+++ /dev/null
-/*
- * chopseqscommand.cpp
- * Mothur
- *
- * Created by westcott on 5/10/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "chopseqscommand.h"
-#include "sequence.hpp"
-
-//**********************************************************************************************************************
-vector<string> ChopSeqsCommand::setParameters(){
- try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "",false,true); parameters.push_back(pnumbases);
- CommandParameter pcountgaps("countgaps", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcountgaps);
- CommandParameter pshort("short", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pshort);
- CommandParameter pkeep("keep", "Multiple", "front-back", "front", "", "", "",false,false); parameters.push_back(pkeep);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-
- vector<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string ChopSeqsCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences. Note: If a sequence is completely 'chopped', an accnos file will be created with the names of the sequences removed. \n";
- helpString += "The chop.seqs command parameters are fasta, numbases, countgaps and keep. fasta is required unless you have a valid current fasta file. numbases is required.\n";
- helpString += "The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n";
- helpString += "The numbases parameter allows you to specify the number of bases you want to keep.\n";
- helpString += "The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n";
- helpString += "The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n";
- helpString += "The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.\n";
- helpString += "For example, if you ran chop.seqs with numbases=200 and short=t, if a sequence had 100 bases mothur would keep the sequence rather than eliminate it.\n";
- helpString += "Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n";
- helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "getHelpString");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-ChopSeqsCommand::ChopSeqsCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["accnos"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-ChopSeqsCommand::ChopSeqsCommand(string option) {
- try {
- abort = false; calledHelp = false;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
-
- ValidParameters validParameter;
- map<string,string>::iterator it;
-
- //check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["accnos"] = tempOutNames;
-
- //if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false);
- if (inputDir == "not found"){ inputDir = ""; }
- else {
- string path;
- it = parameters.find("fasta");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["fasta"] = inputDir + it->second; }
- }
- }
-
- //check for required parameters
- fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { //if there is a current fasta file, use it
- fastafile = m->getFastaFile();
- if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setFastaFile(fastafile); }
-
- //if the user changes the output directory command factory will send this info to us in the output parameter
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
-
- string temp = validParameter.validFile(parameters, "numbases", false); if (temp == "not found") { temp = "0"; }
- m->mothurConvert(temp, numbases);
-
- temp = validParameter.validFile(parameters, "countgaps", false); if (temp == "not found") { temp = "f"; }
- countGaps = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "short", false); if (temp == "not found") { temp = "f"; }
- Short = m->isTrue(temp);
-
- keep = validParameter.validFile(parameters, "keep", false); if (keep == "not found") { keep = "front"; }
-
- 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; }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int ChopSeqsCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.fasta";
- string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.accnos";
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- ofstream outAcc;
- m->openOutputFile(outputFileNameAccnos, outAcc);
-
- ifstream in;
- m->openInputFile(fastafile, in);
-
- bool wroteAccnos = false;
-
- while (!in.eof()) {
-
- Sequence seq(in);
-
- if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputFileNameAccnos); return 0; }
-
- if (seq.getName() != "") {
- string newSeqString = getChopped(seq);
-
- //output trimmed sequence
- if (newSeqString != "") {
- out << ">" << seq.getName() << endl << newSeqString << endl;
- }else{
- outAcc << seq.getName() << endl;
- wroteAccnos = true;
- }
- }
- }
- in.close();
- out.close();
- outAcc.close();
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
-
- if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
- else { m->mothurRemove(outputFileNameAccnos); }
-
- m->mothurOutEndLine();
-
- //set fasta file as new current fastafile
- string current = "";
- itTypes = outputTypes.find("fasta");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
- }
-
- if (wroteAccnos) { //set accnos file as new current accnosfile
- itTypes = outputTypes.find("accnos");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
- }
- }
-
-
- return 0;
- }
-
- catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string ChopSeqsCommand::getChopped(Sequence seq) {
- try {
- string temp = seq.getAligned();
- string tempUnaligned = seq.getUnaligned();
-
- if (countGaps) {
- //if needed trim sequence
- if (keep == "front") {//you want to keep the beginning
- int tempLength = temp.length();
-
- if (tempLength > numbases) { //you have enough bases to remove some
-
- int stopSpot = 0;
- int numBasesCounted = 0;
-
- for (int i = 0; i < temp.length(); i++) {
- //eliminate N's
- if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
-
- numBasesCounted++;
-
- if (numBasesCounted >= numbases) { stopSpot = i; break; }
- }
-
- if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(0, stopSpot+1); }
-
- }else {
- if (!Short) { temp = ""; } //sequence too short
- }
- }else { //you are keeping the back
- int tempLength = temp.length();
- if (tempLength > numbases) { //you have enough bases to remove some
-
- int stopSpot = 0;
- int numBasesCounted = 0;
-
- for (int i = (temp.length()-1); i >= 0; i--) {
- //eliminate N's
- if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
-
- numBasesCounted++;
-
- if (numBasesCounted >= numbases) { stopSpot = i; break; }
- }
-
- if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(stopSpot+1); }
- }else {
- if (!Short) { temp = ""; } //sequence too short
- }
- }
-
- }else{
-
- //if needed trim sequence
- 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 numBasesCounted = 0;
-
- for (int i = 0; i < temp.length(); i++) {
- //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; }
- }
-
- if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(0, stopSpot+1); }
-
- }else {
- if (!Short) { temp = ""; } //sequence too short
- }
- }else { //you are keeping the back
- int tempLength = tempUnaligned.length();
- if (tempLength > numbases) { //you have enough bases to remove some
-
- int stopSpot = 0;
- int numBasesCounted = 0;
-
- for (int i = (temp.length()-1); i >= 0; i--) {
- //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; }
- }
-
- if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(stopSpot); }
- }else {
- if (!Short) { temp = ""; } //sequence too short
- }
- }
- }
-
- return temp;
- }
- catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "getChopped");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
projects / mothur.git / blobdiff