# HG changeset patch # User gkumar09 # Date 1443492156 14400 # Node ID 0845cefc6cfe0b1f592a438e1d894270d750ace0 # Parent ecf8be6538f84485d498cc22cb44714e33d779dc Deleted selected files diff -r ecf8be6538f8 -r 0845cefc6cfe Final/alignreads.xml --- a/Final/alignreads.xml Mon Sep 28 22:02:25 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,138 +0,0 @@ - - - alignReads: short read alignment tool wrapper - - trinity - - - - trinityToolWrapper.py util/alignReads.pl --target $target -o alignment --aligner $aligner_selection.aligner - - - ## Inputs. - #if str($inputs.paired_or_single) == "paired": - --left $inputs.left_input --right $inputs.right_input - #if $inputs.left_input.ext == 'fa': - --seqType fa - #else: - --seqType fq - #end if - #if str($inputs.library_type) != "None": - --SS_lib_type $inputs.library_type - #end if - --max_dist_between_pairs $inputs.max_dist_between_pairs - #else: - --single $inputs.input - #if str($inputs.input.ext) == 'fa': - --seqType fa - #else: - --seqType fq - #end if - #if str($inputs.library_type) != "None": - --SS_lib_type $inputs.library_type - #end if - #end if - - ## Additional parameters. - ##if str($inputs.use_additional) == "yes": - ## -- $inputs.additional_params - ##end if - - - ## direct to output - > outCapture.txt - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - .. _Trinity: http://trinityrnaseq.sourceforge.net - - diff -r ecf8be6538f8 -r 0845cefc6cfe Final/analyze_diff_exp.xml --- a/Final/analyze_diff_exp.xml Mon Sep 28 22:02:25 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ - - - Analyze differential expression - - trinity - - - - analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - .. _Trinity: http://trinityrnaseq.sourceforge.net - - diff -r ecf8be6538f8 -r 0845cefc6cfe Final/analyze_diff_exp_wrapper.py --- a/Final/analyze_diff_exp_wrapper.py Mon Sep 28 22:02:25 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,63 +0,0 @@ -import sys, os, subprocess - -TRINITY_BASE_DIR = "" -if os.environ.has_key('TRINITY_HOME'): - TRINITY_BASE_DIR = os.environ['TRINITY_HOME']; -else: - sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this"); - sys.exit() - -usage= "usage: " + sys.argv[0] + " " + "edgeR.tar.gz " + "TMM_normalized_FPKM_matrix " + "P-value " + "C-value" -print sys.argv -print usage -print " " - -if len(sys.argv)<5: - print "Require atleast two parameters" -else: - print "All good- command going ahead" -print " " - -Normalized_Matrix=sys.argv[2] -Pvalue=sys.argv[3] -Cvalue=sys.argv[4] - -def run_command(cmd): - print "The command used: " + cmd - pipe= subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE) - pipe.wait() - ret= pipe.returncode - if ret: - print "command died: " + str(ret) - print pipe.stderr.readlines() - sys.exit(1) - else: - return -print " " - -Final_tar_gz= "edgeR.tar.gz" -run_command("cp "+ sys.argv[1] + " " + "Final_tar_gz") -run_command("tar -xvf " + "Final_tar_gz") -run_command("mv " + "edgeR_results" + "/* ." ) - -# run the analyze command -cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " + Normalized_Matrix + " -P " + Pvalue + " -C " + Cvalue -run_command(cmd) - -origMatrixName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix" -# diffExpr.P0.001_C2.0.matrix -run_command("mv " + origMatrixName + " diffExpr.matrix") - -SampleCorName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor.dat" -# diffExpr.P0.001_C2.0.matrix.log2.sample_cor.dat -run_command("mv " + SampleCorName + " diffExpr.matrix.log2.sample_cor.dat") - -CorMatrix= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor_matrix.pdf" -# diffExpr.P0.001_C2.0.matrix.log2.sample_cor_matrix.pdf -run_command("mv " + CorMatrix + " diffExpr.matrix.log2.sample_cor_matrix.pdf") - -Heatmap= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.centered.genes_vs_samples_heatmap.pdf" -#diffExpr.P0.001_C2.0.matrix.log2.centered.genes_vs_samples_heatmap.pdf -run_command("mv " + Heatmap + " diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf") - -sys.exit(0) diff -r ecf8be6538f8 -r 0845cefc6cfe Final/cat.xml --- a/Final/cat.xml Mon Sep 28 22:02:25 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ - - tail-to-head - - bash_command_executer.py cat - $input1 - #for $q in $queries - ${q.input2} - #end for - > $out_file1 - - - - - - - - - - - - - - - - - - - - - no help - - - diff -r ecf8be6538f8 -r 0845cefc6cfe Final/diffExpress_edgeR.xml --- a/Final/diffExpress_edgeR.xml Mon Sep 28 22:02:25 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ - - - Identify Differentially Expressed Transcripts Using EdgeR - - edgeR - - - - trinityToolWrapper.py Analysis/DifferentialExpression/run_EdgeR.pl - --matrix $counts_matrix - --transcripts $transcripts_fasta_file - --output edgeR_results - --dispersion $dispersion - - > stdout.txt - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - help info here. - -