# HG changeset patch
# User deepakjadmin
# Date 1452089661 18000
# Node ID 1b8c54b9de559445b3b70d2b806988fe46d0dc7c
# Parent 64c804de0681020dc3d0740af46a373454fe9dd7
Uploaded
diff -r 64c804de0681 -r 1b8c54b9de55 addact.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/addact.xml Wed Jan 06 09:14:21 2016 -0500
@@ -0,0 +1,29 @@
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+"Merge data files of Active and Inactive compounds "
+tool2/addact.pl $Input1 $Activity1 $Input2 $Activity2 $Merged_file
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+Provide descriptor files of active/positive and inactive/negative molecules and assign them properly.
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diff -r 64c804de0681 -r 1b8c54b9de55 padelnew.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/padelnew.xml Wed Jan 06 09:14:21 2016 -0500
@@ -0,0 +1,76 @@
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+"PaDEL Descriptor Calculation Tool"
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+#if '.smi' in $input.name
+/bin/mkdir $input.extra_files_path;
+ln -s $input $input.extra_files_path/molecule.smi;
+/usr/bin/java -jar PaDEL-Descriptor.jar -dir $input.extra_files_path/molecule.smi -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate $fingerprint $retainorder -file $descriptor -log > $log ;
+/bin/rm -rf $input.extra_files_path;
+#else
+/usr/bin/java -jar PaDEL-Descriptor.jar -dir $input -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate $fingerprint $retainorder -file $descriptor -log >$log
+#end if
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+Input may be any sdf,smile or mol2 file and output file will be in CSV format.
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diff -r 64c804de0681 -r 1b8c54b9de55 removeduplecate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/removeduplecate.xml Wed Jan 06 09:14:21 2016 -0500
@@ -0,0 +1,13 @@
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+"Removes Repeated Entry From File"
+tool3/removeduplecate.R $Input1 $Non_redudant_mega_file
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+run command with Descriptor file and in csv format only .output file will be in CSV format.
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diff -r 64c804de0681 -r 1b8c54b9de55 tool2/addact.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool2/addact.pl Wed Jan 06 09:14:21 2016 -0500
@@ -0,0 +1,25 @@
+#!/usr/bin/perl
+use warnings;
+use strict;
+open(FH,$ARGV[0]) or die "Couldn't open file, $!";
+open(DH,">$ARGV[4]") or die "Couldn't open file, $!";
+my $first_line = scalar ;
+chomp($first_line);
+$first_line = join(",",$first_line,"outcome\n");
+print DH $first_line;
+while(){chomp($_);
+my $line= join(",",$_,"$ARGV[1]\n");
+print DH $line;
+}
+close FH;
+open(SH,$ARGV[2]) or die "Coudn't open file,$!";
+scalar ;
+while(){
+if($ARGV[1] ne $ARGV[3]){chomp($_);
+my $line1= join(",",$_,"$ARGV[3]\n");
+print DH $line1;
+}
+else{ print ("There is error to assign activity\n");exit;}
+}
+close SH;
+close DH;
diff -r 64c804de0681 -r 1b8c54b9de55 tool2/addact.pl.copy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool2/addact.pl.copy Wed Jan 06 09:14:21 2016 -0500
@@ -0,0 +1,25 @@
+#!/usr/bin/perl
+use warnings;
+use strict;
+open(FH,$ARGV[0]) or die "Couldn't open file, $!";
+open(DH,">tmp.txt") or die "Couldn't open file, $!";
+my $first_line = scalar ;
+chomp($first_line);
+$first_line = join(",",$first_line,"outcome\n");
+print DH $first_line;
+while(){chomp($_);
+my $line= join(",",$_,"$ARGV[1]\n");
+print DH $line;
+}
+close FH;
+open(SH,$ARGV[2]) or die "Coudn't open file,$!";
+scalar ;
+while(){
+if($ARGV[1] ne $ARGV[3]){chomp($_);
+my $line1= join(",",$_,"$ARGV[3]\n");
+print DH $line1;
+}
+else{ print ("There is error to assign activity\n");exit;}
+}
+close SH;
+close DH;
diff -r 64c804de0681 -r 1b8c54b9de55 tool3/removeduplecate.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool3/removeduplecate.R Wed Jan 06 09:14:21 2016 -0500
@@ -0,0 +1,11 @@
+args <- commandArgs(TRUE)
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+res1 <- read.csv(args[1])
+#res11 <- duplicated(res1[,1:length(res1) - 1])
+res11 <- duplicated(res1[,1])
+result <- res1[!res11,]
+names1 <- result[,1]
+rownames(result) <- names1
+result$Name <- NULL
+write.csv(result,file=args[2])
diff -r 64c804de0681 -r 1b8c54b9de55 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Jan 06 09:14:21 2016 -0500
@@ -0,0 +1,21 @@
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+ http://www.yapcwsoft.com/dd/padeldescriptor/PaDEL-Descriptor.zip
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+ .
+ $INSTALL_DIR/bin/
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+ $INSTALL_DIR/bin
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