Mercurial > repos > gkumar09 > trinityrnaseq_protocol
changeset 21:9be8023b486a draft
Deleted selected files
| author | gkumar09 |
|---|---|
| date | Mon, 28 Sep 2015 22:03:10 -0400 |
| parents | 0845cefc6cfe |
| children | 8bce7f287a2a |
| files | Final/EdgeR_differentialExpression.xml Final/EdgeR_differentialExpression_wrapper.py Final/RSEM_estimates_to_matrix.xml Final/abundance_estimation_to_matrix.xml Final/abundance_estimation_to_matrix_wrapper.py Final/align_and_estimate_abundance.xml |
| diffstat | 6 files changed, 0 insertions(+), 301 deletions(-) [+] |
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--- a/Final/EdgeR_differentialExpression.xml Mon Sep 28 22:02:36 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -<tool id="EdgeR_differentialExpression" name="EdgeR_differentialExpression" version="0.0.1"> - - <description>Identify Differentially Expressed Transcripts Using EdgeR</description> - <requirements> - <requirement type="package">trinity</requirement> - </requirements> - <command interpreter="python"> - - EdgeR_differentialExpression_wrapper.py - $counts_matrix - $dispersion - - </command> - <inputs> - - <param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" /> - <param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" /> - <param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" /> - - </inputs> - <outputs> - - <data format="tar.gz" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" /> - - </outputs> - <tests> - - <test> - <param name="myname" value="This is just a simple test" /> - - </test> - - - </tests> - <help> - help info here. - </help> -</tool>
--- a/Final/EdgeR_differentialExpression_wrapper.py Mon Sep 28 22:02:36 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)
--- a/Final/RSEM_estimates_to_matrix.xml Mon Sep 28 22:02:36 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ -<tool id="RSEM_estimates_to_matrix" name="RSEM_estimates_to_matrix" version="0.0.1"> - - <description>Join RSEM estimates from multiple samples into a single matrix</description> - <requirements> - <requirement type="package">trinity</requirement> - </requirements> - <command interpreter="python"> - - 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: - ${entry.file} - #end for - - > RSEM.counts.matrix - - </command> - <inputs> - - <repeat name="RSEM_samples" title="RSEM abundance estimates for samples"> - <param name="file" label="Add file" type="data" format="text"/> - <param name="column_label" label="column label" type="text" /> - </repeat> - - </inputs> - <outputs> - <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="RSEM.counts.matrix"/> - </outputs> - <tests> - - - <test> - <param name="target" value="trinity/Trinity.fasta" /> - <param name="aligner" value="bowtie" /> - <param name="paired_or_single" value="single" /> - <param name="library_type" value="None" /> - <param name="input" value="trinity/reads.left.fq" /> - </test> - - - </tests> - <help> - .. _Trinity: http://trinityrnaseq.sourceforge.net - </help> -</tool>
--- a/Final/abundance_estimation_to_matrix.xml Mon Sep 28 22:02:36 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -<tool id="abundance_estimation_to_matrix" name="abundance_estimation_to_matrix" version="0.0.1"> - - <description>Join RSEM estimates from multiple samples into a single matrix</description> - <requirements> - <requirement type="package">trinity</requirement> - </requirements> - <command interpreter="python"> - - abundance_estimation_to_matrix_wrapper.py - #for $q in $RSEM_samples - ${q.file} "${q.column_label}" - #end for - - </command> - <inputs> - - <repeat name="RSEM_samples" title="RSEM abundance estimates for samples"> - <param name="file" label="Add file" type="data" format="text"/> - <param name="column_label" label="column label" type="text" /> - </repeat> - - </inputs> - <outputs> - <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/> - </outputs> - <tests> - - - <test> - <param name="target" value="trinity/Trinity.fasta" /> - <param name="aligner" value="bowtie" /> - <param name="paired_or_single" value="single" /> - <param name="library_type" value="None" /> - <param name="input" value="trinity/reads.left.fq" /> - </test> - - - </tests> - <help> - .. _Trinity: http://trinityrnaseq.sourceforge.net - </help> -</tool>
--- a/Final/abundance_estimation_to_matrix_wrapper.py Mon Sep 28 22:02:36 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) -
--- a/Final/align_and_estimate_abundance.xml Mon Sep 28 22:02:36 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,90 +0,0 @@ -<tool id="RSEM_abundance_estimation" name="RSEM_abundance_estimation" version="0.0.1"> - - <description>run RSEM to estimate transcript abundances</description> - <requirements> - <requirement type="package">trinity</requirement> - </requirements> - <command interpreter="python"> - - 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 $inputs.library_type - #end if - #end if - - - </command> - <inputs> - <param format="fasta" name="transcripts" type="data" label="transcripts_fasta" help="Fasta sequences for which reads are aligned." /> - - <conditional name="inputs"> - <param name="paired_or_single" type="select" label="Paired or Single-end data?"> - <option value="paired">Paired</option> - <option value="single">Single</option> - </param> - <when value="paired"> - <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> - <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> - <param name="library_type" type="select" label="Strand-specific Library Type"> - <option value="None">None</option> - <option value="FR">FR</option> - <option value="RF">RF</option> - </param> - - </when> - <when value="single"> - <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> - <param name="library_type" type="select" label="Strand-specific Library Type"> - <option value="None">None</option> - <option value="F">F</option> - <option value="R">R</option> - </param> - - </when> - </conditional> - - - </inputs> - <outputs> - <data format="text" name="transcript_counts" label="${tool.name} on ${on_string}: Isoform Counts" from_work_dir="RSEM.isoforms.results"/> - <data format="text" name="gene_counts" label="${tool.name} on ${on_string}: Gene counts" from_work_dir="RSEM.genes.results"/> - - - </outputs> - <tests> - - - <test> - <param name="target" value="trinity/Trinity.fasta" /> - <param name="aligner" value="bowtie" /> - <param name="paired_or_single" value="single" /> - <param name="library_type" value="None" /> - <param name="input" value="trinity/reads.left.fq" /> - </test> - - - </tests> - <help> - .. _Trinity: http://trinityrnaseq.sourceforge.net - </help> -</tool>