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changeset 0:6ff325b36382 draft

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Imported from capsule None
author devteam
date Tue, 01 Apr 2014 09:11:53 -0400
parents
children 3fde957695f6
files tables_arithmetic_operations.pl tables_arithmetic_operations.xml test-data/numericalTable1.tabular test-data/table_addition_result.tabular test-data/table_division_result.tabular test-data/table_multiplication_result.tabular test-data/table_subtraction_result.tabular
diffstat 7 files changed, 262 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tables_arithmetic_operations.pl	Tue Apr 01 09:11:53 2014 -0400
@@ -0,0 +1,117 @@
+# A program to implement arithmetic operations on tabular files data. The program takes three inputs:
+# The first input is a TABULAR format file containing numbers only.
+# The second input is a TABULAR format file containing numbers only.
+# The two files must have the same number of columns and the same number of rows
+# The third input is an arithmetic operation: +, -, *, or / for addition, subtraction, multiplication, or division, respectively 
+# The output file is a TABULAR format file containing the result of implementing the arithmetic operation on both input files.
+# The output file has the same number of columns and the same number of rows as each of the two input files.
+# Note: in case of division, none of the values in the second input file could be 0.
+
+use strict;
+use warnings;
+
+#variables to handle information of the first input tabular file
+my $lineData1 = "";
+my @lineDataArray1 = ();
+my $lineArraySize = 0;
+my $lineCounter1 = 0;
+
+#variables to handle information of the second input tabular file
+my $lineData2= "";
+my @lineDataArray2 = ();
+my $lineCounter2 = 0;
+
+my $result = 0;
+
+# check to make sure having the correct number of arguments
+my $usage = "usage: tables_arithmetic_operations.pl [TABULAR.in] [TABULAR.in] [ArithmeticOperation] [TABULAR.out] \n";
+die $usage unless @ARGV == 4;
+
+#variables to store the names of input and output files
+my $inputTabularFile1 = $ARGV[0];
+my $inputTabularFile2 = $ARGV[1];
+my $arithmeticOperation = $ARGV[2];
+my $outputTabularFile = $ARGV[3];
+
+#open the input and output files
+open (INPUT1, "<", $inputTabularFile1) || die("Could not open file $inputTabularFile1 \n"); 
+open (INPUT2, "<", $inputTabularFile2) || die("Could not open file $inputTabularFile2 \n"); 
+open (OUTPUT, ">", $outputTabularFile) || die("Could not open file $outputTabularFile \n");
+
+#store the first input file in the array @motifsFrequencyData1
+my @tabularData1 = <INPUT1>;
+	
+#store the second input file in the array @motifsFrequencyData2
+my @tabularData2 = <INPUT2>;
+
+#reset the $lineCounter1 to 0	
+$lineCounter1 = 0;
+
+#iterated through the lines of the first input file 
+INDEL1:
+foreach $lineData1 (@tabularData1){
+	chomp ($lineData1);
+	$lineCounter1++;
+	
+	#reset the $lineCounter2 to 0
+	$lineCounter2 = 0;
+	
+	#iterated through the lines of the second input file 
+	foreach $lineData2 (@tabularData2){
+		chomp ($lineData2);
+		$lineCounter2++;
+
+		#check if the two motifs are the same in the two input files
+		if ($lineCounter1 == $lineCounter2){
+			
+			@lineDataArray1 = split(/\t/, $lineData1);
+			@lineDataArray2 = split(/\t/, $lineData2);
+			
+			$lineArraySize = @lineDataArray1;
+			
+			for (my $index = 0; $index < $lineArraySize; $index++){
+				
+				if ($arithmeticOperation eq "Addition"){
+					#compute the additin of both values
+					$result = $lineDataArray1[$index] + $lineDataArray2[$index];
+				}
+				
+				if ($arithmeticOperation eq "Subtraction"){
+					#compute the subtraction of both values
+					$result = $lineDataArray1[$index] - $lineDataArray2[$index];
+				}	
+				
+				if ($arithmeticOperation eq "Multiplication"){
+					#compute the multiplication of both values
+					$result = $lineDataArray1[$index] * $lineDataArray2[$index];
+				}
+				
+				if ($arithmeticOperation eq "Division"){
+					
+					#check if the denominator is 0
+					if ($lineDataArray2[$index] != 0){
+						#compute the division of both values
+						$result = $lineDataArray1[$index] / $lineDataArray2[$index];
+					}
+					else{
+						die("A denominator could not be zero \n"); 
+					}
+				}
+				
+				#store the result in the output file
+				if ($index < $lineArraySize - 1){
+					print OUTPUT $result . "\t";
+				}
+				else{
+					print OUTPUT $result . "\n";
+				}
+			}
+			next INDEL1;
+		}
+	}
+}	 
+
+#close the input and output files
+close(OUTPUT);
+close(INPUT2);
+close(INPUT1);
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tables_arithmetic_operations.xml	Tue Apr 01 09:11:53 2014 -0400
@@ -0,0 +1,105 @@
+<tool id="tables_arithmetic_operations" name="Arithmetic Operations " version="1.0.0">
+  <description>on tables</description>
+  
+  <command interpreter="perl">
+  	tables_arithmetic_operations.pl $inputFile1 $inputFile2 $inputArithmeticOperation3 $outputFile1
+  </command>
+
+  <inputs>
+  	<param format="tabular" name="inputFile1" type="data" label="Select the first input tabular file"/>
+  	<param format="tabular" name="inputFile2" type="data" label="Select the second input tabular file"/>
+  	
+    <param name="inputArithmeticOperation3" type="select" label="Choose the arithmetic operation:">
+    	<option value="Addition">Addition</option>
+      	<option value="Subtraction">Subtraction</option>
+      	<option value="Multiplication">Multiplication</option>
+      	<option value="Division">Division</option>
+    </param>
+  </inputs>
+  
+  <outputs>
+    <data format="tabular" name="outputFile1"/>
+  </outputs>
+  
+  <tests>
+  	<test>
+  		<param name="inputFile1" value="numericalTable1.tabular" />
+  		<param name="inputFile2" value="numericalTable1.tabular" />
+    	<param name="inputArithmeticOperation3" value="Addition" />
+    	<output name="outputFile1" file="table_addition_result.tabular" />
+  	</test>
+  	
+  	<test>
+  		<param name="inputFile1" value="numericalTable1.tabular" />
+  		<param name="inputFile2" value="numericalTable1.tabular" />
+    	<param name="inputArithmeticOperation3" value="Subtraction" />
+    	<output name="outputFile1" file="table_subtraction_result.tabular" />
+  	</test>
+  	
+  	<test>
+  		<param name="inputFile1" value="numericalTable1.tabular" />
+  		<param name="inputFile2" value="numericalTable1.tabular" />
+    	<param name="inputArithmeticOperation3" value="Multiplication" />
+    	<output name="outputFile1" file="table_multiplication_result.tabular" />
+  	</test>
+  	
+  	<test>
+  		<param name="inputFile1" value="numericalTable1.tabular" />
+  		<param name="inputFile2" value="numericalTable1.tabular" />
+    	<param name="inputArithmeticOperation3" value="Division" />
+    	<output name="outputFile1" file="table_division_result.tabular" />
+  	</test>
+  	
+  </tests>
+  
+  
+  <help> 
+
+.. class:: infomark
+
+**What it does**
+
+This program implements arithmetic operations on tabular files data. The program takes three inputs:
+
+- The first input is a TABULAR format file containing numbers only.
+- The second input is a TABULAR format file containing numbers only.
+- The third input is an arithmetic operation: +, -, x, or / for addition, subtraction, multiplication, or division, respectively. 
+- The output file is a TABULAR format file containing the result of implementing the arithmetic operation on both input files.
+
+
+Notes: 
+
+- The two files must have the same number of columns and the same number of rows.
+- The output file has the same number of columns and the same number of rows as each of the two input files.
+- In case of division, none of the values in the second input file could be 0, otherwise the program will stop and report an error.
+
+**Example**
+
+Let us have the first input file as follows::
+
+	5	4	0
+	10	11	12
+	1	3	1
+	1	2	1
+	2	0	4
+	
+And the second input file as follows::
+
+	5	4	4
+	2	5	8
+	1	2	1
+	3	2	5
+	2	4	4
+
+Running the program and choosing "Addition" as an arithmetic operation will give the following output::
+
+	10	8	4
+	12	16	20
+	2	5	2
+	4	4	6
+	4	4	8
+
+
+  </help>  
+  
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/numericalTable1.tabular	Tue Apr 01 09:11:53 2014 -0400
@@ -0,0 +1,8 @@
+5	4	4	5	4	5	6	6
+10	11	12	14	15	14	19	23
+1	1	1	1	1	1	1	1
+1	2	1	2	2	1	4	3
+2	4	4	5	4	4	5	5
+3	1	2	1	1	2	3	3
+6	7	5	1	1	2	2	2
+4	4	4	5	8	7	6	6
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/table_addition_result.tabular	Tue Apr 01 09:11:53 2014 -0400
@@ -0,0 +1,8 @@
+10	8	8	10	8	10	12	12
+20	22	24	28	30	28	38	46
+2	2	2	2	2	2	2	2
+2	4	2	4	4	2	8	6
+4	8	8	10	8	8	10	10
+6	2	4	2	2	4	6	6
+12	14	10	2	2	4	4	4
+8	8	8	10	16	14	12	12
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/table_division_result.tabular	Tue Apr 01 09:11:53 2014 -0400
@@ -0,0 +1,8 @@
+1	1	1	1	1	1	1	1
+1	1	1	1	1	1	1	1
+1	1	1	1	1	1	1	1
+1	1	1	1	1	1	1	1
+1	1	1	1	1	1	1	1
+1	1	1	1	1	1	1	1
+1	1	1	1	1	1	1	1
+1	1	1	1	1	1	1	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/table_multiplication_result.tabular	Tue Apr 01 09:11:53 2014 -0400
@@ -0,0 +1,8 @@
+25	16	16	25	16	25	36	36
+100	121	144	196	225	196	361	529
+1	1	1	1	1	1	1	1
+1	4	1	4	4	1	16	9
+4	16	16	25	16	16	25	25
+9	1	4	1	1	4	9	9
+36	49	25	1	1	4	4	4
+16	16	16	25	64	49	36	36
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/table_subtraction_result.tabular	Tue Apr 01 09:11:53 2014 -0400
@@ -0,0 +1,8 @@
+0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0