From a8c74e7c7283b5bd04d4bd084a28f0c32992416d Mon Sep 17 00:00:00 2001 From: pschloss Date: Thu, 4 Jun 2009 15:32:33 +0000 Subject: [PATCH] modified filter.seqs to not store all seqs in memory but to read off disc --- Mothur.xcodeproj/project.pbxproj | 20 ++-- filterseqscommand.cpp | 192 ++++++++++++++++--------------- filterseqscommand.h | 12 +- 3 files changed, 116 insertions(+), 108 deletions(-) diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index ec6d06c..2bdb5b9 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -189,8 +189,8 @@ 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = matrixoutputcommand.cpp; sourceTree = SOURCE_ROOT; }; 370B88050F8A4EE4005AB382 /* getoturepcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getoturepcommand.h; sourceTree = SOURCE_ROOT; }; 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */ = {isa = PBXFileReference; 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sourceTree = SOURCE_ROOT; }; 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = SOURCE_ROOT; }; 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = SOURCE_ROOT; }; 37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = SOURCE_ROOT; }; diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp index e8c96b3..e493cbf 100644 --- a/filterseqscommand.cpp +++ b/filterseqscommand.cpp @@ -12,18 +12,13 @@ /**************************************************************************************/ FilterSeqsCommand::FilterSeqsCommand(){ + globaldata = GlobalData::getInstance(); if(globaldata->getFastaFile() == "") { cout << "You must enter a fasta formatted file" << endl; } trump = globaldata->getTrump()[0]; -// vertical = -// readSeqs->read(); -// db = readSeqs->getDB(); -// numSeqs = db->size(); -// -// alignmentLength = db->get(0).getAlignLength(); -// -// filter = string(alignmentLength, '1'); + numSeqs = 0; + } /**************************************************************************************/ @@ -36,82 +31,66 @@ void FilterSeqsCommand::doHard() { ifstream fileHandle; openInputFile(hardName, fileHandle); - fileHandle >> hardFilter; + fileHandle >> filter; + +} + +/**************************************************************************************/ + +void FilterSeqsCommand::doTrump(Sequence seq) { - if(hardFilter.length() != filter.length()){ - cout << "The hard filter is not the same length as the alignment: Hard filter will not be applied." << endl; - } - else{ - filter = hardFilter; + string curAligned = seq.getAligned(); + + for(int j = 0; j < alignmentLength; j++) { + if(curAligned[j] == trump){ + filter[j] = '0'; + } } } /**************************************************************************************/ -void FilterSeqsCommand::doTrump(Sequence seq) { +void FilterSeqsCommand::doVertical() { + for(int i=0;iget(i).getAligned();; -// -// for(int j = 0; j < alignmentLength; j++) { -// if(curAligned[j] == trump){ -// filter[j] = '0'; -// } -// } -// } - } /**************************************************************************************/ -void FilterSeqsCommand::doVertical(Sequence seq) { - -// vector counts(alignmentLength, 0); -// -// for(int i = 0; i < numSeqs; i++) { -// string curAligned = db->get(i).getAligned();; -// -// for(int j = 0; j < alignmentLength; j++) { -// if(curAligned[j] == '-' || curAligned[j] == '.'){ -// counts[j]++; -// } -// } -// } -// for(int i=0;i= threshold) { keep = 1; } + else if(t[i] >= threshold) { keep = 1; } + else if(g[i] >= threshold) { keep = 1; } + else if(c[i] >= threshold) { keep = 1; } + + if(keep == 0) { filter[i] = 0; } + } + } /**************************************************************************************/ -void FilterSeqsCommand::doSoft(Sequence seq) { - -// int softThreshold = numSeqs * (float)atoi(globaldata->getSoft().c_str()) / 100.0; -// -// vector a(alignmentLength, 0); -// vector t(alignmentLength, 0); -// vector g(alignmentLength, 0); -// vector c(alignmentLength, 0); -// vector x(alignmentLength, 0); -// -// for(int i=0;iget(i).getAligned();; -// -// for(int j=0;jgetSoft() != "" || isTrue(globaldata->getVertical())){ + a.assign(alignmentLength, 0); + t.assign(alignmentLength, 0); + g.assign(alignmentLength, 0); + c.assign(alignmentLength, 0); + gap.assign(alignmentLength, 0); + } + if(globaldata->getSoft() != ""){ + soft = (float)atoi(globaldata->getSoft().c_str()) / 100.0; + } if(globaldata->getHard().compare("") != 0) { doHard(); } else { filter = string(alignmentLength, '1'); } - while(!inFASTA.eof()){ - Sequence seq(inFASTA); - if(globaldata->getTrump().compare("") != 0) { doTrump(seq); } - if(isTrue(globaldata->getVertical()) == 1) { doVertical(seq); } -// if(globaldata->getSoft().compare("") != 0) { doSoft(seq); } - numSeqs++; + + if(globaldata->getTrump().compare("") != 0 || isTrue(globaldata->getVertical()) || globaldata->getSoft().compare("") != 0){ + + while(!inFASTA.eof()){ + Sequence seq(inFASTA); + if(globaldata->getTrump().compare("") != 0) { doTrump(seq); } + if(isTrue(globaldata->getVertical()) || globaldata->getSoft().compare("") != 0){ getFreqs(seq); } + numSeqs++; + cout.flush(); + } + } + inFASTA.close(); - ofstream outfile; - string filterFile = getRootName(globaldata->inputFileName) + "filter"; - openOutputFile(filterFile, outfile); + if(isTrue(globaldata->getVertical()) == 1) { doVertical(); } + if(globaldata->getSoft().compare("") != 0) { doSoft(); } - outfile << filter << endl; - outfile.close(); + ofstream outFilter; + string filterFile = getRootName(globaldata->inputFileName) + "filter"; + openOutputFile(filterFile, outFilter); + outFilter << filter << endl; + outFilter.close(); + + openInputFile(globaldata->getFastaFile(), inFASTA); string filteredFasta = getRootName(globaldata->inputFileName) + "filter.fasta"; - openOutputFile(filteredFasta, outfile); - -// for(int i=0;iget(i).getAligned(); -// outfile << '>' << db->get(i).getName() << endl; -// for(int j=0;j' << seq.getName() << endl << filterSeq << endl; + numSeqs++; + gobble(inFASTA); + } + outFASTA.close(); + inFASTA.close(); + int filteredLength = 0; for(int i=0;i a, t, g, c, gap; }; #endif -- 2.39.5