5 * Created by westcott on 7/7/10.
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6 * Copyright 2010 Schloss Lab. All rights reserved.
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10 #include "sffinfocommand.h"
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11 #include "endiannessmacros.h"
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12 #include "trimoligos.h"
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13 #include "sequence.hpp"
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14 #include "qualityscores.h"
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16 //**********************************************************************************************************************
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17 vector<string> SffInfoCommand::setParameters(){
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19 CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(psff);
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20 CommandParameter poligos("oligos", "InputTypes", "", "", "oligosGroup", "none", "none","",false,false); parameters.push_back(poligos);
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21 CommandParameter preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient);
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22 CommandParameter pgroup("group", "InputTypes", "", "", "oligosGroup", "none", "none","",false,false); parameters.push_back(pgroup);
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23 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
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24 CommandParameter psfftxt("sfftxt", "String", "", "", "", "", "","",false,false); parameters.push_back(psfftxt);
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25 CommandParameter pflow("flow", "Boolean", "", "T", "", "", "","flow",false,false); parameters.push_back(pflow);
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26 CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptrim);
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27 CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "","fasta",false,false); parameters.push_back(pfasta);
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28 CommandParameter pqfile("qfile", "Boolean", "", "T", "", "", "","qfile",false,false); parameters.push_back(pqfile);
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29 CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ppdiffs);
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30 CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pbdiffs);
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31 CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
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32 CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
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33 CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
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34 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
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35 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
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37 vector<string> myArray;
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38 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
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41 catch(exception& e) {
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42 m->errorOut(e, "SffInfoCommand", "setParameters");
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46 //**********************************************************************************************************************
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47 string SffInfoCommand::getHelpString(){
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49 string helpString = "";
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50 helpString += "The sffinfo command reads a sff file and extracts the sequence data, or you can use it to parse a sfftxt file.\n";
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51 helpString += "The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, oligos, group, bdiffs, tdiffs, ldiffs, sdiffs, pdiffs, checkorient and trim. sff is required. \n";
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52 helpString += "The sff parameter allows you to enter the sff file you would like to extract data from. You may enter multiple files by separating them by -'s.\n";
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53 helpString += "The fasta parameter allows you to indicate if you would like a fasta formatted file generated. Default=True. \n";
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54 helpString += "The qfile parameter allows you to indicate if you would like a quality file generated. Default=True. \n";
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55 helpString += "The oligos parameter allows you to provide an oligos file to split your sff file into separate sff files by barcode. \n";
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56 helpString += "The group parameter allows you to provide a group file to split your sff file into separate sff files by group. \n";
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57 helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
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58 helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
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59 helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
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60 helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
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61 helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
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62 helpString += "The checkorient parameter will check look for the reverse compliment of the barcode or primer in the sequence. The default is false.\n";
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63 helpString += "The flow parameter allows you to indicate if you would like a flowgram file generated. Default=True. \n";
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64 helpString += "The sfftxt parameter allows you to indicate if you would like a sff.txt file generated. Default=False. \n";
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65 helpString += "If you want to parse an existing sfftxt file into flow, fasta and quality file, enter the file name using the sfftxt parameter. \n";
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66 helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values. Default=True. \n";
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67 helpString += "The accnos parameter allows you to provide a accnos file containing the names of the sequences you would like extracted. You may enter multiple files by separating them by -'s. \n";
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68 helpString += "Example sffinfo(sff=mySffFile.sff, trim=F).\n";
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69 helpString += "Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n";
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72 catch(exception& e) {
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73 m->errorOut(e, "SffInfoCommand", "getHelpString");
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78 //**********************************************************************************************************************
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79 string SffInfoCommand::getOutputPattern(string type) {
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81 string pattern = "";
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83 if (type == "fasta") { pattern = "[filename],fasta-[filename],[tag],fasta"; }
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84 else if (type == "flow") { pattern = "[filename],flow"; }
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85 else if (type == "sfftxt") { pattern = "[filename],sff.txt"; }
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86 else if (type == "sff") { pattern = "[filename],[group],sff"; }
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87 else if (type == "qfile") { pattern = "[filename],qual-[filename],[tag],qual"; }
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88 else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
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92 catch(exception& e) {
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93 m->errorOut(e, "SffInfoCommand", "getOutputPattern");
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97 //**********************************************************************************************************************
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98 SffInfoCommand::SffInfoCommand(){
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100 abort = true; calledHelp = true;
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102 vector<string> tempOutNames;
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103 outputTypes["fasta"] = tempOutNames;
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104 outputTypes["flow"] = tempOutNames;
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105 outputTypes["sfftxt"] = tempOutNames;
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106 outputTypes["qfile"] = tempOutNames;
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107 outputTypes["sff"] = tempOutNames;
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109 catch(exception& e) {
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110 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
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114 //**********************************************************************************************************************
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116 SffInfoCommand::SffInfoCommand(string option) {
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118 abort = false; calledHelp = false;
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119 hasAccnos = false; hasOligos = false; hasGroup = false;
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122 //allow user to run help
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123 if(option == "help") { help(); abort = true; calledHelp = true; }
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124 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
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127 //valid paramters for this command
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128 vector<string> myArray = setParameters();
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130 OptionParser parser(option);
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131 map<string, string> parameters = parser.getParameters();
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133 ValidParameters validParameter;
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134 //check to make sure all parameters are valid for command
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135 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
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136 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
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139 //initialize outputTypes
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140 vector<string> tempOutNames;
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141 outputTypes["fasta"] = tempOutNames;
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142 outputTypes["flow"] = tempOutNames;
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143 outputTypes["sfftxt"] = tempOutNames;
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144 outputTypes["qfile"] = tempOutNames;
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145 outputTypes["sff"] = tempOutNames;
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147 //if the user changes the output directory command factory will send this info to us in the output parameter
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148 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
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150 //if the user changes the input directory command factory will send this info to us in the output parameter
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151 string inputDir = validParameter.validFile(parameters, "inputdir", false); if (inputDir == "not found"){ inputDir = ""; }
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153 sffFilename = validParameter.validFile(parameters, "sff", false);
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154 if (sffFilename == "not found") { sffFilename = ""; }
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156 m->splitAtDash(sffFilename, filenames);
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158 //go through files and make sure they are good, if not, then disregard them
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159 for (int i = 0; i < filenames.size(); i++) {
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160 bool ignore = false;
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161 if (filenames[i] == "current") {
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162 filenames[i] = m->getSFFFile();
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163 if (filenames[i] != "") { m->mothurOut("Using " + filenames[i] + " as input file for the sff parameter where you had given current."); m->mothurOutEndLine(); }
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165 m->mothurOut("You have no current sfffile, ignoring current."); m->mothurOutEndLine(); ignore=true;
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166 //erase from file list
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167 filenames.erase(filenames.begin()+i);
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173 if (inputDir != "") {
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174 string path = m->hasPath(filenames[i]);
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175 //if the user has not given a path then, add inputdir. else leave path alone.
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176 if (path == "") { filenames[i] = inputDir + filenames[i]; }
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180 int ableToOpen = m->openInputFile(filenames[i], in, "noerror");
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182 //if you can't open it, try default location
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183 if (ableToOpen == 1) {
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184 if (m->getDefaultPath() != "") { //default path is set
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185 string tryPath = m->getDefaultPath() + m->getSimpleName(filenames[i]);
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186 m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
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188 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
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190 filenames[i] = tryPath;
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194 //if you can't open it, try default location
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195 if (ableToOpen == 1) {
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196 if (m->getOutputDir() != "") { //default path is set
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197 string tryPath = m->getOutputDir() + m->getSimpleName(filenames[i]);
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198 m->mothurOut("Unable to open " + filenames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
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200 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
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202 filenames[i] = tryPath;
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208 if (ableToOpen == 1) {
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209 m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
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210 //erase from file list
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211 filenames.erase(filenames.begin()+i);
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213 }else { m->setSFFFile(filenames[i]); }
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217 //make sure there is at least one valid file left
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218 if (filenames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
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221 accnosName = validParameter.validFile(parameters, "accnos", false);
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222 if (accnosName == "not found") { accnosName = ""; }
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225 m->splitAtDash(accnosName, accnosFileNames);
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227 //go through files and make sure they are good, if not, then disregard them
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228 for (int i = 0; i < accnosFileNames.size(); i++) {
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229 bool ignore = false;
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230 if (accnosFileNames[i] == "current") {
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231 accnosFileNames[i] = m->getAccnosFile();
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232 if (accnosFileNames[i] != "") { m->mothurOut("Using " + accnosFileNames[i] + " as input file for the accnos parameter where you had given current."); m->mothurOutEndLine(); }
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234 m->mothurOut("You have no current accnosfile, ignoring current."); m->mothurOutEndLine(); ignore=true;
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235 //erase from file list
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236 accnosFileNames.erase(accnosFileNames.begin()+i);
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243 if (inputDir != "") {
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244 string path = m->hasPath(accnosFileNames[i]);
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245 //if the user has not given a path then, add inputdir. else leave path alone.
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246 if (path == "") { accnosFileNames[i] = inputDir + accnosFileNames[i]; }
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250 int ableToOpen = m->openInputFile(accnosFileNames[i], in, "noerror");
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252 //if you can't open it, try default location
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253 if (ableToOpen == 1) {
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254 if (m->getDefaultPath() != "") { //default path is set
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255 string tryPath = m->getDefaultPath() + m->getSimpleName(accnosFileNames[i]);
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256 m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
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258 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
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260 accnosFileNames[i] = tryPath;
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263 //if you can't open it, try default location
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264 if (ableToOpen == 1) {
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265 if (m->getOutputDir() != "") { //default path is set
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266 string tryPath = m->getOutputDir() + m->getSimpleName(accnosFileNames[i]);
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267 m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
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269 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
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271 accnosFileNames[i] = tryPath;
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276 if (ableToOpen == 1) {
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277 m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
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278 //erase from file list
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279 accnosFileNames.erase(accnosFileNames.begin()+i);
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285 //make sure there is at least one valid file left
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286 if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
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289 oligosfile = validParameter.validFile(parameters, "oligos", false);
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290 if (oligosfile == "not found") { oligosfile = ""; }
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293 m->splitAtDash(oligosfile, oligosFileNames);
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295 //go through files and make sure they are good, if not, then disregard them
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296 for (int i = 0; i < oligosFileNames.size(); i++) {
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297 bool ignore = false;
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298 if (oligosFileNames[i] == "current") {
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299 oligosFileNames[i] = m->getOligosFile();
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300 if (oligosFileNames[i] != "") { m->mothurOut("Using " + oligosFileNames[i] + " as input file for the oligos parameter where you had given current."); m->mothurOutEndLine(); }
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302 m->mothurOut("You have no current oligosfile, ignoring current."); m->mothurOutEndLine(); ignore=true;
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303 //erase from file list
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304 oligosFileNames.erase(oligosFileNames.begin()+i);
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311 if (inputDir != "") {
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312 string path = m->hasPath(oligosFileNames[i]);
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313 //if the user has not given a path then, add inputdir. else leave path alone.
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314 if (path == "") { oligosFileNames[i] = inputDir + oligosFileNames[i]; }
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318 int ableToOpen = m->openInputFile(oligosFileNames[i], in, "noerror");
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320 //if you can't open it, try default location
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321 if (ableToOpen == 1) {
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322 if (m->getDefaultPath() != "") { //default path is set
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323 string tryPath = m->getDefaultPath() + m->getSimpleName(oligosFileNames[i]);
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324 m->mothurOut("Unable to open " + oligosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
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326 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
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328 oligosFileNames[i] = tryPath;
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331 //if you can't open it, try default location
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332 if (ableToOpen == 1) {
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333 if (m->getOutputDir() != "") { //default path is set
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334 string tryPath = m->getOutputDir() + m->getSimpleName(oligosFileNames[i]);
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335 m->mothurOut("Unable to open " + oligosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
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337 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
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339 oligosFileNames[i] = tryPath;
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344 if (ableToOpen == 1) {
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345 m->mothurOut("Unable to open " + oligosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
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346 //erase from file list
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347 oligosFileNames.erase(oligosFileNames.begin()+i);
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353 //make sure there is at least one valid file left
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354 if (oligosFileNames.size() == 0) { m->mothurOut("no valid oligos files."); m->mothurOutEndLine(); abort = true; }
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357 groupfile = validParameter.validFile(parameters, "group", false);
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358 if (groupfile == "not found") { groupfile = ""; }
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361 m->splitAtDash(groupfile, groupFileNames);
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363 //go through files and make sure they are good, if not, then disregard them
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364 for (int i = 0; i < groupFileNames.size(); i++) {
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365 bool ignore = false;
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366 if (groupFileNames[i] == "current") {
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367 groupFileNames[i] = m->getGroupFile();
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368 if (groupFileNames[i] != "") { m->mothurOut("Using " + groupFileNames[i] + " as input file for the group parameter where you had given current."); m->mothurOutEndLine(); }
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370 m->mothurOut("You have no current group file, ignoring current."); m->mothurOutEndLine(); ignore=true;
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371 //erase from file list
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372 groupFileNames.erase(groupFileNames.begin()+i);
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379 if (inputDir != "") {
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380 string path = m->hasPath(groupFileNames[i]);
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381 //if the user has not given a path then, add inputdir. else leave path alone.
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382 if (path == "") { groupFileNames[i] = inputDir + groupFileNames[i]; }
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386 int ableToOpen = m->openInputFile(groupFileNames[i], in, "noerror");
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388 //if you can't open it, try default location
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389 if (ableToOpen == 1) {
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390 if (m->getDefaultPath() != "") { //default path is set
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391 string tryPath = m->getDefaultPath() + m->getSimpleName(groupFileNames[i]);
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392 m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
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394 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
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396 groupFileNames[i] = tryPath;
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399 //if you can't open it, try default location
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400 if (ableToOpen == 1) {
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401 if (m->getOutputDir() != "") { //default path is set
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402 string tryPath = m->getOutputDir() + m->getSimpleName(groupFileNames[i]);
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403 m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
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405 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
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407 groupFileNames[i] = tryPath;
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412 if (ableToOpen == 1) {
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413 m->mothurOut("Unable to open " + groupFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
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414 //erase from file list
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415 groupFileNames.erase(groupFileNames.begin()+i);
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421 //make sure there is at least one valid file left
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422 if (groupFileNames.size() == 0) { m->mothurOut("no valid group files."); m->mothurOutEndLine(); abort = true; }
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427 if (groupFileNames.size() != filenames.size()) { abort = true; m->mothurOut("If you provide a group file, you must have one for each sff file."); m->mothurOutEndLine(); }
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432 if (oligosFileNames.size() != filenames.size()) { abort = true; m->mothurOut("If you provide an oligos file, you must have one for each sff file."); m->mothurOutEndLine(); }
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435 if (hasGroup && hasOligos) { m->mothurOut("You must enter ONLY ONE of the following: oligos or group."); m->mothurOutEndLine(); abort = true;}
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438 if (accnosFileNames.size() != filenames.size()) { abort = true; m->mothurOut("If you provide a accnos file, you must have one for each sff file."); m->mothurOutEndLine(); }
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441 string temp = validParameter.validFile(parameters, "qfile", false); if (temp == "not found"){ temp = "T"; }
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442 qual = m->isTrue(temp);
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444 temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ temp = "T"; }
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445 fasta = m->isTrue(temp);
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447 temp = validParameter.validFile(parameters, "flow", false); if (temp == "not found"){ temp = "T"; }
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448 flow = m->isTrue(temp);
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450 temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found"){ temp = "T"; }
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451 trim = m->isTrue(temp);
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453 temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found") { temp = "0"; }
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454 m->mothurConvert(temp, bdiffs);
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456 temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
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457 m->mothurConvert(temp, pdiffs);
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459 temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
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460 m->mothurConvert(temp, ldiffs);
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462 temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
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463 m->mothurConvert(temp, sdiffs);
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465 temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
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466 m->mothurConvert(temp, tdiffs);
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468 if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
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470 temp = validParameter.validFile(parameters, "sfftxt", false);
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471 if (temp == "not found") { temp = "F"; sfftxt = false; sfftxtFilename = ""; }
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472 else if (m->isTrue(temp)) { sfftxt = true; sfftxtFilename = ""; }
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474 //you are a filename
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475 if (inputDir != "") {
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476 map<string,string>::iterator it = parameters.find("sfftxt");
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477 //user has given a template file
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478 if(it != parameters.end()){
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479 string path = m->hasPath(it->second);
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480 //if the user has not given a path then, add inputdir. else leave path alone.
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481 if (path == "") { parameters["sfftxt"] = inputDir + it->second; }
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485 sfftxtFilename = validParameter.validFile(parameters, "sfftxt", true);
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486 if (sfftxtFilename == "not found") { sfftxtFilename = ""; }
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487 else if (sfftxtFilename == "not open") { sfftxtFilename = ""; }
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490 if ((sfftxtFilename == "") && (filenames.size() == 0)) {
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491 //if there is a current sff file, use it
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492 string filename = m->getSFFFile();
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493 if (filename != "") { filenames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the sff parameter."); m->mothurOutEndLine(); }
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494 else { m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true; }
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497 temp = validParameter.validFile(parameters, "checkorient", false); if (temp == "not found") { temp = "F"; }
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498 reorient = m->isTrue(temp);
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502 catch(exception& e) {
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503 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
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507 //**********************************************************************************************************************
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508 int SffInfoCommand::execute(){
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510 if (abort == true) { if (calledHelp) { return 0; } return 2; }
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512 for (int s = 0; s < filenames.size(); s++) {
\r
514 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
\r
516 int start = time(NULL);
\r
518 filenames[s] = m->getFullPathName(filenames[s]);
\r
519 m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
\r
521 string accnos = "";
\r
522 if (hasAccnos) { accnos = accnosFileNames[s]; }
\r
524 string oligos = "";
\r
525 if (hasOligos) { oligos = oligosFileNames[s]; }
\r
526 if (hasGroup) { oligos = groupFileNames[s]; }
\r
528 int numReads = extractSffInfo(filenames[s], accnos, oligos);
\r
530 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
\r
533 if (sfftxtFilename != "") { parseSffTxt(); }
\r
535 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
\r
537 //set fasta file as new current fastafile
\r
538 string current = "";
\r
539 itTypes = outputTypes.find("fasta");
\r
540 if (itTypes != outputTypes.end()) {
\r
541 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
\r
544 itTypes = outputTypes.find("qfile");
\r
545 if (itTypes != outputTypes.end()) {
\r
546 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
\r
549 itTypes = outputTypes.find("flow");
\r
550 if (itTypes != outputTypes.end()) {
\r
551 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); }
\r
554 //report output filenames
\r
555 m->mothurOutEndLine();
\r
556 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
\r
557 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
\r
558 m->mothurOutEndLine();
\r
562 catch(exception& e) {
\r
563 m->errorOut(e, "SffInfoCommand", "execute");
\r
567 //**********************************************************************************************************************
\r
568 int SffInfoCommand::extractSffInfo(string input, string accnos, string oligos){
\r
570 oligosObject = new Oligos();
\r
571 currentFileName = input;
\r
572 if (outputDir == "") { outputDir += m->hasPath(input); }
\r
574 if (accnos != "") { readAccnosFile(accnos); }
\r
575 else { seqNames.clear(); }
\r
577 TrimOligos* trimOligos = NULL; TrimOligos* rtrimOligos = NULL;
\r
579 readOligos(oligos); split = 2;
\r
580 if (m->control_pressed) { delete oligosObject; return 0; }
\r
581 trimOligos = new TrimOligos(pdiffs, bdiffs, ldiffs, sdiffs, oligosObject->getPrimers(), oligosObject->getBarcodes(), oligosObject->getReversePrimers(), oligosObject->getLinkers(), oligosObject->getSpacers()); numFPrimers = oligosObject->getPrimers().size(); numBarcodes = oligosObject->getBarcodes().size();
\r
583 rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligosObject->getReorientedPairedPrimers(), oligosObject->getReorientedPairedBarcodes()); numBarcodes = oligosObject->getReorientedPairedBarcodes().size();
\r
586 if (hasGroup) { readGroup(oligos); split = 2; }
\r
588 ofstream outSfftxt, outFasta, outQual, outFlow;
\r
589 string outFastaFileName, outQualFileName;
\r
590 string rootName = outputDir + m->getRootName(m->getSimpleName(input));
\r
591 if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
\r
593 map<string, string> variables;
\r
594 variables["[filename]"] = rootName;
\r
595 string sfftxtFileName = getOutputFileName("sfftxt",variables);
\r
596 string outFlowFileName = getOutputFileName("flow",variables);
\r
597 if (!trim) { variables["[tag]"] = "raw"; }
\r
598 outFastaFileName = getOutputFileName("fasta",variables);
\r
599 outQualFileName = getOutputFileName("qfile",variables);
\r
601 if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint); outputNames.push_back(sfftxtFileName); outputTypes["sfftxt"].push_back(sfftxtFileName); }
\r
602 if (fasta) { m->openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
\r
603 if (qual) { m->openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName); }
\r
604 if (flow) { m->openOutputFile(outFlowFileName, outFlow); outputNames.push_back(outFlowFileName); outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName); }
\r
607 m->openInputFileBinary(input, in);
\r
609 CommonHeader header;
\r
610 readCommonHeader(in, header);
\r
614 //check magic number and version
\r
615 if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); delete oligosObject; if (hasOligos) { delete trimOligos; if (reorient) { delete rtrimOligos; } } return count; }
\r
616 if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); delete oligosObject; if (hasOligos) { delete trimOligos; if (reorient) { delete rtrimOligos; } } return count; }
\r
618 //print common header
\r
619 if (sfftxt) { printCommonHeader(outSfftxt, header); }
\r
620 if (flow) { outFlow << header.numFlowsPerRead << endl; }
\r
622 //read through the sff file
\r
623 while (!in.eof()) {
\r
628 seqRead read; Header readheader;
\r
629 readSeqData(in, read, header.numFlowsPerRead, readheader, trimOligos, rtrimOligos);
\r
631 bool okay = sanityCheck(readheader, read);
\r
632 if (!okay) { break; }
\r
634 //if you have provided an accosfile and this seq is not in it, then dont print
\r
635 if (seqNames.size() != 0) { if (seqNames.count(readheader.name) == 0) { print = false; } }
\r
639 if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }
\r
640 if (fasta) { printFastaSeqData(outFasta, read, readheader); }
\r
641 if (qual) { printQualSeqData(outQual, read, readheader); }
\r
642 if (flow) { printFlowSeqData(outFlow, read, readheader); }
\r
648 if((count+1) % 10000 == 0){ m->mothurOut(toString(count+1)); m->mothurOutEndLine(); }
\r
650 if (m->control_pressed) { count = 0; break; }
\r
652 if (count >= header.numReads) { break; }
\r
656 if (!m->control_pressed) { if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } }
\r
660 if (sfftxt) { outSfftxt.close(); }
\r
661 if (fasta) { outFasta.close(); }
\r
662 if (qual) { outQual.close(); }
\r
663 if (flow) { outFlow.close(); }
\r
666 //create new common headers for each file with the correct number of reads
\r
667 adjustCommonHeader(header);
\r
669 if (hasGroup) { delete groupMap; }
\r
671 //cout << "here" << endl;
\r
672 map<string, string>::iterator it;
\r
673 set<string> namesToRemove;
\r
674 for(int i=0;i<filehandles.size();i++){
\r
675 for(int j=0;j<filehandles[0].size();j++){
\r
676 //cout << i << '\t' << '\t' << j << '\t' << filehandles[i][j] << endl;
\r
677 if (filehandles[i][j] != "") {
\r
678 if (namesToRemove.count(filehandles[i][j]) == 0) {
\r
679 if(m->isBlank(filehandles[i][j])){
\r
680 //cout << i << '\t' << '\t' << j << '\t' << filehandles[i][j] << " is blank removing" << endl;
\r
681 m->mothurRemove(filehandles[i][j]);
\r
682 m->mothurRemove(filehandlesHeaders[i][j]);
\r
683 namesToRemove.insert(filehandles[i][j]);
\r
689 //cout << "here2" << endl;
\r
690 //append new header to reads
\r
691 for (int i = 0; i < filehandles.size(); i++) {
\r
692 for (int j = 0; j < filehandles[i].size(); j++) {
\r
693 if (filehandles[i][j] != "") {
\r
694 m->appendBinaryFiles(filehandles[i][j], filehandlesHeaders[i][j]);
\r
695 m->renameFile(filehandlesHeaders[i][j], filehandles[i][j]);
\r
696 m->mothurRemove(filehandlesHeaders[i][j]);
\r
697 //cout << i << '\t' << '\t' << j << '\t' << filehandles[i][j] << " done appending headers and removing " << filehandlesHeaders[i][j] << endl;
\r
698 if (numSplitReads[i][j] == 0) { m->mothurRemove(filehandles[i][j]); }
\r
702 //cout << "here3" << endl;
\r
703 //remove names for outputFileNames, just cleans up the output
\r
704 for(int i = 0; i < outputNames.size(); i++) {
\r
705 if (namesToRemove.count(outputNames[i]) != 0) {
\r
706 //cout << "erasing " << i << '\t' << outputNames[i] << endl;
\r
707 outputNames.erase(outputNames.begin()+i);
\r
711 //cout << "here4" << endl;
\r
712 if(m->isBlank(noMatchFile)){ m->mothurRemove(noMatchFile); }
\r
713 else { outputNames.push_back(noMatchFile); outputTypes["sff"].push_back(noMatchFile); }
\r
716 delete oligosObject;
\r
717 if (hasOligos) { delete trimOligos; if (reorient) { delete rtrimOligos; } }
\r
721 catch(exception& e) {
\r
722 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
\r
726 //**********************************************************************************************************************
\r
727 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
\r
732 //read magic number
\r
734 in.read(buffer, 4);
\r
735 header.magicNumber = be_int4(*(unsigned int *)(&buffer));
\r
739 in.read(buffer9, 4);
\r
740 header.version = "";
\r
741 for (int i = 0; i < 4; i++) { header.version += toString((int)(buffer9[i])); }
\r
745 in.read(buffer2, 8);
\r
746 header.indexOffset = be_int8(*(unsigned long long *)(&buffer2));
\r
748 //read index length
\r
750 in.read(buffer3, 4);
\r
751 header.indexLength = be_int4(*(unsigned int *)(&buffer3));
\r
755 in.read(buffer4, 4);
\r
756 header.numReads = be_int4(*(unsigned int *)(&buffer4));
\r
758 if (m->debug) { m->mothurOut("[DEBUG]: numReads = " + toString(header.numReads) + "\n"); }
\r
760 //read header length
\r
762 in.read(buffer5, 2);
\r
763 header.headerLength = be_int2(*(unsigned short *)(&buffer5));
\r
767 in.read(buffer6, 2);
\r
768 header.keyLength = be_int2(*(unsigned short *)(&buffer6));
\r
770 //read number of flow reads
\r
772 in.read(buffer7, 2);
\r
773 header.numFlowsPerRead = be_int2(*(unsigned short *)(&buffer7));
\r
777 in.read(buffer8, 1);
\r
778 header.flogramFormatCode = (int)(buffer8[0]);
\r
781 char* tempBuffer = new char[header.numFlowsPerRead];
\r
782 in.read(&(*tempBuffer), header.numFlowsPerRead);
\r
783 header.flowChars = tempBuffer;
\r
784 if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead); }
\r
785 delete[] tempBuffer;
\r
788 char* tempBuffer2 = new char[header.keyLength];
\r
789 in.read(&(*tempBuffer2), header.keyLength);
\r
790 header.keySequence = tempBuffer2;
\r
791 if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength); }
\r
792 delete[] tempBuffer2;
\r
794 /* Pad to 8 chars */
\r
795 unsigned long long spotInFile = in.tellg();
\r
796 unsigned long long spot = (spotInFile + 7)& ~7; // ~ inverts
\r
800 m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
\r
806 catch(exception& e) {
\r
807 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
\r
811 //**********************************************************************************************************************
\r
812 int SffInfoCommand::adjustCommonHeader(CommonHeader header){
\r
814 string endian = m->findEdianness();
\r
815 char* mybuffer = new char[4];
\r
817 m->openInputFileBinary(currentFileName, in);
\r
819 ofstream outNoMatchHeader;
\r
820 string tempNoHeader = "tempNoMatchHeader";
\r
821 m->openOutputFileBinary(tempNoHeader, outNoMatchHeader);
\r
824 in.read(mybuffer,4);
\r
825 for (int i = 0; i < filehandlesHeaders.size(); i++) {
\r
826 for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
\r
828 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
\r
829 out.write(mybuffer, in.gcount());
\r
833 outNoMatchHeader.write(mybuffer, in.gcount());
\r
837 mybuffer = new char[4];
\r
838 in.read(mybuffer,4);
\r
839 for (int i = 0; i < filehandlesHeaders.size(); i++) {
\r
840 for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
\r
842 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
\r
843 out.write(mybuffer, in.gcount());
\r
847 outNoMatchHeader.write(mybuffer, in.gcount());
\r
851 mybuffer = new char[8];
\r
852 in.read(mybuffer,8);
\r
853 unsigned long long offset = 0;
\r
854 char* thisbuffer = new char[8];
\r
855 thisbuffer[0] = (offset >> 56) & 0xFF;
\r
856 thisbuffer[1] = (offset >> 48) & 0xFF;
\r
857 thisbuffer[2] = (offset >> 40) & 0xFF;
\r
858 thisbuffer[3] = (offset >> 32) & 0xFF;
\r
859 thisbuffer[4] = (offset >> 24) & 0xFF;
\r
860 thisbuffer[5] = (offset >> 16) & 0xFF;
\r
861 thisbuffer[6] = (offset >> 8) & 0xFF;
\r
862 thisbuffer[7] = offset & 0xFF;
\r
863 for (int i = 0; i < filehandlesHeaders.size(); i++) {
\r
864 for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
\r
866 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
\r
867 out.write(thisbuffer, 8);
\r
871 outNoMatchHeader.write(thisbuffer, 8);
\r
872 delete[] thisbuffer;
\r
876 //read index length
\r
877 mybuffer = new char[4];
\r
878 in.read(mybuffer,4);
\r
880 char* thisbuffer2 = new char[4];
\r
881 thisbuffer2[0] = (offset >> 24) & 0xFF;
\r
882 thisbuffer2[1] = (offset >> 16) & 0xFF;
\r
883 thisbuffer2[2] = (offset >> 8) & 0xFF;
\r
884 thisbuffer2[3] = offset & 0xFF;
\r
885 for (int i = 0; i < filehandlesHeaders.size(); i++) {
\r
886 for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
\r
888 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
\r
889 out.write(thisbuffer2, 4);
\r
893 outNoMatchHeader.write(thisbuffer2, 4);
\r
894 delete[] thisbuffer2;
\r
898 mybuffer = new char[4];
\r
899 in.read(mybuffer,4);
\r
901 for (int i = 0; i < filehandlesHeaders.size(); i++) {
\r
902 for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
\r
903 char* thisbuffer = new char[4];
\r
904 if (endian == "BIG_ENDIAN") {
\r
905 thisbuffer[0] = (numSplitReads[i][j] >> 24) & 0xFF;
\r
906 thisbuffer[1] = (numSplitReads[i][j] >> 16) & 0xFF;
\r
907 thisbuffer[2] = (numSplitReads[i][j] >> 8) & 0xFF;
\r
908 thisbuffer[3] = numSplitReads[i][j] & 0xFF;
\r
910 thisbuffer[0] = numSplitReads[i][j] & 0xFF;
\r
911 thisbuffer[1] = (numSplitReads[i][j] >> 8) & 0xFF;
\r
912 thisbuffer[2] = (numSplitReads[i][j] >> 16) & 0xFF;
\r
913 thisbuffer[3] = (numSplitReads[i][j] >> 24) & 0xFF;
\r
916 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
\r
917 out.write(thisbuffer, 4);
\r
919 delete[] thisbuffer;
\r
922 char* thisbuffer3 = new char[4];
\r
923 if (endian == "BIG_ENDIAN") {
\r
924 thisbuffer3[0] = (numNoMatch >> 24) & 0xFF;
\r
925 thisbuffer3[1] = (numNoMatch >> 16) & 0xFF;
\r
926 thisbuffer3[2] = (numNoMatch >> 8) & 0xFF;
\r
927 thisbuffer3[3] = numNoMatch & 0xFF;
\r
929 thisbuffer3[0] = numNoMatch & 0xFF;
\r
930 thisbuffer3[1] = (numNoMatch >> 8) & 0xFF;
\r
931 thisbuffer3[2] = (numNoMatch >> 16) & 0xFF;
\r
932 thisbuffer3[3] = (numNoMatch >> 24) & 0xFF;
\r
934 outNoMatchHeader.write(thisbuffer3, 4);
\r
935 delete[] thisbuffer3;
\r
938 //read header length
\r
939 mybuffer = new char[2];
\r
940 in.read(mybuffer,2);
\r
941 for (int i = 0; i < filehandlesHeaders.size(); i++) {
\r
942 for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
\r
944 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
\r
945 out.write(mybuffer, in.gcount());
\r
949 outNoMatchHeader.write(mybuffer, in.gcount());
\r
953 mybuffer = new char[2];
\r
954 in.read(mybuffer,2);
\r
955 for (int i = 0; i < filehandlesHeaders.size(); i++) {
\r
956 for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
\r
958 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
\r
959 out.write(mybuffer, in.gcount());
\r
963 outNoMatchHeader.write(mybuffer, in.gcount());
\r
966 //read number of flow reads
\r
967 mybuffer = new char[2];
\r
968 in.read(mybuffer,2);
\r
969 for (int i = 0; i < filehandlesHeaders.size(); i++) {
\r
970 for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
\r
972 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
\r
973 out.write(mybuffer, in.gcount());
\r
977 outNoMatchHeader.write(mybuffer, in.gcount());
\r
981 mybuffer = new char[1];
\r
982 in.read(mybuffer,1);
\r
983 for (int i = 0; i < filehandlesHeaders.size(); i++) {
\r
984 for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
\r
986 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
\r
987 out.write(mybuffer, in.gcount());
\r
991 outNoMatchHeader.write(mybuffer, in.gcount());
\r
995 mybuffer = new char[header.numFlowsPerRead];
\r
996 in.read(mybuffer,header.numFlowsPerRead);
\r
997 for (int i = 0; i < filehandlesHeaders.size(); i++) {
\r
998 for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
\r
1000 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
\r
1001 out.write(mybuffer, in.gcount());
\r
1005 outNoMatchHeader.write(mybuffer, in.gcount());
\r
1006 delete[] mybuffer;
\r
1009 mybuffer = new char[header.keyLength];
\r
1010 in.read(mybuffer,header.keyLength);
\r
1011 for (int i = 0; i < filehandlesHeaders.size(); i++) {
\r
1012 for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
\r
1014 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
\r
1015 out.write(mybuffer, in.gcount());
\r
1019 outNoMatchHeader.write(mybuffer, in.gcount());
\r
1020 delete[] mybuffer;
\r
1023 /* Pad to 8 chars */
\r
1024 unsigned long long spotInFile = in.tellg();
\r
1025 unsigned long long spot = (spotInFile + 7)& ~7; // ~ inverts
\r
1028 mybuffer = new char[spot-spotInFile];
\r
1029 for (int i = 0; i < filehandlesHeaders.size(); i++) {
\r
1030 for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
\r
1032 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
\r
1033 out.write(mybuffer, spot-spotInFile);
\r
1037 outNoMatchHeader.write(mybuffer, spot-spotInFile);
\r
1038 outNoMatchHeader.close();
\r
1039 delete[] mybuffer;
\r
1042 m->appendBinaryFiles(noMatchFile, tempNoHeader);
\r
1043 m->renameFile(tempNoHeader, noMatchFile);
\r
1044 m->mothurRemove(tempNoHeader);
\r
1049 catch(exception& e) {
\r
1050 m->errorOut(e, "SffInfoCommand", "adjustCommonHeader");
\r
1054 //**********************************************************************************************************************
\r
1055 bool SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, Header& header, TrimOligos*& trimOligos, TrimOligos*& rtrimOligos){
\r
1057 unsigned long long startSpotInFile = in.tellg();
\r
1060 /*****************************************/
\r
1063 //read header length
\r
1065 in.read(buffer, 2);
\r
1066 header.headerLength = be_int2(*(unsigned short *)(&buffer));
\r
1068 //read name length
\r
1070 in.read(buffer2, 2);
\r
1071 header.nameLength = be_int2(*(unsigned short *)(&buffer2));
\r
1075 in.read(buffer3, 4);
\r
1076 header.numBases = be_int4(*(unsigned int *)(&buffer3));
\r
1079 //read clip qual left
\r
1081 in.read(buffer4, 2);
\r
1082 header.clipQualLeft = be_int2(*(unsigned short *)(&buffer4));
\r
1083 header.clipQualLeft = 5;
\r
1086 //read clip qual right
\r
1088 in.read(buffer5, 2);
\r
1089 header.clipQualRight = be_int2(*(unsigned short *)(&buffer5));
\r
1092 //read clipAdapterLeft
\r
1094 in.read(buffer6, 2);
\r
1095 header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
\r
1098 //read clipAdapterRight
\r
1100 in.read(buffer7, 2);
\r
1101 header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
\r
1105 char* tempBuffer = new char[header.nameLength];
\r
1106 in.read(&(*tempBuffer), header.nameLength);
\r
1107 header.name = tempBuffer;
\r
1108 if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength); }
\r
1110 delete[] tempBuffer;
\r
1112 //extract info from name
\r
1113 decodeName(header.timestamp, header.region, header.xy, header.name);
\r
1115 /* Pad to 8 chars */
\r
1116 unsigned long long spotInFile = in.tellg();
\r
1117 unsigned long long spot = (spotInFile + 7)& ~7;
\r
1120 /*****************************************/
\r
1124 read.flowgram.resize(numFlowReads);
\r
1125 for (int i = 0; i < numFlowReads; i++) {
\r
1127 in.read(buffer, 2);
\r
1128 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
\r
1132 read.flowIndex.resize(header.numBases);
\r
1133 for (int i = 0; i < header.numBases; i++) {
\r
1136 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
\r
1140 char* tempBuffer6 = new char[header.numBases];
\r
1141 in.read(&(*tempBuffer6), header.numBases);
\r
1142 read.bases = tempBuffer6;
\r
1143 if (read.bases.length() > header.numBases) { read.bases = read.bases.substr(0, header.numBases); }
\r
1144 delete[] tempBuffer6;
\r
1146 //read qual scores
\r
1147 read.qualScores.resize(header.numBases);
\r
1148 for (int i = 0; i < header.numBases; i++) {
\r
1151 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
\r
1154 /* Pad to 8 chars */
\r
1155 spotInFile = in.tellg();
\r
1156 spot = (spotInFile + 7)& ~7;
\r
1161 int barcodeIndex, primerIndex, trashCodeLength;
\r
1163 if (hasOligos) { trashCodeLength = findGroup(header, read, barcodeIndex, primerIndex, trimOligos, rtrimOligos); }
\r
1164 else if (hasGroup) { trashCodeLength = findGroup(header, read, barcodeIndex, primerIndex, "groupMode"); }
\r
1165 else { m->mothurOut("[ERROR]: uh oh, we shouldn't be here...\n"); }
\r
1168 mybuffer = new char [spot-startSpotInFile];
\r
1171 m->openInputFileBinary(currentFileName, in2);
\r
1172 in2.seekg(startSpotInFile);
\r
1173 in2.read(mybuffer,spot-startSpotInFile);
\r
1176 if(trashCodeLength == 0){
\r
1178 m->openOutputFileBinaryAppend(filehandles[barcodeIndex][primerIndex], out);
\r
1179 out.write(mybuffer, in2.gcount());
\r
1181 numSplitReads[barcodeIndex][primerIndex]++;
\r
1185 m->openOutputFileBinaryAppend(noMatchFile, out);
\r
1186 out.write(mybuffer, in2.gcount());
\r
1190 delete[] mybuffer;
\r
1195 m->mothurOut("Error reading."); m->mothurOutEndLine();
\r
1198 if (in.eof()) { return true; }
\r
1202 catch(exception& e) {
\r
1203 m->errorOut(e, "SffInfoCommand", "readSeqData");
\r
1207 //**********************************************************************************************************************
\r
1208 int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& primer, TrimOligos*& trimOligos, TrimOligos*& rtrimOligos) {
\r
1212 string trashCode = "";
\r
1213 int currentSeqsDiffs = 0;
\r
1215 string seq = read.bases;
\r
1218 if(header.clipQualRight < header.clipQualLeft){
\r
1219 if (header.clipQualRight == 0) { //don't trim right
\r
1220 seq = seq.substr(header.clipQualLeft-1);
\r
1225 else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
\r
1226 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
\r
1229 seq = seq.substr(header.clipQualLeft-1);
\r
1232 //if you wanted the sfftxt then you already converted the bases to the right case
\r
1234 int endValue = header.clipQualRight;
\r
1235 //make the bases you want to clip lowercase and the bases you want to keep upper case
\r
1236 if(endValue == 0){ endValue = seq.length(); }
\r
1237 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]); }
\r
1238 for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { seq[i] = toupper(seq[i]); }
\r
1239 for (int i = (endValue-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
\r
1243 Sequence currSeq(header.name, seq);
\r
1244 QualityScores currQual;
\r
1247 Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
\r
1248 QualityScores savedQual(currQual.getName(), currQual.getScores());
\r
1250 if(numLinkers != 0){
\r
1251 success = trimOligos->stripLinker(currSeq, currQual);
\r
1252 if(success > ldiffs) { trashCode += 'k'; }
\r
1253 else{ currentSeqsDiffs += success; }
\r
1257 if(numBarcodes != 0){
\r
1258 success = trimOligos->stripBarcode(currSeq, currQual, barcode);
\r
1259 if(success > bdiffs) { trashCode += 'b'; }
\r
1260 else{ currentSeqsDiffs += success; }
\r
1263 if(numSpacers != 0){
\r
1264 success = trimOligos->stripSpacer(currSeq, currQual);
\r
1265 if(success > sdiffs) { trashCode += 's'; }
\r
1266 else{ currentSeqsDiffs += success; }
\r
1270 if(numFPrimers != 0){
\r
1271 success = trimOligos->stripForward(currSeq, currQual, primer, true);
\r
1272 if(success > pdiffs) { trashCode += 'f'; }
\r
1273 else{ currentSeqsDiffs += success; }
\r
1276 if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
\r
1278 if(numRPrimers != 0){
\r
1279 success = trimOligos->stripReverse(currSeq, currQual);
\r
1280 if(!success) { trashCode += 'r'; }
\r
1283 if (reorient && (trashCode != "")) { //if you failed and want to check the reverse
\r
1284 int thisSuccess = 0;
\r
1285 string thisTrashCode = "";
\r
1286 int thisCurrentSeqsDiffs = 0;
\r
1288 int thisBarcodeIndex = 0;
\r
1289 int thisPrimerIndex = 0;
\r
1290 //cout << currSeq.getName() << '\t' << savedSeq.getUnaligned() << endl;
\r
1291 if(numBarcodes != 0){
\r
1292 thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex);
\r
1293 if(thisSuccess > bdiffs) { thisTrashCode += "b"; }
\r
1294 else{ thisCurrentSeqsDiffs += thisSuccess; }
\r
1296 //cout << currSeq.getName() << '\t' << savedSeq.getUnaligned() << endl;
\r
1297 if(numFPrimers != 0){
\r
1298 thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, true);
\r
1299 if(thisSuccess > pdiffs) { thisTrashCode += "f"; }
\r
1300 else{ thisCurrentSeqsDiffs += thisSuccess; }
\r
1303 if (thisCurrentSeqsDiffs > tdiffs) { thisTrashCode += 't'; }
\r
1305 if (thisTrashCode == "") {
\r
1306 trashCode = thisTrashCode;
\r
1307 success = thisSuccess;
\r
1308 currentSeqsDiffs = thisCurrentSeqsDiffs;
\r
1309 barcode = thisBarcodeIndex;
\r
1310 primer = thisPrimerIndex;
\r
1311 savedSeq.reverseComplement();
\r
1312 currSeq.setAligned(savedSeq.getAligned());
\r
1313 savedQual.flipQScores();
\r
1314 currQual.setScores(savedQual.getScores());
\r
1315 }else { trashCode += "(" + thisTrashCode + ")"; }
\r
1318 if (trashCode.length() == 0) { //is this sequence in the ignore group
\r
1319 string thisGroup = oligosObject->getGroupName(barcode, primer);
\r
1321 int pos = thisGroup.find("ignore");
\r
1322 if (pos != string::npos) { trashCode += "i"; }
\r
1325 return trashCode.length();
\r
1327 catch(exception& e) {
\r
1328 m->errorOut(e, "SffInfoCommand", "findGroup");
\r
1332 //**********************************************************************************************************************
\r
1333 int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& primer, string groupMode) {
\r
1335 string trashCode = "";
\r
1338 string group = groupMap->getGroup(header.name);
\r
1339 if (group == "not found") { trashCode += "g"; } //scrap for group
\r
1341 return trashCode.length();
\r
1343 catch(exception& e) {
\r
1344 m->errorOut(e, "SffInfoCommand", "findGroup");
\r
1348 //**********************************************************************************************************************
\r
1349 int SffInfoCommand::decodeName(string& timestamp, string& region, string& xy, string name) {
\r
1352 if (name.length() >= 6) {
\r
1353 string time = name.substr(0, 6);
\r
1354 unsigned int timeNum = m->fromBase36(time);
\r
1356 int q1 = timeNum / 60;
\r
1357 int sec = timeNum - 60 * q1;
\r
1359 int minute = q1 - 60 * q2;
\r
1361 int hr = q2 - 24 * q3;
\r
1363 int day = q3 - 32 * q4;
\r
1365 int mon = q4 - 13 * q5;
\r
1366 int year = 2000 + q5;
\r
1368 timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
\r
1371 if (name.length() >= 9) {
\r
1372 region = name.substr(7, 2);
\r
1374 string xyNum = name.substr(9);
\r
1375 unsigned int myXy = m->fromBase36(xyNum);
\r
1376 int x = myXy >> 12;
\r
1377 int y = myXy & 4095;
\r
1379 xy = toString(x) + "_" + toString(y);
\r
1384 catch(exception& e) {
\r
1385 m->errorOut(e, "SffInfoCommand", "decodeName");
\r
1389 //**********************************************************************************************************************
\r
1390 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
\r
1393 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
\r
1394 out << "Version: " << header.version << endl;
\r
1395 out << "Index Offset: " << header.indexOffset << endl;
\r
1396 out << "Index Length: " << header.indexLength << endl;
\r
1397 out << "Number of Reads: " << header.numReads << endl;
\r
1398 out << "Header Length: " << header.headerLength << endl;
\r
1399 out << "Key Length: " << header.keyLength << endl;
\r
1400 out << "Number of Flows: " << header.numFlowsPerRead << endl;
\r
1401 out << "Format Code: " << header.flogramFormatCode << endl;
\r
1402 out << "Flow Chars: " << header.flowChars << endl;
\r
1403 out << "Key Sequence: " << header.keySequence << endl << endl;
\r
1407 catch(exception& e) {
\r
1408 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
\r
1412 //**********************************************************************************************************************
\r
1413 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
\r
1416 out << ">" << header.name << endl;
\r
1417 out << "Run Prefix: " << header.timestamp << endl;
\r
1418 out << "Region #: " << header.region << endl;
\r
1419 out << "XY Location: " << header.xy << endl << endl;
\r
1421 out << "Run Name: " << endl;
\r
1422 out << "Analysis Name: " << endl;
\r
1423 out << "Full Path: " << endl << endl;
\r
1425 out << "Read Header Len: " << header.headerLength << endl;
\r
1426 out << "Name Length: " << header.nameLength << endl;
\r
1427 out << "# of Bases: " << header.numBases << endl;
\r
1428 out << "Clip Qual Left: " << header.clipQualLeft << endl;
\r
1429 out << "Clip Qual Right: " << header.clipQualRight << endl;
\r
1430 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
\r
1431 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
\r
1435 catch(exception& e) {
\r
1436 m->errorOut(e, "SffInfoCommand", "printHeader");
\r
1440 //**********************************************************************************************************************
\r
1441 bool SffInfoCommand::sanityCheck(Header& header, seqRead& read) {
\r
1444 string message = "[WARNING]: Your sff file may be corrupted! Sequence: " + header.name + "\n";
\r
1446 if (header.clipQualLeft > read.bases.length()) {
\r
1447 okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
\r
1449 if (header.clipQualRight > read.bases.length()) {
\r
1450 okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
\r
1452 if (header.clipQualLeft > read.qualScores.size()) {
\r
1453 okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
\r
1455 if (header.clipQualRight > read.qualScores.size()) {
\r
1456 okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
\r
1459 if (okay == false) {
\r
1460 m->mothurOut(message); m->mothurOutEndLine();
\r
1465 catch(exception& e) {
\r
1466 m->errorOut(e, "SffInfoCommand", "sanityCheck");
\r
1470 //**********************************************************************************************************************
\r
1471 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
\r
1473 out << "Flowgram: ";
\r
1474 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t'; }
\r
1476 out << endl << "Flow Indexes: ";
\r
1478 for (int i = 0; i < read.flowIndex.size(); i++) { sum += read.flowIndex[i]; out << sum << '\t'; }
\r
1480 //make the bases you want to clip lowercase and the bases you want to keep upper case
\r
1481 int endValue = header.clipQualRight;
\r
1482 if(endValue == 0){ endValue = read.bases.length(); }
\r
1483 for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
\r
1484 for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { read.bases[i] = toupper(read.bases[i]); }
\r
1485 for (int i = (endValue-1); i < read.bases.length(); i++) { read.bases[i] = tolower(read.bases[i]); }
\r
1487 out << endl << "Bases: " << read.bases << endl << "Quality Scores: ";
\r
1488 for (int i = 0; i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
\r
1491 out << endl << endl;
\r
1495 catch(exception& e) {
\r
1496 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
\r
1500 //**********************************************************************************************************************
\r
1501 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
\r
1503 string seq = read.bases;
\r
1506 if(header.clipQualRight < header.clipQualLeft){
\r
1507 if (header.clipQualRight == 0) { //don't trim right
\r
1508 seq = seq.substr(header.clipQualLeft-1);
\r
1513 else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
\r
1514 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
\r
1517 seq = seq.substr(header.clipQualLeft-1);
\r
1520 //if you wanted the sfftxt then you already converted the bases to the right case
\r
1522 int endValue = header.clipQualRight;
\r
1523 //make the bases you want to clip lowercase and the bases you want to keep upper case
\r
1524 if(endValue == 0){ endValue = seq.length(); }
\r
1525 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]); }
\r
1526 for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { seq[i] = toupper(seq[i]); }
\r
1527 for (int i = (endValue-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
\r
1531 out << ">" << header.name << " xy=" << header.xy << endl;
\r
1532 out << seq << endl;
\r
1536 catch(exception& e) {
\r
1537 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
\r
1542 //**********************************************************************************************************************
\r
1543 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
\r
1547 if(header.clipQualRight < header.clipQualLeft){
\r
1548 if (header.clipQualRight == 0) { //don't trim right
\r
1549 out << ">" << header.name << " xy=" << header.xy << " length=" << (read.qualScores.size()-header.clipQualLeft) << endl;
\r
1550 for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
\r
1552 out << ">" << header.name << " xy=" << header.xy << endl;
\r
1553 out << "0\t0\t0\t0";
\r
1556 else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
\r
1557 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
\r
1558 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { out << read.qualScores[i] << '\t'; }
\r
1561 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
\r
1562 for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
\r
1565 out << ">" << header.name << " xy=" << header.xy << " length=" << read.qualScores.size() << endl;
\r
1566 for (int i = 0; i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
\r
1573 catch(exception& e) {
\r
1574 m->errorOut(e, "SffInfoCommand", "printQualSeqData");
\r
1579 //**********************************************************************************************************************
\r
1580 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
\r
1583 int endValue = header.clipQualRight;
\r
1584 if (header.clipQualRight == 0) {
\r
1585 endValue = read.flowIndex.size();
\r
1586 if (m->debug) { m->mothurOut("[DEBUG]: " + header.name + " has clipQualRight=0.\n"); }
\r
1588 if(endValue > header.clipQualLeft){
\r
1590 int rightIndex = 0;
\r
1591 for (int i = 0; i < endValue; i++) { rightIndex += read.flowIndex[i]; }
\r
1593 out << header.name << ' ' << rightIndex;
\r
1594 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100); }
\r
1601 catch(exception& e) {
\r
1602 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
\r
1606 //**********************************************************************************************************************
\r
1607 int SffInfoCommand::readAccnosFile(string filename) {
\r
1609 //remove old names
\r
1613 m->openInputFile(filename, in);
\r
1617 in >> name; m->gobble(in);
\r
1619 seqNames.insert(name);
\r
1621 if (m->control_pressed) { seqNames.clear(); break; }
\r
1627 catch(exception& e) {
\r
1628 m->errorOut(e, "SffInfoCommand", "readAccnosFile");
\r
1632 //**********************************************************************************************************************
\r
1633 int SffInfoCommand::parseSffTxt() {
\r
1637 m->openInputFile(sfftxtFilename, inSFF);
\r
1639 if (outputDir == "") { outputDir += m->hasPath(sfftxtFilename); }
\r
1641 //output file names
\r
1642 ofstream outFasta, outQual, outFlow;
\r
1643 string outFastaFileName, outQualFileName;
\r
1644 string fileRoot = m->getRootName(m->getSimpleName(sfftxtFilename));
\r
1645 if (fileRoot.length() > 0) {
\r
1647 fileRoot = fileRoot.substr(0, fileRoot.length()-1);
\r
1648 fileRoot = m->getRootName(fileRoot);
\r
1651 map<string, string> variables;
\r
1652 variables["[filename]"] = fileRoot;
\r
1653 string sfftxtFileName = getOutputFileName("sfftxt",variables);
\r
1654 string outFlowFileName = getOutputFileName("flow",variables);
\r
1655 if (!trim) { variables["[tag]"] = "raw"; }
\r
1656 outFastaFileName = getOutputFileName("fasta",variables);
\r
1657 outQualFileName = getOutputFileName("qfile",variables);
\r
1659 if (fasta) { m->openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
\r
1660 if (qual) { m->openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName); }
\r
1661 if (flow) { m->openOutputFile(outFlowFileName, outFlow); outputNames.push_back(outFlowFileName); outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName); }
\r
1663 //read common header
\r
1664 string commonHeader = m->getline(inSFF);
\r
1665 string magicNumber = m->getline(inSFF);
\r
1666 string version = m->getline(inSFF);
\r
1667 string indexOffset = m->getline(inSFF);
\r
1668 string indexLength = m->getline(inSFF);
\r
1669 int numReads = parseHeaderLineToInt(inSFF);
\r
1670 string headerLength = m->getline(inSFF);
\r
1671 string keyLength = m->getline(inSFF);
\r
1672 int numFlows = parseHeaderLineToInt(inSFF);
\r
1673 string flowgramCode = m->getline(inSFF);
\r
1674 string flowChars = m->getline(inSFF);
\r
1675 string keySequence = m->getline(inSFF);
\r
1680 if (flow) { outFlow << numFlows << endl; }
\r
1682 for(int i=0;i<numReads;i++){
\r
1685 if (inSFF.eof()) { m->mothurOut("[ERROR]: Expected " + toString(numReads) + " but reached end of file at " + toString(i+1) + "."); m->mothurOutEndLine(); break; }
\r
1689 //parse read header
\r
1691 seqName = seqName.substr(1);
\r
1693 header.name = seqName;
\r
1695 string runPrefix = parseHeaderLineToString(inSFF); header.timestamp = runPrefix;
\r
1696 string regionNumber = parseHeaderLineToString(inSFF); header.region = regionNumber;
\r
1697 string xyLocation = parseHeaderLineToString(inSFF); header.xy = xyLocation;
\r
1700 string runName = parseHeaderLineToString(inSFF);
\r
1701 string analysisName = parseHeaderLineToString(inSFF);
\r
1702 string fullPath = parseHeaderLineToString(inSFF);
\r
1705 string readHeaderLen = parseHeaderLineToString(inSFF); convert(readHeaderLen, header.headerLength);
\r
1706 string nameLength = parseHeaderLineToString(inSFF); convert(nameLength, header.nameLength);
\r
1707 int numBases = parseHeaderLineToInt(inSFF); header.numBases = numBases;
\r
1708 string clipQualLeft = parseHeaderLineToString(inSFF); convert(clipQualLeft, header.clipQualLeft);
\r
1709 int clipQualRight = parseHeaderLineToInt(inSFF); header.clipQualRight = clipQualRight;
\r
1710 string clipAdapLeft = parseHeaderLineToString(inSFF); convert(clipAdapLeft, header.clipAdapterLeft);
\r
1711 string clipAdapRight = parseHeaderLineToString(inSFF); convert(clipAdapRight, header.clipAdapterRight);
\r
1717 vector<unsigned short> flowVector = parseHeaderLineToFloatVector(inSFF, numFlows); read.flowgram = flowVector;
\r
1718 vector<unsigned int> flowIndices = parseHeaderLineToIntVector(inSFF, numBases);
\r
1720 //adjust for print
\r
1721 vector<unsigned int> flowIndicesAdjusted; flowIndicesAdjusted.push_back(flowIndices[0]);
\r
1722 for (int j = 1; j < flowIndices.size(); j++) { flowIndicesAdjusted.push_back(flowIndices[j] - flowIndices[j-1]); }
\r
1723 read.flowIndex = flowIndicesAdjusted;
\r
1725 string bases = parseHeaderLineToString(inSFF); read.bases = bases;
\r
1726 vector<unsigned int> qualityScores = parseHeaderLineToIntVector(inSFF, numBases); read.qualScores = qualityScores;
\r
1729 //if you have provided an accosfile and this seq is not in it, then dont print
\r
1730 bool print = true;
\r
1731 if (seqNames.size() != 0) { if (seqNames.count(header.name) == 0) { print = false; } }
\r
1735 if (fasta) { printFastaSeqData(outFasta, read, header); }
\r
1736 if (qual) { printQualSeqData(outQual, read, header); }
\r
1737 if (flow) { printFlowSeqData(outFlow, read, header); }
\r
1741 if((i+1) % 10000 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine(); }
\r
1743 if (m->control_pressed) { break; }
\r
1747 if (!m->control_pressed) { if((numReads) % 10000 != 0){ m->mothurOut(toString(numReads)); m->mothurOutEndLine(); } }
\r
1751 if (fasta) { outFasta.close(); }
\r
1752 if (qual) { outQual.close(); }
\r
1753 if (flow) { outFlow.close(); }
\r
1757 catch(exception& e) {
\r
1758 m->errorOut(e, "SffInfoCommand", "parseSffTxt");
\r
1762 //**********************************************************************************************************************
\r
1764 int SffInfoCommand::parseHeaderLineToInt(ifstream& file){
\r
1768 while (!file.eof()) {
\r
1770 char c = file.get();
\r
1780 catch(exception& e) {
\r
1781 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToInt");
\r
1787 //**********************************************************************************************************************
\r
1789 string SffInfoCommand::parseHeaderLineToString(ifstream& file){
\r
1793 while (!file.eof()) {
\r
1794 char c = file.get();
\r
1797 //m->gobble(file);
\r
1798 //text = m->getline(file);
\r
1807 catch(exception& e) {
\r
1808 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToString");
\r
1813 //**********************************************************************************************************************
\r
1815 vector<unsigned short> SffInfoCommand::parseHeaderLineToFloatVector(ifstream& file, int length){
\r
1817 vector<unsigned short> floatVector(length);
\r
1819 while (!file.eof()) {
\r
1820 char c = file.get();
\r
1823 for(int i=0;i<length;i++){
\r
1825 floatVector[i] = temp * 100;
\r
1831 return floatVector;
\r
1833 catch(exception& e) {
\r
1834 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToFloatVector");
\r
1839 //**********************************************************************************************************************
\r
1841 vector<unsigned int> SffInfoCommand::parseHeaderLineToIntVector(ifstream& file, int length){
\r
1843 vector<unsigned int> intVector(length);
\r
1845 while (!file.eof()) {
\r
1846 char c = file.get();
\r
1848 for(int i=0;i<length;i++){
\r
1849 file >> intVector[i];
\r
1857 catch(exception& e) {
\r
1858 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToIntVector");
\r
1862 //***************************************************************************************************************
\r
1864 bool SffInfoCommand::readOligos(string oligoFile){
\r
1866 filehandles.clear();
\r
1867 numSplitReads.clear();
\r
1868 filehandlesHeaders.clear();
\r
1870 bool allBlank = false;
\r
1871 oligosObject->read(oligoFile);
\r
1873 if (m->control_pressed) { return false; } //error in reading oligos
\r
1875 if (oligosObject->hasPairedBarcodes()) {
\r
1876 pairedOligos = true;
\r
1877 m->mothurOut("[ERROR]: sffinfo does not support paired barcodes and primers, aborting.\n"); m->control_pressed = true; return true;
\r
1879 pairedOligos = false;
\r
1880 numFPrimers = oligosObject->getPrimers().size();
\r
1881 numBarcodes = oligosObject->getBarcodes().size();
\r
1884 numLinkers = oligosObject->getLinkers().size();
\r
1885 numSpacers = oligosObject->getSpacers().size();
\r
1886 numRPrimers = oligosObject->getReversePrimers().size();
\r
1888 vector<string> groupNames = oligosObject->getGroupNames();
\r
1889 if (groupNames.size() == 0) { allBlank = true; }
\r
1891 filehandles.resize(oligosObject->getBarcodeNames().size());
\r
1892 for(int i=0;i<filehandles.size();i++){
\r
1893 for(int j=0;j<oligosObject->getPrimerNames().size();j++){ filehandles[i].push_back(""); }
\r
1897 set<string> uniqueNames; //used to cleanup outputFileNames
\r
1898 map<string, int> barcodes = oligosObject->getBarcodes() ;
\r
1899 map<string, int> primers = oligosObject->getPrimers();
\r
1900 for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
\r
1901 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
\r
1903 string primerName = oligosObject->getPrimerName(itPrimer->second);
\r
1904 string barcodeName = oligosObject->getBarcodeName(itBar->second);
\r
1906 if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
\r
1907 else if ((primerName == "") && (barcodeName == "")) { } //do nothing
\r
1909 string comboGroupName = "";
\r
1910 string fastaFileName = "";
\r
1911 string qualFileName = "";
\r
1912 string nameFileName = "";
\r
1913 string countFileName = "";
\r
1915 if(primerName == ""){
\r
1916 comboGroupName = barcodeName;
\r
1918 if(barcodeName == ""){
\r
1919 comboGroupName = primerName;
\r
1922 comboGroupName = barcodeName + "." + primerName;
\r
1927 map<string, string> variables;
\r
1928 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
\r
1929 variables["[group]"] = comboGroupName;
\r
1930 string thisFilename = getOutputFileName("sff",variables);
\r
1931 if (uniqueNames.count(thisFilename) == 0) {
\r
1932 outputNames.push_back(thisFilename);
\r
1933 outputTypes["sff"].push_back(thisFilename);
\r
1934 uniqueNames.insert(thisFilename);
\r
1937 filehandles[itBar->second][itPrimer->second] = thisFilename;
\r
1938 temp.open(thisFilename.c_str(), ios::binary); temp.close();
\r
1944 map<string, string> variables;
\r
1945 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
\r
1946 variables["[group]"] = "scrap";
\r
1947 noMatchFile = getOutputFileName("sff",variables);
\r
1948 m->mothurRemove(noMatchFile);
\r
1951 filehandlesHeaders.resize(filehandles.size());
\r
1952 numSplitReads.resize(filehandles.size());
\r
1953 for (int i = 0; i < filehandles.size(); i++) {
\r
1954 numSplitReads[i].resize(filehandles[i].size(), 0);
\r
1955 for (int j = 0; j < filehandles[i].size(); j++) {
\r
1956 filehandlesHeaders[i].push_back(filehandles[i][j]+"headers");
\r
1961 m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a split the sff file."); m->mothurOutEndLine();
\r
1969 catch(exception& e) {
\r
1970 m->errorOut(e, "SffInfoCommand", "readOligos");
\r
1974 //***************************************************************************************************************
\r
1976 bool SffInfoCommand::readGroup(string oligoFile){
\r
1978 filehandles.clear();
\r
1979 numSplitReads.clear();
\r
1980 filehandlesHeaders.clear();
\r
1982 groupMap = new GroupMap();
\r
1983 groupMap->readMap(oligoFile);
\r
1985 //like barcodeNameVector - no primer names
\r
1986 vector<string> groups = groupMap->getNamesOfGroups();
\r
1988 filehandles.resize(groups.size());
\r
1989 for (int i = 0; i < filehandles.size(); i++) {
\r
1990 for (int j = 0; j < 1; j++) {
\r
1992 map<string, string> variables;
\r
1993 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
\r
1994 variables["[group]"] = groups[i];
\r
1995 string thisFilename = getOutputFileName("sff",variables);
\r
1996 outputNames.push_back(thisFilename);
\r
1997 outputTypes["sff"].push_back(thisFilename);
\r
2000 m->openOutputFileBinary(thisFilename, temp); temp.close();
\r
2001 filehandles[i].push_back(thisFilename);
\r
2005 map<string, string> variables;
\r
2006 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
\r
2007 variables["[group]"] = "scrap";
\r
2008 noMatchFile = getOutputFileName("sff",variables);
\r
2009 m->mothurRemove(noMatchFile);
\r
2013 filehandlesHeaders.resize(groups.size());
\r
2014 numSplitReads.resize(filehandles.size());
\r
2015 for (int i = 0; i < filehandles.size(); i++) {
\r
2016 numSplitReads[i].resize(filehandles[i].size(), 0);
\r
2017 for (int j = 0; j < filehandles[i].size(); j++) {
\r
2019 string thisHeader = filehandles[i][j]+"headers";
\r
2020 m->openOutputFileBinary(thisHeader, temp); temp.close();
\r
2021 filehandlesHeaders[i].push_back(thisHeader);
\r
2028 catch(exception& e) {
\r
2029 m->errorOut(e, "SffInfoCommand", "readGroup");
\r
2034 //********************************************************************/
\r
2035 string SffInfoCommand::reverseOligo(string oligo){
\r
2037 string reverse = "";
\r
2039 for(int i=oligo.length()-1;i>=0;i--){
\r
2041 if(oligo[i] == 'A') { reverse += 'T'; }
\r
2042 else if(oligo[i] == 'T'){ reverse += 'A'; }
\r
2043 else if(oligo[i] == 'U'){ reverse += 'A'; }
\r
2045 else if(oligo[i] == 'G'){ reverse += 'C'; }
\r
2046 else if(oligo[i] == 'C'){ reverse += 'G'; }
\r
2048 else if(oligo[i] == 'R'){ reverse += 'Y'; }
\r
2049 else if(oligo[i] == 'Y'){ reverse += 'R'; }
\r
2051 else if(oligo[i] == 'M'){ reverse += 'K'; }
\r
2052 else if(oligo[i] == 'K'){ reverse += 'M'; }
\r
2054 else if(oligo[i] == 'W'){ reverse += 'W'; }
\r
2055 else if(oligo[i] == 'S'){ reverse += 'S'; }
\r
2057 else if(oligo[i] == 'B'){ reverse += 'V'; }
\r
2058 else if(oligo[i] == 'V'){ reverse += 'B'; }
\r
2060 else if(oligo[i] == 'D'){ reverse += 'H'; }
\r
2061 else if(oligo[i] == 'H'){ reverse += 'D'; }
\r
2063 else { reverse += 'N'; }
\r
2069 catch(exception& e) {
\r
2070 m->errorOut(e, "SffInfoCommand", "reverseOligo");
\r
2075 //**********************************************************************************************************************
\r