--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mosaics/R/generateWig.R	Thu Jan 10 16:01:28 2013 -0500
@@ -0,0 +1,181 @@
+
+# read alignment files and construct bin-level files
+
+generateWig <- function( infile=NULL, fileFormat=NULL, outfileLoc="./", 
+    byChr=FALSE, useChrfile=FALSE, chrfile=NULL, excludeChr=NULL, 
+    PET=FALSE, fragLen=200, span=200, capping=0, normConst=1, perl = "perl" )
+{   
+    # preprocessing perl script embedded in "mosaics/inst/Perl/"
+    
+    if ( PET == TRUE ) {
+        script <- "readfile2wig_PET.pl"
+        allFormat <- c( "eland_result", "sam" )
+        allFormatName <- c( "Eland result", "SAM" )
+    } else {
+        script <- "readfile2wig_SET.pl"
+        allFormat <- c( "eland_result", "eland_extended", "eland_export", 
+            "bowtie", "sam", "bed", "csem" )
+        allFormatName <- c( "Eland result", "Eland extended", "Eland export", 
+            "Bowtie default", "SAM", "BED", "CSEM" )
+    }
+    
+    # Check whether perl exists
+    
+    CMD <- paste( perl, "-v" )
+    res <- system( CMD, intern = TRUE, ignore.stderr = TRUE )
+  
+    if ( length(res) == 0 ) {
+        # cannot proceed if perl does not exist
+        
+        stop( "Perl is not found on your system! Either check $PATH if installed or please install Perl." )
+    } else {
+        # process read files into bin-level files if perl exists
+        
+        # check whether minimal options are missing
+        
+        if ( length(infile) != 1 || is.null(infile) )
+        {
+            stop( "Please specify the name of the aligned read file!" )
+        }       
+        
+        if ( length(fileFormat) != 1 || is.null(fileFormat) )
+        {
+            stop( "Please specify aligned read file format! Read '?generateWig' for supported file formats" )
+        }   
+        
+        # check file format specification
+        
+        if ( length(which(!is.na(match( fileFormat, allFormat )))) == 0 )
+        {
+            stop( "Unsupported aligned read file format! Read '?generateWig' for supported file formats" )
+        }
+        
+        # if useChrfile is TRUE & excludeChr is NOT null, then ignore excludeChr
+        
+        if ( useChrfile & !is.null(excludeChr) ) {
+            message( "User set 'useChrfile' as TRUE and also provided 'excludeChr'." )
+            message( "'excludeChr' argument will be ignored." )
+            excludeChr <- NULL
+        }
+        
+        # print out processing settings:
+        # by default, set fragment length = 200, bin size = fragment length, capping = 0.
+        
+        fileFormatName <- allFormatName[ match( fileFormat, allFormat ) ]
+        
+        cat( "------------------------------------------------------------\n" )
+        cat( "Info: setting summary\n" )
+        cat( "------------------------------------------------------------\n" )
+        cat( "Name of aligned read file:", infile, "\n" )
+        cat( "Aligned read file format:", fileFormatName, "\n" )
+        cat( "Directory of processed wig files:", outfileLoc, "\n" )
+        cat( "span of the wig files:", span, "\n" )
+        cat( "Normalizing constant:", normConst, "\n" )
+        cat( "Construct wig files by chromosome?", ifelse(byChr,"Y","N"), "\n" ) 
+        cat( "Is file for chromosome info provided?", ifelse(useChrfile,"Y","N"), "\n" )   
+        if ( useChrfile == TRUE ) {
+            cat( "Name of file for chromosome info: ", chrfile, "\n" )
+        }
+        if ( !is.null(excludeChr) ) {
+            cat( "List of chromosomes to be excluded:", paste(excludeChr,collapse=", "), "\n" )
+        }
+        if ( PET == FALSE ) {
+            cat( "Data type: Single-end tag (SET)\n" )
+            cat( "Average fragment length:", fragLen, "\n" )
+        } else {
+            cat( "Data type: Paired-end tag (PET)\n" )
+        }
+        if ( capping > 0 ) {
+            cat( "Maximum number of reads allowed in each nucleotide:", capping, "\n" )
+        }
+        cat( "------------------------------------------------------------\n" )
+        
+        
+        # get path to the perl code (unified script for all file formats)
+        
+        Fn.Path <- system.file( file.path("Perl",script), package="mosaics")
+        
+        
+        # process read file to bin-level files using perl codes
+        
+        message( "Info: reading the aligned read file and processing it into bin-level files..." )
+        
+        if ( capping <= 0 ) {
+            capping <- 0
+        }
+        if ( is.null(excludeChr) ) {
+            excludeChrVec <- ""
+        } else {
+            excludeChrVec <- paste( excludeChr, collapse=" " )
+        }
+        
+        if ( PET == TRUE ) {
+            CMD <- paste( perl, 
+                " ", Fn.Path,
+                " ", infile, 
+                " ", outfileLoc, 
+                " ", fileFormat,
+                " ", span, 
+                " ", normConst,
+                " ", capping,
+                " ", ifelse(byChr,"Y","N"),
+                " ", ifelse(useChrfile,"Y","N"),
+                " ", ifelse(!is.null(chrfile),chrfile,"-"),
+                " ", paste(excludeChrVec,collpase=" "), sep="" )
+        } else {    
+            CMD <- paste( perl, 
+                " ", Fn.Path,
+                " ", infile, 
+                " ", outfileLoc, 
+                " ", fileFormat, 
+                " ", span,
+                " ", normConst,
+                " ", fragLen,
+                " ", capping, 
+                " ", ifelse(byChr,"Y","N"),
+                " ", ifelse(useChrfile,"Y","N"),
+                " ", ifelse(!is.null(chrfile),chrfile,"-"),
+                " ", paste(excludeChrVec,collpase=" "), sep="" )
+        }
+        
+        res <- system( CMD, intern = TRUE )
+        
+        message( "Info: done!" )   
+            
+        
+        # print out processing results
+        
+        infilename <- basename( infile )
+            # extract only filename from infile
+        
+        if ( PET == TRUE ) {    
+            if ( byChr ) {
+                outfileName <- list.files( path=outfileLoc,
+                    pattern=paste(infilename,"_span",span,"_.*.wig",sep="") )
+            } else {
+                outfileName <- paste(infilename,"_span",span,".wig",sep="")
+            }
+        } else {
+            if ( byChr ) {
+                outfileName <- list.files( path=outfileLoc,
+                    pattern=paste(infilename,"_fragL",fragLen,"_span",span,"_.*.wig",sep="") )
+            } else {
+                outfileName <- paste(infilename,"_fragL",fragLen,"_span",span,".wig",sep="")
+            }
+        }
+        
+        cat( "------------------------------------------------------------\n" )
+        cat( "Info: processing summary\n" )
+        cat( "------------------------------------------------------------\n" )    
+        cat( "Directory of processed wig files:", outfileLoc, "\n" )
+        if ( byChr ) {
+            cat( "List of processed wig files:\n" )
+            for ( i in 1:length(outfileName) ) {                
+                cat( "- ",outfileName[i],"\n", sep="" )
+            }
+        } else {
+            cat( "Processed wig file: ",outfileName,"\n", sep="" )   
+        }
+        cat( "------------------------------------------------------------\n" )
+    }
+}