//**********************************************************************************************************************
-AlignCommand::AlignCommand(string option){
+AlignCommand::AlignCommand(string option) {
try {
- // globaldata = GlobalData::getInstance();
+
abort = false;
//allow user to run help
templateFileName = validParameter.validFile(parameters, "template", true);
if (templateFileName == "not found") {
- mothurOut("template is a required parameter for the align.seqs command.");
- mothurOutEndLine();
+ m->mothurOut("template is a required parameter for the align.seqs command.");
+ m->mothurOutEndLine();
abort = true;
}else if (templateFileName == "not open") { abort = true; }
candidateFileName = validParameter.validFile(parameters, "candidate", false);
- if (candidateFileName == "not found") { mothurOut("candidate is a required parameter for the align.seqs command."); mothurOutEndLine(); abort = true; }
+ if (candidateFileName == "not found") { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true; }
else {
splitAtDash(candidateFileName, candidateFileNames);
ifstream in;
ableToOpen = openInputFile(candidateFileNames[i], in);
if (ableToOpen == 1) {
- mothurOut(candidateFileNames[i] + " will be disregarded."); mothurOutEndLine();
+ m->mothurOut(candidateFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
//erase from file list
candidateFileNames.erase(candidateFileNames.begin()+i);
i--;
}
//make sure there is at least one valid file left
- if (candidateFileNames.size() == 0) { mothurOut("no valid files."); mothurOutEndLine(); abort = true; }
+ if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
//check for optional parameter and set defaults
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "AlignCommand");
+ m->errorOut(e, "AlignCommand", "AlignCommand");
exit(1);
}
}
void AlignCommand::help(){
try {
- mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
- mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
- mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
- mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.\n");
- mothurOut("The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
- mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
- mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
- mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
- mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
- mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
- mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold. The default is false.\n");
- mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.\n");
- mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
- mothurOut("The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.\n");
- mothurOut("The align.seqs command should be in the following format: \n");
- mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
- mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n");
- mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
+ m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
+ m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
+ m->mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
+ m->mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.\n");
+ m->mothurOut("The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
+ m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
+ m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
+ m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
+ m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
+ m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
+ m->mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold. The default is false.\n");
+ m->mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.\n");
+ m->mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
+ m->mothurOut("The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.\n");
+ m->mothurOut("The align.seqs command should be in the following format: \n");
+ m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
+ m->mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "help");
+ m->errorOut(e, "AlignCommand", "help");
exit(1);
}
}
else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
else if(align == "noalign") { alignment = new NoAlign(); }
else {
- mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
- mothurOutEndLine();
+ m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+ m->mothurOutEndLine();
alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
}
+ vector<string> outputNames;
for (int s = 0; s < candidateFileNames.size(); s++) {
- mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); mothurOutEndLine();
+ m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
if (outputDir == "") { outputDir += hasPath(candidateFileNames[s]); }
string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
//delete accnos file if its blank else report to user
- if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); }
+ if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
else {
- mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
+ m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
if (!flip) {
- mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
- }else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
- mothurOutEndLine();
+ m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
+ }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
+ m->mothurOutEndLine();
}
}
else{
appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
remove(nonBlankAccnosFiles[h].c_str());
}
- mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
+ m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
if (!flip) {
- mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
- }else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
- mothurOutEndLine();
+ m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
+ }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
+ m->mothurOutEndLine();
}else{ hasAccnos = false; }
}
#else
//delete accnos file if its blank else report to user
if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
else {
- mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
+ m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
if (!flip) {
- mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
- }else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
- mothurOutEndLine();
+ m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
+ }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
+ m->mothurOutEndLine();
}
#endif
- mothurOut("Output File Names: " + alignFileName + ", " + reportFileName);
- if (hasAccnos) { mothurOut(", " + accnosFileName + "."); }
- else { mothurOut("."); }
- mothurOutEndLine();
-
- mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
- mothurOutEndLine();
- mothurOutEndLine();
+ outputNames.push_back(alignFileName);
+ outputNames.push_back(reportFileName);
+ if (hasAccnos) { outputNames.push_back(accnosFileName); }
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
+ m->mothurOutEndLine();
+ m->mothurOutEndLine();
}
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "execute");
+ m->errorOut(e, "AlignCommand", "execute");
exit(1);
}
}
delete candidateSeq;
//report progress
- if((i+1) % 100 == 0){ mothurOut(toString(i+1)); mothurOutEndLine(); }
+ if((i+1) % 100 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine(); }
}
//report progress
- if((line->numSeqs) % 100 != 0){ mothurOut(toString(line->numSeqs)); mothurOutEndLine(); }
+ if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine(); }
alignmentFile.close();
inFASTA.close();
return 1;
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "driver");
+ m->errorOut(e, "AlignCommand", "driver");
exit(1);
}
}
}else if (pid == 0){
driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
exit(0);
- }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
//force parent to wait until all the processes are done
#endif
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "createProcesses");
+ m->errorOut(e, "AlignCommand", "createProcesses");
exit(1);
}
}
output.close();
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "appendAlignFiles");
+ m->errorOut(e, "AlignCommand", "appendAlignFiles");
exit(1);
}
}
output.close();
}
catch(exception& e) {
- errorOut(e, "AlignCommand", "appendReportFiles");
+ m->errorOut(e, "AlignCommand", "appendReportFiles");
exit(1);
}
}
projects / mothur.git / blobdiff