Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/com_uni.cpp @ 0:cdd489d98766

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:50:41 -0400
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 /*
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2 * Copyright 2009 Matteo Cesaroni, Lucilla Luzi
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3 *
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4 * This program is free software; ; you can redistribute it and/or modify
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5 * it under the terms of the GNU Lesser General Public License as published by
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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6 * the Free Software Foundation; either version 3 of the License, or (at your
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7 * option) any later version.
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8 *
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9 * This program is distributed in the hope that it will be useful,
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10 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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12 * GNU General Public License for more details.
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13
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14 */
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15
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16 #include <iostream>
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17 #include <fstream>
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18 #include <string>
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19 #include <vector>
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20 #include <algorithm>
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21 #include <sstream>
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22 #include <deque>
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23 #include <map>
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24 #include <ctime>
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25 #include <cstdlib>
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26
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27 using namespace std;
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28
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29 inline void Tokenize(const string& str,
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30 vector<string>& tokens,
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31 const string& delimiters = " ")
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32 {
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33 // Skip delimiters at beginning.
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34 string::size_type lastPos = str.find_first_not_of(delimiters, 0);
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35 // Find first "non-delimiter".
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36 string::size_type pos = str.find_first_of(delimiters, lastPos);
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37
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38 while (string::npos != pos || string::npos != lastPos)
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39 {
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40 // Found a token, add it to the vector.
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41 tokens.push_back(str.substr(lastPos, pos - lastPos));
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42 // Skip delimiters. Note the "not_of"
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43 lastPos = str.find_first_not_of(delimiters, pos);
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44 // Find next "non-delimiter"
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45 pos = str.find_first_of(delimiters, lastPos);
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46 }
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47 }
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48
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49
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50 typedef struct {
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51 int inizioprobe;
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52 int fineprobe;
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53 string score;
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54 string campo1;
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55 string campo2;
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56 string strand;
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57 string index;
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58 int file;
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59 } Probe;
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60
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61 struct Comparatore2 {
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62 bool operator()(const Probe& s1, const Probe& s2) const {
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63 if (s1.inizioprobe < s2.inizioprobe) {
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64 return true;
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65 }
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66 else if (s1.inizioprobe == s2.inizioprobe) {
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67 if (s1.fineprobe < s2.fineprobe) {
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68 return true;
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69 }
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70 else if (s1.fineprobe == s2.fineprobe){
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71 return true;
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72 }
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73 else {
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74 return false;
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75 }
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76
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77 }
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78 else {
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79 return false;
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80 }
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81
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82 }
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83 };
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84
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85 int main (int argc, char * const argv[]) {
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86
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87 string concatenate=argv[3];
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88 int dist_t=atoi(argv[1]);
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89 string choice=argv[2];
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90
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91 string name_out= argv[6];
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92 ofstream resfile;
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93 resfile.open (name_out.c_str());
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94
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95
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96
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97 if (concatenate=="no" && choice!="union"){
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98
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99 //print "flank=$win , type=$type col6=%overlap, concatenate=$concatenate";
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100 if (choice=="common"){
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101 cout<<"flank="<<dist_t<<" , type="<<choice<<" , col6=%overlap, concatenate="<<concatenate;
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102 }
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103 if (choice=="unique"){
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104 cout<<"flank="<<dist_t<<" , type="<<choice<<" , col6=score o p-value";
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105 }
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106
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107 string line;
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108 Probe thisprobe;
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109 Probe thisanno;
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110 int overlap=0;
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111 vector<string> arraypro;
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112 map<string, vector<Probe> > seq;
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113 map<string, vector<Probe> > annotation;
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114 map<string, vector<Probe> >::iterator itseq;
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115
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116 ifstream seque_file(argv[4]);
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117 while (getline(seque_file, line)) {
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118 string s4;
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119 s4.assign(line, 0, 1);
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120 if (line=="" || s4=="#"){
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121 continue;
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122 }
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123 arraypro.clear();
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124 Tokenize(line, arraypro, "\t");
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125 string chr2 = (arraypro[0].c_str());
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126 thisprobe.inizioprobe=atoi(arraypro[3].c_str());
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127 thisprobe.fineprobe=atoi(arraypro[4].c_str());
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128 thisprobe.campo1=(arraypro[1].c_str());
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129 thisprobe.campo2=(arraypro[2].c_str());
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130 thisprobe.score=(arraypro[5].c_str());
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131 thisprobe.strand=(arraypro[6].c_str());
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132 thisprobe.index=(arraypro[8].c_str());
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133 seq[chr2].push_back(thisprobe);
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134 }
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135
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136
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137 ifstream anno_file(argv[5]);
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138 while (getline(anno_file, line)) {
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139 string s4;
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140 s4.assign(line, 0, 1);
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141 if (line=="" || s4=="#"){
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142 continue;
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143 }
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144 arraypro.clear();
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145 Tokenize(line, arraypro, "\t");
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146 string chr3= (arraypro[0].c_str());
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147 thisanno.inizioprobe=atoi(arraypro[3].c_str());
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148 thisanno.fineprobe=atoi(arraypro[4].c_str());
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149 thisanno.campo1=(arraypro[1].c_str());
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150 thisanno.campo2=(arraypro[2].c_str());
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151 thisanno.score=(arraypro[5].c_str());
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152 thisanno.strand=(arraypro[6].c_str());
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153 thisanno.index=(arraypro[8].c_str());
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154 annotation[chr3].push_back(thisanno);
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155 }
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156
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157
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158 for ( itseq=seq.begin() ; itseq != seq.end(); itseq++ ){
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diff changeset
159
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
160 vector <Probe> seq_chr = (*itseq).second;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
161 vector <Probe> anno_chr = annotation[(*itseq).first];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
162 if(anno_chr.size()==0 && choice=="unique"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
163 for (int i=0; i<seq_chr.size();i++){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
164 resfile<<(*itseq).first<<"\t"<<seq_chr[i].campo1<<"\t"<<seq_chr[i].campo2<<"\t"<<seq_chr[i].inizioprobe<<"\t"<<seq_chr[i].fineprobe<<"\t"<<seq_chr[i].score<<"\t"<<seq_chr[i].strand<<"\t.\t"<<seq_chr[i].index<<endl;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
165 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
166 continue;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
167 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
168 if(anno_chr.size()==0 && choice=="common"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
169 continue;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
170 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
171 sort (seq_chr.begin(),seq_chr.end(),Comparatore2());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
172 sort (anno_chr.begin(),anno_chr.end(),Comparatore2());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
173
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
174 int finefine=0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
175
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
176 for (int i=0; i<anno_chr.size();i++){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
177 if(anno_chr[i].fineprobe<=finefine){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
178 anno_chr[i].fineprobe=finefine;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
179 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
180 if(anno_chr[i].fineprobe>finefine){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
181 finefine=anno_chr[i].fineprobe;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
182 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
183 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
184
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
185 for (int i=0; i<seq_chr.size();i++){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
186 int start_array=0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
187 int fine_array=anno_chr.size();
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
188 int pos=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
189 int trovato=0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
190
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
191 while (pos>0){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
192 pos=(fine_array-start_array)/2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
193 int position=start_array+pos;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
194
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
195 if((seq_chr[i].inizioprobe-dist_t)<anno_chr[position].inizioprobe){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
196 fine_array=position;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
197 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
198 if((seq_chr[i].inizioprobe-dist_t)>anno_chr[position].inizioprobe){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
199 start_array=position;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
200 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
201 if((seq_chr[i].inizioprobe-dist_t)<=anno_chr[position].fineprobe && (seq_chr[i].fineprobe+dist_t)>=anno_chr[position].inizioprobe){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
202 if (choice=="common"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
203 if (seq_chr[i].inizioprobe<=anno_chr[position].inizioprobe && seq_chr[i].fineprobe<=anno_chr[position].fineprobe){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
204 overlap=(seq_chr[i].fineprobe-anno_chr[position].inizioprobe)*100/(seq_chr[i].fineprobe-seq_chr[i].inizioprobe);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
205 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
206 if (seq_chr[i].inizioprobe<=anno_chr[position].inizioprobe && seq_chr[i].fineprobe>=anno_chr[position].fineprobe){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
207 overlap=(anno_chr[position].fineprobe-anno_chr[position].inizioprobe)*100/(seq_chr[i].fineprobe-seq_chr[i].inizioprobe);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
208 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
209 if (seq_chr[i].inizioprobe>=anno_chr[position].inizioprobe && seq_chr[i].fineprobe>=anno_chr[position].fineprobe){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
210 overlap=(anno_chr[position].fineprobe-seq_chr[i].inizioprobe)*100/(seq_chr[i].fineprobe-seq_chr[i].inizioprobe);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
211 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
212 if (seq_chr[i].inizioprobe>=anno_chr[position].inizioprobe && seq_chr[i].fineprobe<=anno_chr[position].fineprobe){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
213 overlap=100;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
214 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
215 if (overlap<0){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
216 overlap=-1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
217 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
218 resfile<<(*itseq).first<<"\t"<<seq_chr[i].campo1<<"\t"<<seq_chr[i].campo2<<"\t"<<seq_chr[i].inizioprobe<<"\t"<<seq_chr[i].fineprobe<<"\t"<<overlap<<"\t"<<seq_chr[i].strand<<"\t.\t"<<"ValueA:"<<seq_chr[i].score<<"~"<<"ValueB:"<<anno_chr[position].score<<endl;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
219 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
220 trovato=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
221 break;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
222 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
223 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
224 if (choice=="unique" && trovato==0){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
225 resfile<<(*itseq).first<<"\t"<<seq_chr[i].campo1<<"\t"<<seq_chr[i].campo2<<"\t"<<seq_chr[i].inizioprobe<<"\t"<<seq_chr[i].fineprobe<<"\t"<<seq_chr[i].score<<"\t"<<seq_chr[i].strand<<"\t.\t"<<seq_chr[i].index<<endl;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
226 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
227 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
228 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
229 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
230
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
231 if (concatenate=="yes" || choice == "union"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
232
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
233 cout<<"flank="<<dist_t<<" , type="<<choice<<" , col6=#overlaping regions, concatenate="<<concatenate;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
234
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
235 string line;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
236 Probe thisprobe;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
237 Probe thisanno;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
238 vector<string> arraypro;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
239 map<string, vector<Probe> > seq;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
240 map<string, vector<Probe> > annotation;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
241 map<string, vector<Probe> >::iterator itseq;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
242 string concatenate=argv[3];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
243 int dist_t=atoi(argv[1]);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
244 string choice=argv[2];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
245
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
246 ifstream seque_file(argv[4]);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
247 while (getline(seque_file, line)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
248 string s4;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
249 s4.assign(line, 0, 1);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
250 if (line=="" || s4=="#"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
251 continue;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
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diff changeset
252 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
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diff changeset
253 arraypro.clear();
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
254 Tokenize(line, arraypro, "\t");
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
255 string chr2 = (arraypro[0].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
256 thisprobe.inizioprobe=atoi(arraypro[3].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
257 thisprobe.fineprobe=atoi(arraypro[4].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
258 thisprobe.campo2=(arraypro[2].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
259 thisprobe.campo1=(arraypro[1].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
260 thisprobe.score=(arraypro[5].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
261 thisprobe.index=(arraypro[8].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
262 thisprobe.strand=(arraypro[6].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
263 thisprobe.file=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
264 seq[chr2].push_back(thisprobe);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
265 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
266
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
267 ifstream anno_file(argv[5]);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
268 while (getline(anno_file, line)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
269 string s4;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
270 s4.assign(line, 0, 1);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
271 if (line=="" || s4=="#"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
272 continue;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
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diff changeset
273 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
274 arraypro.clear();
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
275 Tokenize(line, arraypro, "\t");
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
276 string chr3= (arraypro[0].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
277 thisanno.inizioprobe=atoi(arraypro[3].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
278 thisanno.fineprobe=atoi(arraypro[4].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
279 thisanno.campo2=(arraypro[2].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
280 thisanno.campo1=(arraypro[1].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
281 thisanno.score=(arraypro[5].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
282 thisanno.index=(arraypro[8].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
283 thisanno.strand=(arraypro[6].c_str());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
284 thisanno.file=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
285 seq[chr3].push_back(thisanno);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
286 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
287
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
288 int inizio;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
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diff changeset
289 int fine;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
290 string annot;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
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diff changeset
291 int overlap;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
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diff changeset
292 int inizio_ann;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
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diff changeset
293 int fine_ann;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
294
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
295 for ( itseq=seq.begin() ; itseq != seq.end(); itseq++ ){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
296
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
297 vector <Probe> seq_chr = (*itseq).second;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
298 sort (seq_chr.begin(),seq_chr.end(),Comparatore2());
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
299
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
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diff changeset
300 for (int i=0; i<seq_chr.size();i++){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
301 inizio = seq_chr[i].inizioprobe;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
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diff changeset
302 fine=seq_chr[i].fineprobe;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
303 int file_t=0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
304 int file_t2=0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
305 int entrato=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
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diff changeset
306 int z=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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307 if(seq_chr[i].file==1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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308 file_t=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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309 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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310 if(seq_chr[i].file==2){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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311 file_t2=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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312 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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313 if(i==(seq_chr.size()-1)){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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314 if (choice=="union"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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315 resfile<<(*itseq).first<<"\tfile_"<<seq_chr[i].file<<"\tunique\t"<<seq_chr[i].inizioprobe<<"\t"<<seq_chr[i].fineprobe<<"\t"<<seq_chr[i].score<<"\t"<<seq_chr[i].strand<<"\t.\t"<<seq_chr[i].index<<endl;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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316 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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317 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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318
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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319 //cout<<"x"<<(*itseq).first<<"\t"<<seq_chr[i].inizioprobe<<"\t"<<seq_chr[i].fineprobe<<"\t"<<seq_chr[i].file<<endl;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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320 for (int y=i+1; y<seq_chr.size(); y++){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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321 if((inizio-dist_t)<=seq_chr[y].fineprobe && (fine+dist_t)>=seq_chr[y].inizioprobe){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
322 if(seq_chr[y].file==1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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323 file_t=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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324 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
325 if(seq_chr[y].file==2){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
326 file_t2=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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327 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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328 if(seq_chr[y].fineprobe>fine){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
329 fine=seq_chr[y].fineprobe;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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330 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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331 entrato=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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332 i++;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
333 z++;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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334 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
335 if(seq_chr[y].inizioprobe>fine || y==seq_chr.size()-1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
336 if (choice == "union" && entrato==1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
337 resfile<<(*itseq).first<<"\tfile_"<<seq_chr[i].file<<"\tunique\t"<<inizio<<"\t"<<fine<<"\t"<<seq_chr[i].score<<"\t"<<seq_chr[i].strand<<"\t.\t"<<seq_chr[i].index<<endl;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
338 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
339 if (choice == "union" && entrato==2){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
340 resfile<<(*itseq).first<<"\tcommon\tcommon\t"<<inizio<<"\t"<<fine<<"\t"<<z<<"\t.\t.\tcommon"<<endl;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
341 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
342 if (choice == "common" && entrato==2 && file_t == 1 && file_t2 == 1 && concatenate=="yes"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
343 resfile<<(*itseq).first<<"\t"<<seq_chr[i].campo1<<"\t"<<seq_chr[i].campo2<<"\t"<<inizio<<"\t"<<fine<<"\t"<<z<<"\t"<<seq_chr[i].strand<<"\t.\t"<<seq_chr[i].index<<endl;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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344 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
345 break;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
346 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
347 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
348 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
349 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
350 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
351 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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diff changeset
352