# HG changeset patch # User gkumar09 # Date 1443581639 14400 # Node ID 4eaf6b15b1b233b820c4a971c5282e6cc536ed5c # Parent 1c37a800375581a6bc9313a98956f92b3cb7e96e Deleted selected files diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/EdgeR_differentialExpression.xml --- a/trinityrnaseq_protocol/EdgeR_differentialExpression.xml Mon Sep 28 22:44:29 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - - Identify Differentially Expressed Transcripts Using EdgeR - - trinity - - - - EdgeR_differentialExpression_wrapper.py - $counts_matrix - $dispersion - - - - - - - - - - - - - - - - - - - - - - - - - help info here. - - diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/EdgeR_differentialExpression_wrapper.py --- a/trinityrnaseq_protocol/EdgeR_differentialExpression_wrapper.py Mon Sep 28 22:44:29 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +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(1) - -usage= "usage: " + " $counts_matrix" + " $dispersion" - -if len(sys.argv)<2: - print "Require atleast two parameters" -else: - print "All good- command going ahead" -print " " - -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 " " - -countmatrix= "counts_matrix" - -cmd= "cp " + sys.argv[1] + " " + countmatrix -run_command(cmd) - -cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/run_DE_analysis.pl "+ " --matrix "+ countmatrix + " --method edgeR " + " --output edgeR_results "+ " --dispersion " + sys.argv[2] + " --tar_gz_outdir" - -run_command(cmd) - -sys.exit(0) diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/RSEM_estimates_to_matrix.xml --- a/trinityrnaseq_protocol/RSEM_estimates_to_matrix.xml Mon Sep 28 22:44:29 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ - - - Join RSEM estimates from multiple samples into a single matrix - - trinity - - - - trinityToolWrapper.py util/RSEM_util/merge_RSEM_counts_and_labels_single_table.pl - - --labels - #for $entry in $RSEM_samples: - ${entry.column_label} - #end for - - --RSEM_counts - #for $entry in $RSEM_samples: - ${entry.file} - #end for - - > RSEM.counts.matrix - - - - - - - - - - - - - - - - - - - - - - - - - - - - .. _Trinity: http://trinityrnaseq.sourceforge.net - - diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/abundance_estimation_to_matrix.xml --- a/trinityrnaseq_protocol/abundance_estimation_to_matrix.xml Mon Sep 28 22:44:29 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ - - - Join RSEM estimates from multiple samples into a single matrix - - trinity - - - - abundance_estimation_to_matrix_wrapper.py - #for $q in $RSEM_samples - ${q.file} "${q.column_label}" - #end for - - - - - - - - - - - - - - - - - - - - - - - - - - - - .. _Trinity: http://trinityrnaseq.sourceforge.net - - diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/abundance_estimation_to_matrix_wrapper.py --- a/trinityrnaseq_protocol/abundance_estimation_to_matrix_wrapper.py Mon Sep 28 22:44:29 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -#!/usr/bin/env python - -import sys, os, string, subprocess - -#aliasing the filenames using the labels - - -def run_command(command): - print "Running command: " + command - - err_capture_file = open("my.stderr", 'w') # writing stderr to a file - cmd_run = subprocess.Popen(args=command, shell=True, stderr=err_capture_file, stdout=sys.stdout) - err = cmd_run.wait() # get exit code from command execution - err_capture_file.close() - - if err: - # report the error messages we captured, and exit non-zero - sys.stderr.write("Error, cmd: " + command + " died with ret: " + `err`) - for line in open(err_capture_file): - sys.stderr.write(line) - sys.exit(err) - return - -label_list = [] # symlink files to the labels -for i in range(1, len(sys.argv), 2): - filename=sys.argv[i] - label= sys.argv[i+1] - cmd= "ln -sf " + filename + " " + label - label_list.append(label) - run_command(cmd) - - -# run the abundance estimation script - -cmd = os.path.dirname(sys.argv[0]) + "/trinityToolWrapper.py " + " util/abundance_estimates_to_matrix.pl --est_method RSEM --cross_sample_fpkm_norm TMM " + " ".join(label_list) - -run_command(cmd) - -sys.exit(0) - diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/align_and_estimate_abundance.xml --- a/trinityrnaseq_protocol/align_and_estimate_abundance.xml Mon Sep 28 22:44:29 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,90 +0,0 @@ - - - run RSEM to estimate transcript abundances - - trinity - - - - trinityToolWrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference - - ## Inputs. - #if str($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 - - #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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - .. _Trinity: http://trinityrnaseq.sourceforge.net - - diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/alignreads.xml --- a/trinityrnaseq_protocol/alignreads.xml Mon Sep 28 22:44:29 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 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/analyze_diff_exp.xml --- a/trinityrnaseq_protocol/analyze_diff_exp.xml Mon Sep 28 22:44:29 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 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/analyze_diff_exp_wrapper.py --- a/trinityrnaseq_protocol/analyze_diff_exp_wrapper.py Mon Sep 28 22:44:29 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 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/cat.xml --- a/trinityrnaseq_protocol/cat.xml Mon Sep 28 22:44:29 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 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/diffExpress_edgeR.xml --- a/trinityrnaseq_protocol/diffExpress_edgeR.xml Mon Sep 28 22:44:29 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. - - diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/trinityToolWrapper.py --- a/trinityrnaseq_protocol/trinityToolWrapper.py Mon Sep 28 22:44:29 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -#!/usr/bin/env python - - -# borrowed from: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr and modified for use with Trinity tools. - -""" -Wrapper that execute a program and its arguments but reports standard error -messages only if the program exit status was not 0 -Example: ./stderr_wrapper.py myprog arg1 -f arg2 -""" - -import sys, subprocess, os - -assert sys.version_info[:2] >= ( 2, 4 ) - -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() - - - -# get bindir -bindir = sys.argv[0] -bindir = bindir.split("/") -if len(bindir) > 1: - bindir.pop() - bindir = "/".join(bindir) -else: - bindir = "." - - -## add locations of tools to path setting. -TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt"; -for line in open(TOOL_PATHS_FILE): - line = line.rstrip() - os.environ['PATH'] += ":" + line - - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - -def __main__(): - # Get command-line arguments - args = sys.argv - # Remove name of calling program, i.e. ./stderr_wrapper.py - args.pop(0) - # If there are no arguments left, we're done - if len(args) == 0: - return - - # If one needs to silence stdout - #args.append( ">" ) - #args.append( "/dev/null" ) - - args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]); - - cmdline = " ".join(args) - - - - try: - # Run program - err_capture = open("stderr.txt", 'w') - proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout ) - returncode = proc.wait() - err_capture.close() - - - if returncode != 0: - raise Exception - - except Exception: - # Running Grinder failed: write error message to stderr - err_text = open("stderr.txt").readlines() - stop_err( "ERROR:\n" + "\n".join(err_text)) - - -if __name__ == "__main__": __main__()