -1,end2 = -1;
    bool revcom1 = false, revcom2 = false, both = false, error = false;
    bool version = false;
    for (int i = 0;i < n_args;i++) {
      if (args[i].at(0) == '-') { // Options
	string option = args[i];
	string begin = option.substr(0,7);
	if (begin == "-match=") {
	  string value = option.substr(7);
	  if (!parseValue(value,match)) {
	    cerr<<line<<endl;
	    cerr<<"Error in match specification '"<<option<<"'."<<endl;
	    cerr<<"Using default value "<<match<<"."<<endl;
	  }
	} else if (option.substr(0,10) == "-mismatch=") {
	  string value = option.substr(10);
	  if (!parseValue(value,mismatch)) {
	    cerr<<line<<endl;
	    cerr<<"Error in mismatch specification '"<<option<<"'."<<endl;
	    cerr<<"Using default value "<<mismatch<<"."<<endl;
	  }
	} else if (option.substr(0,4) == "-go=") {
	  string value = option.substr(4);
	  if (!parseValue(value,gap_open)) {
	    cerr<<line<<endl;
	    cerr<<"Error in gap open specification '"<<option<<"'."<<endl;
	    cerr<<"Using default value "<<gap_open<<"."<<endl;
	  }
	} else if (option.substr(0,4) == "-ge=") {
	  string value = option.substr(4);
	  if (!parseValue(value,gap_extend)) {
	    cerr<<line<<endl;
	    cerr<<"Error in gap extend specification '"<<option<<"'."<<endl;
	    cerr<<"Using default value "<<gap_extend<<"."<<endl;
	  }
	} else if (begin == "-coor1=") {
	  string end = option.substr(7);
	  if (!parseStartEnd(end,start1,end1)) {
	    cerr<<line<<endl;
	    cerr<<"Error in coordinate specification '"<<option<<"'."<<endl;
	    cerr<<usage<<endl;
	    error = true;
	    break;
	  }
	} else if (begin == "-coor2=") {
	  string end = option.substr(7);
	  if (!parseStartEnd(end,start2,end2)) {
	    cerr<<line<<endl;
	    cerr<<"Error in coordinate specification '"<<option<<"'."<<endl;
	    cerr<<usage<<endl;
	    error = true;
	    break;
	  }
	} else if (option == "-version") {
	  version = true;
	} else if (option == "-allpos") {
	  flag |= LongAGEaligner::SHOW_ALL_POS;
	} else if (option == "-indel") {
	  flag |= LongAGEaligner::INDEL_FLAG;
	} else if (option == "-inv") {
	  flag |= LongAGEaligner::INVERSION_FLAG;
	} else if (option == "-invl") {
	  flag |= LongAGEaligner::INVL_FLAG;
	} else if (option == "-invr") {
	  flag |= LongAGEaligner::INVR_FLAG;
	} else if (option == "-tdup") {
	  flag |= LongAGEaligner::TDUPLICATION_FLAG;
	} else if (option == "-revcom1") {
	  revcom1 = true;
	} else if (option == "-revcom2") {
	  revcom2 = true;
	} else if (option == "-both") {
	  both = true;
	} else {
	  cerr<<line<<endl;
	  cerr<<"Unknown option '"<<option<<"'."<<endl;
	  cerr<<usage<<endl;
	  error = true;
	  break;
	}
	continue;
      }
      
      if (file1.length()      <= 0) file1 = args[i];
      else if (file2.length() <= 0) file2 = args[i];
      else {
	cerr<<line<<endl;
	cerr<<"Too many input files '"<<args[i]<<"'."<<endl;
	cerr<<usage<<endl;
	error = true;
	break;
      }
    }

    if (version) {
      cout<<age_version<<endl;
      return 0;
    }

    int n_modes = 0;
    if (flag & LongAGEaligner::INDEL_FLAG)        n_modes++;
    if (flag & LongAGEaligner::TDUPLICATION_FLAG) n_modes++;
    if (flag & LongAGEaligner::INVR_FLAG)         n_modes++;
    if (flag & LongAGEaligner::INVL_FLAG)         n_modes++;
    if (flag & LongAGEaligner::INVERSION_FLAG)    n_modes++;

    if (n_modes == 0)
      flag |= LongAGEaligner::INDEL_FLAG;
    if (n_modes > 1) {
      cerr<<"Error: More than one mode is specified."<<endl;
      error = true;
    }

    if (file1 != "" && file2 == "") cerr<<"No second file given."<<endl;

    if (!error && file1 != "" && file2 != "") {


      if (file1 != old_file1) {
	Sequence::deleteSequences(old_seq1);
	//old_seq1  = new Sequence(file1);
	old_seq1  = Sequence::parseSequences(file1);
	old_file1 = file1;
      }

      if (file2 != old_file2) {
	Sequence::deleteSequences(old_seq2);
	//old_seq2  = new Sequence(file2);
	old_seq2  = Sequence::parseSequences(file2);
	old_file2 = file2;
      }

      for (Sequence *s1 = old_seq1;s1;s1 = s1->next())
	for (Sequence *s2 = old_seq2;s2;s2 = s2->next()) {

	  Sequence *seq1 = s1->substr(start1,end1);
	  Sequence *seq2 = s2->substr(start2,end2);

	  if (revcom1) seq1->revcom();
	  if (revcom2) seq2->revcom();

#ifdef LONG_AGE_TIME
	  timeval ali_s,ali_e;
	  gettimeofday(&ali_s,NULL);
#endif

	  Scorer scr(match,mismatch,gap_open,gap_extend);
	  if (both) {
	    Sequence *seq3 = seq2->clone();
	    seq3->revcom();
      LongAGEaligner aligner1(*seq1,*seq2);
      LongAGEaligner aligner2(*seq1,*seq3);

      bool res1 = aligner1.align(scr,flag);
      bool res2 = aligner2.align(scr,flag);

      if (!res1 && !res2) cerr<<"No alignment made."<<endl;
      else if (aligner1.score() >= aligner2.score())
              aligner1.printAlignment();
            else
              aligner2.printAlignment();
      delete seq3;
	  } else {
        LongAGEaligner aligner(*seq1,*seq2);
        if (aligner.align(scr,flag)) aligner.printAlignment();
        else cerr<<"No alignment made."<<endl;
	  }
	  
#ifdef LONG_AGE_TIME
	  gettimeofday(&ali_e,NULL);
	  cout<<endl<<"Alignment time is "<<ali_e.tv_sec - ali_s.tv_sec +
	    (ali_e.tv_usec - ali_s.tv_usec)/1e+6<<" s"<<endl<<endl;
#endif
	  
	}
    }

    n_args = 0;
    while (cin_length > 0) {
      getline(cin,line);
      cin_length -= line.length() + 1;
      if (line.length() > 0) {
	n_args = parseArgs(line,args,MAX_ARGS);
	break;
      }
    }
  }

  Sequence::deleteSequences(old_seq1);
  Sequence::deleteSequences(old_seq2);

  return 0;
}