# 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 @@
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- Identify Differentially Expressed Transcripts Using EdgeR
-
- trinity
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- EdgeR_differentialExpression_wrapper.py
- $counts_matrix
- $dispersion
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- help info here.
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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 @@
-
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- Join RSEM estimates from multiple samples into a single matrix
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- trinity
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-
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- 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
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- .. _Trinity: http://trinityrnaseq.sourceforge.net
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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 @@
-
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- Join RSEM estimates from multiple samples into a single matrix
-
- trinity
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- abundance_estimation_to_matrix_wrapper.py
- #for $q in $RSEM_samples
- ${q.file} "${q.column_label}"
- #end for
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- .. _Trinity: http://trinityrnaseq.sourceforge.net
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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 @@
-
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- run RSEM to estimate transcript abundances
-
- trinity
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- 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
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- .. _Trinity: http://trinityrnaseq.sourceforge.net
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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 @@
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- alignReads: short read alignment tool wrapper
-
- trinity
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- 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
-
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- ## direct to output
- > outCapture.txt
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- .. _Trinity: http://trinityrnaseq.sourceforge.net
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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 @@
-
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- Analyze differential expression
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- trinity
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- analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue
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- .. _Trinity: http://trinityrnaseq.sourceforge.net
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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
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- bash_command_executer.py cat
- $input1
- #for $q in $queries
- ${q.input2}
- #end for
- > $out_file1
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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 @@
-
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- Identify Differentially Expressed Transcripts Using EdgeR
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- edgeR
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- trinityToolWrapper.py Analysis/DifferentialExpression/run_EdgeR.pl
- --matrix $counts_matrix
- --transcripts $transcripts_fasta_file
- --output edgeR_results
- --dispersion $dispersion
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- > stdout.txt
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- help info here.
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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__()