From 3604ddb078ae09215ec1ddc2b8c183232e3b5f89 Mon Sep 17 00:00:00 2001 From: westcott Date: Mon, 14 Jun 2010 18:28:12 +0000 Subject: [PATCH] modified chop.seqs --- chopseqscommand.cpp | 103 +++++++++++++++++++----------------------- chopseqscommand.h | 8 ++-- removeseqscommand.cpp | 6 +-- 3 files changed, 54 insertions(+), 63 deletions(-) diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp index 47f151d..536aec9 100644 --- a/chopseqscommand.cpp +++ b/chopseqscommand.cpp @@ -21,7 +21,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option) { else { //valid paramters for this command - string Array[] = {"fasta","end","fromend","outputdir","inputdir"}; + string Array[] = {"fasta","numbases","keep","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -57,14 +57,12 @@ ChopSeqsCommand::ChopSeqsCommand(string option) { if (fastafile == "not open") { abort = true; } else if (fastafile == "not found") { m->mothurOut("You must provide a fasta file."); m->mothurOutEndLine(); abort = true; } - string temp = validParameter.validFile(parameters, "end", false); if (temp == "not found") { temp = "0"; } - convert(temp, end); + string temp = validParameter.validFile(parameters, "numbases", false); if (temp == "not found") { temp = "0"; } + convert(temp, numbases); - temp = validParameter.validFile(parameters, "fromend", false); if (temp == "not found") { temp = "0"; } - convert(temp, fromend); + keep = validParameter.validFile(parameters, "keep", false); if (keep == "not found") { keep = "front"; } - if ((end == 0) && (fromend == 0)) { m->mothurOut("You must provide either end or fromend for the chops.seqs command."); m->mothurOutEndLine(); abort = true; } - if ((end != 0) && (fromend != 0)) { m->mothurOut("You must provide either end or fromend for the chops.seqs command, not both."); m->mothurOutEndLine(); abort = true; } + if (numbases == 0) { m->mothurOut("You must provide the number of bases you want to keep for the chops.seqs command."); m->mothurOutEndLine(); abort = true; } } } @@ -78,11 +76,11 @@ ChopSeqsCommand::ChopSeqsCommand(string option) { void ChopSeqsCommand::help(){ try { m->mothurOut("The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences.\n"); - m->mothurOut("The chop.seqs command parameters are fasta, end and fromend, fasta is required.\n"); - m->mothurOut("The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, end=yourEnd).\n"); - m->mothurOut("The end parameter allows you to specify an end base position for your sequences, default = 0.\n"); - m->mothurOut("The fromend parameter allows you to remove the last X bases from the end of the sequence, default = 0.\n"); - m->mothurOut("Example chop.seqs(fasta=amazon.fasta, end=200).\n"); + m->mothurOut("The chop.seqs command parameters are fasta, numbases, and keep. fasta and numbases are required required.\n"); + m->mothurOut("The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n"); + m->mothurOut("The numbases parameter allows you to specify the number of bases you want to keep.\n"); + m->mothurOut("The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n"); + m->mothurOut("Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n"); m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); } catch(exception& e) { @@ -119,12 +117,7 @@ int ChopSeqsCommand::execute(){ if (m->control_pressed) { in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0; } if (seq.getName() != "") { - string newSeqString = ""; - if (seq.getIsAligned()) { //sequence is aligned - newSeqString = getChoppedAligned(seq); - }else{ - newSeqString = getChoppedUnaligned(seq); - } + string newSeqString = getChopped(seq); //output trimmed sequence if (newSeqString != "") { @@ -157,62 +150,60 @@ int ChopSeqsCommand::execute(){ } } //********************************************************************************************************************** -string ChopSeqsCommand::getChoppedUnaligned(Sequence seq) { - try { - string temp = seq.getUnaligned(); - - //if needed trim sequence - if (end != 0) { - if (temp.length() > end) { temp = temp.substr(0, end); } - else { temp = ""; } - }else { //you are using fromend - if (temp.length() > fromend) { temp = temp.substr(0, (temp.length()-fromend)); } - else { temp = ""; } //sequence too short - } - - return temp; - } - catch(exception& e) { - m->errorOut(e, "ChopSeqsCommand", "getChoppedUnaligned"); - exit(1); - } -} -//********************************************************************************************************************** -string ChopSeqsCommand::getChoppedAligned(Sequence seq) { +string ChopSeqsCommand::getChopped(Sequence seq) { try { string temp = seq.getAligned(); string tempUnaligned = seq.getUnaligned(); //if needed trim sequence - if (end != 0) { - if (tempUnaligned.length() > end) { //you have enough bases to remove some + if (keep == "front") {//you want to keep the beginning + int tempLength = tempUnaligned.length(); + + if (tempLength > numbases) { //you have enough bases to remove some int stopSpot = 0; - int numBases = 0; + int numBasesCounted = 0; for (int i = 0; i < temp.length(); i++) { - if(isalpha(temp[i])) { numBases++; } - - if (numBases >= end) { stopSpot = i; break; } + //eliminate N's + if (toupper(temp[i]) == 'N') { + temp[i] == '.'; + tempLength--; + if (tempLength < numbases) { stopSpot = 0; break; } + } + + if(isalpha(temp[i])) { numBasesCounted++; } + + if (numBasesCounted >= numbases) { stopSpot = i; break; } } - temp = temp.substr(0, stopSpot); + if (stopSpot == 0) { temp = ""; } + else { temp = temp.substr(0, stopSpot); } + }else { temp = ""; } //sequence too short - }else { //you are using fromend - - if (tempUnaligned.length() > fromend) { + }else { //you are keeping the back + int tempLength = tempUnaligned.length(); + if (tempLength > numbases) { //you have enough bases to remove some int stopSpot = 0; - int numBases = 0; + int numBasesCounted = 0; for (int i = (temp.length()-1); i >= 0; i--) { - if(isalpha(temp[i])) { numBases++; } + //eliminate N's + if (toupper(temp[i]) == 'N') { + temp[i] == '.'; + tempLength--; + if (tempLength < numbases) { stopSpot = 0; break; } + } + + if(isalpha(temp[i])) { numBasesCounted++; } - if (numBases >= fromend) { stopSpot = i; break; } + if (numBasesCounted >= numbases) { stopSpot = i; break; } } - - temp = temp.substr(0, stopSpot); + + if (stopSpot == 0) { temp = ""; } + else { temp = temp.substr(stopSpot+1); } } else { temp = ""; } //sequence too short } @@ -220,7 +211,7 @@ string ChopSeqsCommand::getChoppedAligned(Sequence seq) { return temp; } catch(exception& e) { - m->errorOut(e, "ChopSeqsCommand", "getChoppedUnaligned"); + m->errorOut(e, "ChopSeqsCommand", "getChopped"); exit(1); } } diff --git a/chopseqscommand.h b/chopseqscommand.h index 2da134e..b6af154 100644 --- a/chopseqscommand.h +++ b/chopseqscommand.h @@ -24,12 +24,12 @@ class ChopSeqsCommand : public Command { void help(); private: - string fastafile, outputDir; + string fastafile, outputDir, keep; bool abort; - int end, fromend; + int numbases; + + string getChopped(Sequence); - string getChoppedAligned(Sequence); - string getChoppedUnaligned(Sequence); }; #endif diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp index 5f5fe65..35d9bea 100644 --- a/removeseqscommand.cpp +++ b/removeseqscommand.cpp @@ -334,7 +334,7 @@ int RemoveSeqsCommand::readName(){ string name, firstCol, secondCol; bool wroteSomething = false; - + int numSeqsInNames = 0; while(!in.eof()){ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } @@ -359,7 +359,7 @@ int RemoveSeqsCommand::readName(){ validSecond.push_back(parsedNames[i]); } } - + numSeqsInNames += parsedNames.size(); if ((dups) && (validSecond.size() != parsedNames.size())) { //if dups is true and we want to get rid of anyone, get rid of everyone for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); } }else { @@ -394,7 +394,7 @@ int RemoveSeqsCommand::readName(){ } in.close(); out.close(); - +cout << "your names file contains " << numSeqsInNames << endl; if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); remove(outputFileName.c_str()); -- 2.39.2