# HG changeset patch
# User devteam
# Date 1406561418 14400
# Node ID 263a3b92368b5f14a7b36d042361e846353e1e0b
Imported from capsule None
diff -r 000000000000 -r 263a3b92368b first_matrix_generator_example_file.png
Binary file first_matrix_generator_example_file.png has changed
diff -r 000000000000 -r 263a3b92368b generate_matrix_for_pca_lda.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_matrix_for_pca_lda.pl Mon Jul 28 11:30:18 2014 -0400
@@ -0,0 +1,147 @@
+#!/usr/bin/perl -w
+
+use strict;
+use warnings;
+
+my $Input_Matrix = $ARGV[0];
+my $Input_Label = $ARGV[1];
+
+my %Hash_X = ();
+my %Hash_Y = ();
+my $My_Num_X = 0;
+my $My_Num_Y = 0;
+
+open (OUT, "> $ARGV[2]");
+
+open (LABEL, "< $Input_Label") ||
+ die "Sorry, I couldn't open the escape.txt for clone: $!\n";
+
+my $Label_Index = 0;
+my $X_Label;
+my $input_Label;
+while (defined($input_Label = <LABEL>)){
+ chomp($input_Label);
+ my @cArray_Label = $input_Label =~ /(\S+)\s*/g;
+ if ($input_Label =~ /\w/){
+ if ($Label_Index == 0){
+ $Hash_X{$cArray_Label[0]} = $cArray_Label[1];
+ $X_Label = $cArray_Label[1];
+ $Label_Index = 1;
+ }else{
+ if ($cArray_Label[1] eq $X_Label){
+ $Hash_X{$cArray_Label[0]} = $cArray_Label[1];
+ }else{
+ $Hash_Y{$cArray_Label[0]} = $cArray_Label[1];
+ }
+ }
+ }
+}
+close(LABEL);
+
+open (MATRIX, "< $Input_Matrix") ||
+ die "Sorry, I couldn't open the escape.txt for clone: $!\n";
+
+my %Hash_Matrix = ();
+my %Hash_Features = ();
+my @cArray_Features = ();
+
+my %Hash_Sum = ();
+my $Matrix_Index = 0;
+my $input_Matrix;
+while (defined($input_Matrix = <MATRIX>)){
+ chomp($input_Matrix);
+ my @cArray_Matrix = $input_Matrix =~ /(\S+)\s*/g;
+ if ($input_Matrix =~ /\w/){
+ if ($Matrix_Index == 0){
+ @cArray_Features = @cArray_Matrix;
+ my $Temp_Num_Array = scalar(@cArray_Matrix);
+ my $Temp_Index = 0;
+ for(;$Temp_Index < $Temp_Num_Array; $Temp_Index++){
+ $Hash_Features{$cArray_Matrix[$Temp_Index]} = "BOL";
+ $Hash_Sum{$cArray_Matrix[$Temp_Index]} = 0;
+ }
+ $Matrix_Index = 1;
+ }else{
+ $Hash_Matrix{$cArray_Matrix[0]} = $input_Matrix;
+ }
+ }
+}
+close(MATRIX);
+
+my $Trace_Key;
+
+foreach $Trace_Key (sort {$a cmp $b} keys %Hash_X){
+ my @cArray_Trace_X = $Hash_Matrix{$Trace_Key} =~ /(\S+)\s*/g;
+ my $Num_Array_Feature_X = scalar(@cArray_Features);
+ my $Index_Feature_X = 0;
+ for(;$Index_Feature_X < $Num_Array_Feature_X; $Index_Feature_X++){
+ if ($Hash_Features{$cArray_Features[$Index_Feature_X]} eq "BOL"){
+ $Hash_Features{$cArray_Features[$Index_Feature_X]} = $cArray_Trace_X[$Index_Feature_X + 1];
+ }else{
+ $Hash_Features{$cArray_Features[$Index_Feature_X]} = $Hash_Features{$cArray_Features[$Index_Feature_X]} . "\t" . $cArray_Trace_X[$Index_Feature_X + 1];
+ }
+
+ $Hash_Sum{$cArray_Features[$Index_Feature_X]} += $cArray_Trace_X[$Index_Feature_X + 1];
+ }
+ $My_Num_X ++;
+}
+
+my $Append_Key;
+foreach $Append_Key (keys %Hash_Features){
+ $Hash_Features{$Append_Key} = $Hash_Features{$Append_Key} . "\t" . $Hash_Sum{$Append_Key};
+ $Hash_Sum{$Append_Key} = 0;
+}
+
+foreach $Trace_Key (sort {$a cmp $b} keys %Hash_Y){
+ my @cArray_Trace_Y = $Hash_Matrix{$Trace_Key} =~ /(\S+)\s*/g;
+ my $Num_Array_Feature_Y = scalar(@cArray_Features);
+ my $Index_Feature_Y = 0;
+ for(;$Index_Feature_Y < $Num_Array_Feature_Y; $Index_Feature_Y++){
+ if ($Hash_Features{$cArray_Features[$Index_Feature_Y]} eq "BOL"){
+ $Hash_Features{$cArray_Features[$Index_Feature_Y]} = $cArray_Trace_Y[$Index_Feature_Y + 1];
+ }else{
+ $Hash_Features{$cArray_Features[$Index_Feature_Y]} = $Hash_Features{$cArray_Features[$Index_Feature_Y]} . "\t" . $cArray_Trace_Y[$Index_Feature_Y + 1];
+ }
+
+ $Hash_Sum{$cArray_Features[$Index_Feature_Y]} += $cArray_Trace_Y[$Index_Feature_Y + 1];
+ }
+ $My_Num_Y ++;
+}
+
+foreach $Append_Key (keys %Hash_Features){
+ $Hash_Features{$Append_Key} = $Hash_Features{$Append_Key} . "\t" . $Hash_Sum{$Append_Key} . "\t" . "EOL";
+}
+
+my $Prt_Key;
+print OUT " \t";
+foreach $Prt_Key (sort {$a cmp $b} keys %Hash_X){
+ print OUT "$Prt_Key \t";
+}
+print OUT "X(SUM) \t";
+
+foreach $Prt_Key (sort {$a cmp $b} keys %Hash_Y){
+ print OUT "$Prt_Key \t";
+}
+print OUT "Y(SUM) \t";
+print OUT "\n";
+
+my $Prt_Index = 0;
+my $Prt_Array_Num = scalar (@cArray_Features);
+for(;$Prt_Index < $Prt_Array_Num; $Prt_Index++){
+ print OUT "$cArray_Features[$Prt_Index] \t$Hash_Features{$cArray_Features[$Prt_Index]}\n";
+}
+
+print OUT " \t";
+my $My_Label_Index = 0;
+for(;$My_Label_Index < $My_Num_X; $My_Label_Index++){
+ print OUT "X \t";
+}
+print OUT " \t";
+
+$My_Label_Index = 0;
+for(;$My_Label_Index < $My_Num_Y; $My_Label_Index++){
+ print OUT "Y \t";
+}
+print OUT " \t\n";
+
+close(OUT);
diff -r 000000000000 -r 263a3b92368b generate_matrix_for_pca_lda.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_matrix_for_pca_lda.xml Mon Jul 28 11:30:18 2014 -0400
@@ -0,0 +1,48 @@
+<tool id="generate_matrix_for_pca_and_lda1" name="Generate A Matrix" version="1.0.0">
+ <description>for using PC and LDA</description>
+ <command interpreter="perl">generate_matrix_for_pca_lda.pl $input_1 $input_2 $output</command>
+
+ <inputs>
+ <param format="tabular" name="input_1" type="data" label="Source file First: a matrix (samples/observations in rows and variables/features in columns)"> </param>
+ <param format="tabular" name="input_2" type="data" label="Source file Second: a table (samples/observations with response/class label)"> </param>
+ </inputs>
+
+ <outputs>
+ <data format="tabular" name="output" />
+ </outputs>
+
+ <tests>
+ <test>
+ <param name="input_1" value="matrix_generator_for_pc_and_lda_input_1.tabular"/>
+ <param name="input_2" value="matrix_generator_for_pc_and_lda_input_2.tabular"/>
+ <output name="output" file="matrix_generator_for_pc_and_lda_output.tabular"/>
+ </test>
+ </tests>
+
+ <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool consists of a module to generate a matrix to be used for running the Linear Discriminant Analysis as described in Carrel et al., 2006 (PMID: 17009873)
+
+*Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, et al. (2006) Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome. PLoS Genet 2(9): e151. doi:10.1371/journal.pgen.0020151*
+
+-----
+
+**Example**
+
+- Input file (Source file First)
+
+.. image:: tools/lda/first_matrix_generator_example_file.png
+
+
+- Input file (Source file Second)
+
+.. image:: tools/lda/second_matrix_generator_example_file.png
+
+
+</help>
+
+</tool>
diff -r 000000000000 -r 263a3b92368b second_matrix_generator_example_file.png
Binary file second_matrix_generator_example_file.png has changed
diff -r 000000000000 -r 263a3b92368b test-data/matrix_generator_for_pc_and_lda_input_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix_generator_for_pc_and_lda_input_1.tabular Mon Jul 28 11:30:18 2014 -0400
@@ -0,0 +1,88 @@
+ CTCAGAAAAAAA CCATCCATCCATCCATCC AGAGGGAGAGGG ATCTGTTGATGG AGGGGTGACAGA ATCCCATTTACA AAGGGTATCAGT ATAATATATACA TATTATATGTATA CATCATCATCATCA CCCCATGATCCA TGATTCCTTAAAGAA AACACTTGGACA TATTAATATAATTTATAAA ATGTTTATTTTA TATCCAGGAGAA CAATTCTCCTGCC ACCATAAAAATGAGAAC CTCAGCCATAAAAA ATGAGTGAGAATAT ACTGTGAGTCAA TAAACTAAAGAGCTTCTGCACAGCA TCCTTTGGGTATAT ATGCTGCTATAAAGACACATGCACAC TGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTG TCCACAATGGTTGAA TTGGCTGCATAAAT CAATGGAACAGAACAGAGCCCTCAGAAATAA GAACTAGAAATACCATTTGACCCAGC TCAAAGATCAGAT GACCCATCTCACACCAGTTAGAATG CAAAGAGAATAAAATACCTAGGTATTTTATTCTTTTT AAAATGGCCATACTGCCCAAG AAATTTTTCCAATTCTGTGAAGAAA TTCACAATAGCAAAGAC TAGGAAGAATCAATA CTGGGTATATACCCAGTAATGG TTGGAAGTTCTGGCCAGGGCAA TGAAGGACCTCTTCAAGGAGAACTACAAACCACTGCTCAA CTCTCACCACTCCTATTCAACATA ACACACACATAT CCATGAGCATGGAATGTTCT AACCCAAATGTCC TTTACAAGAAAAAAACAAACAACCCCA AGTTCTAGATCC CTGGAAGCATTCCCTTT GATCCCATTTGTC GATATGAACAGACA TGGGTTTGTCATA AGTTTCTTTTGC AATTACCCAGTCT TCATGTCATCTGCAAACA AAAACTCTCAAT CAACTTCAGCAA ATTGGCTGTGGGTTT AATTAGATCCCA GACCTAAAACCA AGAATCTACAAT AAACCAAACACC GGAGTTCCAGACCAGCCT CCTTGCCCATGCC ATCATACTGAAT AGGAAGTCAAATT AGCAAACCACCA AGCATGATTTATA GAGAGCCAAATCATGAGTG AAAGAGCCAAAT AGCAATTGTGAATGG CACTATTCACAATTGC TCAGGATACAAAATCAATG CAATGAACTCAAACAAATT TCCAACAAAGGACATGAACTCATC AATTGAACAATGAGAACATGTGGTAT AACCACAATGAGAACA GTGTATATATATACAT ACATATATATAT GTCAGATGGATA TCATCTGACAAAGGGCTAATATCCAG TTTGTCAGGTTTGTCAAAG TTCTTAATCCAGTCTATCATT TTTAATCCATCTTGA AAACTACCATCAGAGTGAACAGGCA GCCATCAGAGAAAT ACAGGCAACCTACA GCAACCTACTCA TAGAAAACCCCAT
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diff -r 000000000000 -r 263a3b92368b test-data/matrix_generator_for_pc_and_lda_input_2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix_generator_for_pc_and_lda_input_2.tabular Mon Jul 28 11:30:18 2014 -0400
@@ -0,0 +1,87 @@
+ARHGEF9 XLMR
+KIAA2022 XLMR
+ZDHHC15 XLMR
+PGK1 XLMR
+BRWD3 XLMR
+PAK3 XLMR
+AGTR2 XLMR
+GRIA3 XLMR
+ZDHHC9 XLMR
+GPC3 XLMR
+PHF6 XLMR
+SOX3 XLMR
+FMR1 XLMR
+MTM1 XLMR
+SHROOM4 XLMR
+KLF8 XLMR
+UXT XLMR
+PCSK1N XLMR
+PAGE1 XLMR
+PAGE4 XLMR
+CLCN5 XLMR
+NUDT10 XLMR
+NUDT11 XLMR
+GSPT2 XLMR
+TMEM29 XLMR
+GPR173 XLMR
+HUWE1 XLMR
+TSR2 XLMR
+TRO XLMR
+MAGEH1 XLMR
+USP51 XLMR
+RRAGB XLMR
+UBQLN2 CONTROL
+SPIN3 CONTROL
+SPIN2A CONTROL
+ZXDA CONTROL
+SPIN4 CONTROL
+MTMR8 CONTROL
+KIAA1166 CONTROL
+LAS1L CONTROL
+MSN CONTROL
+HEPH CONTROL
+AR CONTROL
+STARD8 CONTROL
+TMEM28 CONTROL
+EDA CONTROL
+SLC7A3 CONTROL
+CXCR3 CONTROL
+NAP1L2 CONTROL
+CHIC1 CONTROL
+FXYD8 CONTROL
+RNF12 CONTROL
+UPRT CONTROL
+MAGEE2 CONTROL
+CXorf26 CONTROL
+MAGEE1 CONTROL
+FGF16 CONTROL
+TAF9B CONTROL
+CYSLTR1 CONTROL
+ZCCHC5 CONTROL
+GPR23 CONTROL
+P2RY10 CONTROL
+ITM2A CONTROL
+TBX22 CONTROL
+NSBP1 CONTROL
+RPS6KA6 CONTROL
+HDX CONTROL
+APOOL CONTROL
+ZNF711 CONTROL
+POF1B CONTROL
+CHM CONTROL
+DACH2 CONTROL
+KLHL4 CONTROL
+CPXCR1 CONTROL
+PABPC5 CONTROL
+DIAPH2 CONTROL
+SYTL4 CONTROL
+CSTF2 CONTROL
+DRP2 CONTROL
+TCEAL2 CONTROL
+BEX5 CONTROL
+NXF3 CONTROL
+BEX4 CONTROL
+TCEAL4 CONTROL
+ESX1 CONTROL
+IL1RAPL2 CONTROL
+NRK CONTROL
diff -r 000000000000 -r 263a3b92368b test-data/matrix_generator_for_pc_and_lda_output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix_generator_for_pc_and_lda_output.tabular Mon Jul 28 11:30:18 2014 -0400
@@ -0,0 +1,88 @@
+ AGTR2 ARHGEF9 BRWD3 CLCN5 FMR1 GPC3 GPR173 GRIA3 GSPT2 HUWE1 KIAA2022 KLF8 MAGEH1 MTM1 NUDT10 NUDT11 PAGE1 PAGE4 PAK3 PCSK1N PGK1 PHF6 RRAGB SHROOM4 SOX3 TMEM29 TRO TSR2 USP51 UXT ZDHHC15 ZDHHC9 X(SUM) APOOL AR BEX4 BEX5 CHIC1 CHM CPXCR1 CSTF2 CXCR3 CXorf26 CYSLTR1 DACH2 DIAPH2 DRP2 EDA ESX1 FGF16 FXYD8 GPR23 HDX HEPH IL1RAPL2 ITM2A KIAA1166 KLHL4 LAS1L MAGEE1 MAGEE2 MSN MTMR8 NAP1L2 NRK NSBP1 NXF3 P2RY10 PABPC5 POF1B RNF12 RPS6KA6 SLC7A3 SPIN2A SPIN3 SPIN4 STARD8 SYTL4 TAF9B TBX22 TCEAL2 TCEAL4 TMEM28 UBQLN2 UPRT ZCCHC5 ZNF711 ZXDA Y(SUM)
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