added get.repseqs command, started matrix output command

[mothur.git] / helpcommand.cpp

diff --git a/helpcommand.cpp b/helpcommand.cpp
index c259e1f065c5861c5fe337715bf5879e9709e1f9..a30caefd44e73df86b498b17ae28f6e671f1cb70 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -82,6 +82,22 @@ int HelpCommand::execute(){
                cout << "dist.seqs(fasta=yourFastaFile, calc=yourCalc, ends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
                cout << "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, ends=F, cutoff= 2.0, processors=3)." << "\n";
                cout << "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc)." << "\n" << "\n";
+       }else if (globaldata->helpRequest == "align.seqs") {
+               cout << "The align.seqs command reads a file containing sequences and creates an alignment file and a report file." << "\n";
+               cout << "The align.seqs command parameters are fasta, phylip, clustal, nexus, template, search, ksize, align, match, mismatch, gapopen and gapextend.  " << "\n";
+               cout << "You must use one of the following parameters for your candidate filename: fasta, phylip, clustal or nexus. " << "\n";
+               cout << "The template parameter is also required." << "\n";
+               cout << "The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer and blast. The default is suffix." << "\n";
+               cout << "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is blast." << "\n";
+               cout << "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 7." << "\n";
+               cout << "The match parameter allows you to specify the bonus for having the same base. The default is 1.0." << "\n";
+               cout << "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0." << "\n";
+               cout << "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -5.0." << "\n";
+               cout << "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -2.0." << "\n";
+               cout << "The align.seqs command should be in the following format: " << "\n";
+               cout << "align.seqs(fasta=yourFastaFile, template=yourTemplateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n";
+               cout << "Example align.seqs(fasta=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)" << "\n";
+               cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
        }else if (globaldata->helpRequest == "collect.single") {
                cout << "The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. " << "\n";
                cout << "The collect.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster." << "\n";
@@ -280,6 +296,17 @@ int HelpCommand::execute(){
                cout << "The default value for line and label are all lines in your inputfile." << "\n";
                cout << "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name." << "\n";
                cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
+       }else if (globaldata->helpRequest == "get.repseqs") { 
+               cout << "The get.repseqs command can only be executed after a successful read.otu command of a list file." << "\n";
+               cout << "The get.repseqs command parameters are fasta, name, group, line and label.  The fasta and group parameters are required, and you may not use line and label at the same time." << "\n";
+               cout << "The line and label allow you to select what distance levels you would like a output files created for, and are separated by dashes." << "\n";
+               cout << "The get.repseqss command should be in the following format: get.repseqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupfile, line=yourLines, label=yourLabels)." << "\n";
+               cout << "Example get.repseqs(fasta=amazon.fasta, group=amazon.groups, line=1-3-5, name=amazon.names)." << "\n";
+               cout << "The default value for line and label are all lines in your inputfile." << "\n";
+               cout << "The get.repseqs command outputs several .fasta files for each distance you specify.  " << "\n";
+               cout << "If the distance level you choose has bins that contain only sequences unique to a specific group those sequences are outputted to a file for that group." << "\n";
+               cout << "If the bin contains sequences from multiple groups then the bin is outputted to the shared fasta file." << "\n";
+               cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
        }else if (globaldata->helpRequest == "get.oturep") { 
                cout << "The get.oturep command can only be executed after a successful read.dist command." << "\n";
                cout << "The get.oturep command parameters are list, fasta, name, line and label.  The fasta and list parameters are required, and you may not use line and label at the same time." << "\n";