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fix of custom substitution matrices in ClustalW; version number bumped to 1.11.1

Ulrich Bodenhofer authored on 23/04/2018 11:29:24
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@@ -1,8 +1,8 @@
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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.11.0
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-Date: 2017-04-17
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+Version: 1.11.1
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+Date: 2018-04-23
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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@@ -154,7 +154,7 @@ msaClustalW <- function(inputSeqs,
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             params[["substitutionMatrixIsStringFlag"]] <- FALSE
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             params[["substitutionMatrixIsDefaultFlag"]] <- TRUE
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-            params[["dnamatrix"]] <- substitutionMatrix
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+            params[["pwdnamatrix"]] <- substitutionMatrix
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             substitutionMatrix <- "default"
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         }
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     } else {
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@@ -334,8 +334,7 @@ msaClustalW <- function(inputSeqs,
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     ###########
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     # convert #
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-    ###########
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-    ##output the input sequences in a different file format.
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+    ###########    ##output the input sequences in a different file format.
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     params[["convert"]] <- checkLogicalParams("convert", params, FALSE)
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     ##delete param in copy
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@@ -655,7 +654,7 @@ msaClustalW <- function(inputSeqs,
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     } else {
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         posVal <- c("iub", "clustalw")
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         params[["pwdnamatrix"]] <- checkSingleValParamsNew("pwdnamatrix",
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-                                    params, posVal)
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+                                                           params, posVal)
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     }
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     ##delete param in copy
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@@ -729,16 +728,16 @@ msaClustalW <- function(inputSeqs,
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     #############
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     ##DNA weight matrix=IUB, CLUSTALW or filename
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-    ##if filename (seperated with ".") check and use file;
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+    ##if filename (separated with ".") check and use file;
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     ##else check whether value is iub or clustalw;
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     ##if nothing is given, use iub
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     if (!is.null(params[["dnamatrix"]]) &&
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             grepl("\\.", params[["dnamatrix"]], perl=TRUE)) {
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         checkInFile("dnamatrix", params)
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-    } else {
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+    } else if (is.null(params[["pwdnamatrix"]])) {
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         posVal <- c("iub", "clustalw")
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-        params[["dnamatrix"]] <- checkSingleValParamsNew("dnamatrix",
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-                                    params, posVal)
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+        params[["pwdnamatrix"]] <- checkSingleValParamsNew("dnamatrix",
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+                                                           params, posVal)
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     }
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     ##delete param in copy
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@@ -1,6 +1,24 @@
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 Change history of package msa:
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 ==============================
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+Version 1.12.0:
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+- release as part of Bioconductor 3.7
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+
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+Version 1.11.1:
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+- fix of code for using custom substitution matrices in ClustalW
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+
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+Version 1.11.0:
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+- new branch for Bioconductor 3.7 devel
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+
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+Version 1.10.0:
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+- release as part of Bioconductor 3.6
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+
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+Version 1.9.0:
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+- new branch for Bioconductor 3.6 devel
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+
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+Version 1.8.0:
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+- release as part of Bioconductor 3.5
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+
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 Version 1.7.2:
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 - fix for new clang 4 compiler on Mac OS
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@@ -116,6 +116,16 @@ SEXP RClustalW(SEXP rInputSeqs,
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             args.push_back(std::string(numiter));
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         }
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+        //type
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+        if (!Rf_isNull(rType)) {
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+            string type = as<string>(rType);
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+            string autoType = "auto";
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+            //clustalW don't know type == "rna"
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+            if (autoType.compare(type) != 0 && type != "rna") {
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+                args.push_back(" TYPE=" + type);
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+            }
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+        }
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+
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         //rSubstitutionMatrix
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         bool defaultFlag = false;
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         if (hasClustalWEntry(rparam, "substitutionMatrixIsDefaultFlag")) {
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@@ -127,8 +137,13 @@ SEXP RClustalW(SEXP rInputSeqs,
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         }
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         if (defaultFlag) {
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-            //do nothing
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-            Rprintf("use default substitution matrix\n");
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+            if (hasClustalWEntry(rparam, "pwdnamatrix")) {
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+		string pwDnaMat = as<string>(rparam["pwdnamatrix"]);
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+		Rprintf("use DNA substitution matrix: %s\n", pwDnaMat.c_str());
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+	    }
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+	    else {
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+		Rprintf("use default substitution matrix\n");
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+	    }
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         } else if (stringFlag) {
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             /*FIXME TODO change hardcoded rows and numbers*/
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             string inputMatrixFile = as<string>(rSubstitutionMatrix);
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@@ -145,16 +160,6 @@ SEXP RClustalW(SEXP rInputSeqs,
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             input.substitutionMatrix = substitutionMatrix;
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         }
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-        //type
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-        if (!Rf_isNull(rType)) {
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-            string type = as<string>(rType);
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-            string autoType = "auto";
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-            //clustalW don't know type == "rna"
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-            if (autoType.compare(type) != 0 && type != "rna") {
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-                args.push_back(" TYPE=" + type);
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-            }
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-        }
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-
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         //verbose
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         bool verbose = false;
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         if (!Rf_isNull(rVerbose)) {
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@@ -465,6 +470,10 @@ SEXP RClustalW(SEXP rInputSeqs,
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             string pwdnamatrix = as<string>(rparam["pwdnamatrix"]);
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             args.push_back(" PWDNAMATRIX=" + pwdnamatrix);
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         }
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+	else if (hasClustalWEntry(rparam, "dnamatrix")) {
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+            string pwdnamatrix = as<string>(rparam["dnamatrix"]);
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+            args.push_back(" PWDNAMATRIX=" + pwdnamatrix);
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+	}
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         //params$pwgapext
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         if (hasClustalWEntry(rparam, "pwgapext")) {
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@@ -889,6 +889,14 @@ bibliography below).
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 \section{Change Log}
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 \begin{description}
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+\item[Version 1.12.0:] release as part of Bioconductor 3.7
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+\item[Version 1.11.1:] \mbox{ }  \begin{itemize}
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+   \item fix of code for using custom substitution matrices in ClustalW
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+  \end{itemize}
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+\item[Version 1.11.0:] new branch for Bioconductor 3.7 devel
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+\item[Version 1.10.0:] release as part of Bioconductor 3.56
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+\item[Version 1.9.0:] new branch for Bioconductor 3.6 devel
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+\item[Version 1.8.0:] release as part of Bioconductor 3.5
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 \item[Version 1.7.2:] \mbox{ }  \begin{itemize}
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    \item fix for new \verb+clang+ 4 compiler on Mac OS
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   \end{itemize}