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Commit message:
Upload ctat tools. |
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added:
ctat_analyze_differential_expression.py ctat_analyze_differential_expression.xml test-data/Sp.TMM.EXPR.matrix test-data/Sp.edgeR.tar.gz |
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| diff -r 000000000000 -r 2ca97cd84ce3 ctat_analyze_differential_expression.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_analyze_differential_expression.py Tue Jul 17 11:49:33 2018 -0400 |
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| @@ -0,0 +1,123 @@ +import sys, os, subprocess + +TRINITY_BASE_DIR = "" +if os.environ.has_key('TRINITY_HOME'): + TRINITY_BASE_DIR = os.environ['TRINITY_HOME']; +elif hasattr(os, 'symlink'): # symlink was implemented to always return false when it was not implemented in earlier versions of python. + # 2017-09-26 + # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility. + # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that. + # I also found distutils.spawn.find_executable() which might work, but already implemented the below. + try: + pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE) + except: + msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.\n".format(sys.argv[0]) + sys.stderr.write(msg) + # t, v, tb = sys.exc_info() + # raise t, v, tb + # For some reason the above was giving a syntax error. + # A simple raise should reraise the existing exception. + raise + else: + TrinityPath, err_info = pipe1.communicate() + # FIX - probably should be checking err_info for errors... + # Determine the TRINITY_BASE_DIR from output1. + # If TrinityPath is a link, we need to dereference the link. + TrinityPath = TrinityPath.rstrip() # Need to strip off a newline. + # print "Trinity that was found is: {:s}".format(repr(TrinityPath)) + # print os.path.islink(TrinityPath) + TrinityPath = os.path.abspath(TrinityPath) + # msg = "The Absolute Trinity path that was found is: {:s}".format(TrinityPath) + # print msg + # print os.path.islink(TrinityPath) + while os.path.islink(TrinityPath): + # print "That path is a link." + TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath)) + # print "The new path is: {:s}".format(TrinityPath) + # Take off the last part of the path (which is the Trinity command) + TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1]) +else: + sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.") + sys.exit(1) + +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): + # 2017-10-02 + # Cicada Dennis put the subprocess command in a try/except statement. + # Errors were going undetected the way it was written previously. + print "Running command:\n\t" + cmd + try: + pipe = subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE) + cmd_stdout, cmd_stderr = pipe.communicate() + except: + msg = "ERROR while running command:\n\t" + cmd + sys.stderr.write(msg) + raise + + sys.stdout.write(cmd_stdout) + ret = pipe.returncode + if ret: + print "command died: " + str(ret) + sys.stderr.write(cmd_stderr) + sys.exit(ret) + else: + # Any error output is written to stdout instead of stderr, since no error has occurred. + sys.stderr.write(cmd_stderr) + return + +print "" +Final_tar_gz= "edgeR.tar.gz" +run_command("cp "+ sys.argv[1] + " " + Final_tar_gz) +run_command("tar -xvf " + Final_tar_gz) + +print "Before moving files." +run_command("pwd") +run_command("ls -lad ./*") +print "\nedgeR_results/" +run_command("ls -la edgeR_results") +print "" + +run_command("mv edgeR_results/* ." ) + +print "After moving files." +run_command("pwd") +run_command("ls -lad ./*") +print "\nedgeR_results/" +run_command("ls -la edgeR_results") +print "" + +# 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.centered.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.centered.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) |
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| diff -r 000000000000 -r 2ca97cd84ce3 ctat_analyze_differential_expression.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_analyze_differential_expression.xml Tue Jul 17 11:49:33 2018 -0400 |
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| @@ -0,0 +1,76 @@ +<tool id="ctat_analyze_differential_expression" name="ctat_analyze_differential_expression" version="1.0.0" profile="17.05"> + + <description>Analyze differential expression</description> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package">subprocess32</requirement> + <requirement type="package">bzip2</requirement> + <requirement type="package" version="1.3.0">rsem</requirement> + <requirement type="package" version="3">bioconductor-edger</requirement> + <requirement type="package" version="2">bioconductor-qvalue</requirement> + <requirement type="package">r-cluster</requirement> + <requirement type="package">r-fastcluster</requirement> + <requirement type="package" version="2.6.6">trinity</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + python $__tool_directory__/ctat_analyze_differential_expression.py $EdgeRTarGz $Counts_matrix $Pvalue $Cvalue + ]]> + </command> + <inputs> + <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/> + <param name="Counts_matrix" label="Counts Matrix" type="data" format="tabular" /> + <param name="Pvalue" label="P-value" value="0.05" type="float" /> + <param name="Cvalue" label="C-value" value="0" type="float" /> + + </inputs> + <outputs> + <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/> + <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/> + <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/> + <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/> + </outputs> + <tests> +<test> +<param name="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" /> +<param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" /> +<param name="Pvalue" value="0.05" /> +<param name="Cvalue" value="0.0" /> + +<output name="diffExpr_matrix" > + <assert_contents> + <has_line_matching expression=".+" /> + <has_line line="Sp_ds	Sp_hs" /> + <has_line_matching expression="TRINITY_DN.+" /> + </assert_contents> + </output> +<output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" /> +<output name="diffExpr_correlation_matrix_pdf" > + <assert_contents> + <has_line_matching expression=".+" /> + </assert_contents> + </output> +<output name="Heatmap" > + <assert_contents> + <has_line_matching expression=".+" /> + </assert_contents> + </output> + + </test> + </tests> + <help> +.. class:: infomark + +This tool filters differentially expressed transcripts derived from edgeR using a minimum fold change (C-value) which will be log2 transformed before use and a required significance (P-value) in the pairwise sample comparisons (after false discovery rate correction). + +If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_. + +.. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki +.. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html + </help> + + <citations> + <citation type="doi">10.1038/nbt.1883</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 2ca97cd84ce3 test-data/Sp.TMM.EXPR.matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Sp.TMM.EXPR.matrix Tue Jul 17 11:49:33 2018 -0400 |
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| b'@@ -0,0 +1,353 @@\n+\tSp_ds\tSp_hs\n+TRINITY_DN126_c0_g2\t208.413\t663.692\n+TRINITY_DN173_c0_g3\t229.681\t359.359\n+TRINITY_DN16_c0_g1\t3576.565\t814.603\n+TRINITY_DN107_c0_g1\t428.409\t323.191\n+TRINITY_DN165_c0_g1\t503.376\t658.359\n+TRINITY_DN192_c0_g1\t39126.126\t19142.811\n+TRINITY_DN9_c0_g1\t353.811\t693.312\n+TRINITY_DN85_c0_g2\t581.711\t684.169\n+TRINITY_DN175_c0_g2\t1744.797\t0.000\n+TRINITY_DN170_c0_g2\t0.000\t0.000\n+TRINITY_DN226_c0_g1\t26319.359\t8886.950\n+TRINITY_DN135_c0_g2\t404.134\t200.734\n+TRINITY_DN176_c0_g3\t316.584\t120.017\n+TRINITY_DN80_c0_g1\t159.653\t264.439\n+TRINITY_DN119_c0_g2\t186.574\t632.215\n+TRINITY_DN134_c0_g1\t354.869\t190.269\n+TRINITY_DN150_c0_g1\t1375.774\t2962.222\n+TRINITY_DN149_c0_g2\t531.548\t366.669\n+TRINITY_DN188_c0_g1\t7070.931\t30112.711\n+TRINITY_DN122_c0_g1\t274.527\t184.376\n+TRINITY_DN118_c0_g2\t1417.370\t0.000\n+TRINITY_DN173_c0_g1\t0.000\t2330.019\n+TRINITY_DN219_c0_g1\t1643.145\t1160.152\n+TRINITY_DN141_c0_g2\t368.939\t544.176\n+TRINITY_DN81_c0_g1\t1377.673\t816.734\n+TRINITY_DN178_c0_g4\t168.220\t280.987\n+TRINITY_DN117_c0_g1\t0.000\t0.000\n+TRINITY_DN125_c0_g1\t478.966\t0.000\n+TRINITY_DN158_c0_g2\t567.684\t392.718\n+TRINITY_DN128_c1_g1\t28463.880\t171.388\n+TRINITY_DN177_c1_g1\t0.000\t3469.241\n+TRINITY_DN180_c0_g2\t383.613\t811.686\n+TRINITY_DN32_c0_g1\t1167.261\t1122.091\n+TRINITY_DN113_c0_g1\t496.589\t353.121\n+TRINITY_DN201_c0_g1\t499.159\t325.013\n+TRINITY_DN60_c0_g2\t0.000\t0.000\n+TRINITY_DN50_c0_g1\t95606.418\t24142.635\n+TRINITY_DN112_c0_g1\t185.549\t143.101\n+TRINITY_DN87_c0_g1\t753.988\t751.946\n+TRINITY_DN179_c0_g1\t292.124\t237.557\n+TRINITY_DN170_c0_g4\t2125.765\t991.693\n+TRINITY_DN74_c0_g1\t352.249\t324.774\n+TRINITY_DN199_c0_g1\t16504.791\t313.512\n+TRINITY_DN89_c0_g2\t278.029\t202.591\n+TRINITY_DN49_c0_g1\t406.150\t412.766\n+TRINITY_DN116_c0_g2\t882.546\t0.000\n+TRINITY_DN215_c0_g1\t8281.072\t6884.290\n+TRINITY_DN129_c0_g1\t1043.097\t2058.318\n+TRINITY_DN143_c0_g1\t447.904\t137.648\n+TRINITY_DN176_c0_g2\t476.480\t147.422\n+TRINITY_DN162_c0_g1\t257.164\t476.506\n+TRINITY_DN77_c0_g1\t0.000\t5166.450\n+TRINITY_DN84_c0_g1\t99.771\t155.149\n+TRINITY_DN104_c0_g1\t146.289\t1195.391\n+TRINITY_DN18_c0_g1\t402.655\t818.520\n+TRINITY_DN102_c0_g1\t3491.367\t0.000\n+TRINITY_DN183_c0_g2\t772.367\t1652.695\n+TRINITY_DN10_c0_g1\t2034.830\t1036.159\n+TRINITY_DN158_c0_g3\t560.804\t517.782\n+TRINITY_DN36_c0_g1\t375.558\t319.572\n+TRINITY_DN104_c0_g2\t245.136\t1118.865\n+TRINITY_DN144_c0_g3\t0.000\t0.000\n+TRINITY_DN152_c0_g1\t1210.922\t106.802\n+TRINITY_DN97_c0_g1\t1299.203\t477.280\n+TRINITY_DN53_c0_g1\t649.446\t328.227\n+TRINITY_DN140_c0_g1\t633.940\t0.000\n+TRINITY_DN75_c0_g1\t770.511\t0.000\n+TRINITY_DN195_c0_g1\t786.495\t1157.152\n+TRINITY_DN128_c0_g1\t6202.362\t48712.107\n+TRINITY_DN24_c0_g1\t313.728\t0.000\n+TRINITY_DN149_c0_g1\t153.689\t506.115\n+TRINITY_DN178_c0_g2\t461.512\t633.203\n+TRINITY_DN24_c0_g2\t739.491\t165.364\n+TRINITY_DN174_c0_g4\t445.678\t431.350\n+TRINITY_DN68_c0_g1\t874.230\t357.680\n+TRINITY_DN25_c0_g1\t438.278\t389.741\n+TRINITY_DN227_c0_g1\t537.814\t941.667\n+TRINITY_DN176_c0_g1\t130.178\t418.457\n+TRINITY_DN194_c0_g1\t0.000\t0.000\n+TRINITY_DN213_c0_g1\t777.172\t1416.602\n+TRINITY_DN211_c0_g1\t3179.781\t5736.531\n+TRINITY_DN127_c0_g1\t450.601\t425.707\n+TRINITY_DN108_c0_g2\t167.817\t518.080\n+TRINITY_DN162_c0_g6\t0.000\t2381.342\n+TRINITY_DN4_c0_g1\t1173.451\t1671.767\n+TRINITY_DN207_c0_g1\t793.761\t1501.713\n+TRINITY_DN172_c0_g1\t106.676\t167.173\n+TRINITY_DN178_c0_g3\t386.503\t0.000\n+TRINITY_DN35_c0_g1\t6061.063\t11700.571\n+TRINITY_DN11_c0_g1\t1065.390\t2992.699\n+TRINITY_DN38_c0_g1\t755.097\t431.850\n+TRINITY_DN85_c0_g1\t627.960\t643.858\n+TRINITY_DN197_c0_g1\t775.080\t1034.588\n+TRINITY_DN162_c0_g4\t415.759\t339.704\n+TRINITY_DN206_c0_g1\t1620.121\t518.246\n+TRINITY_DN143_c0_g5\t239.979\t0.000\n+TRINITY_DN186_c0_g1\t117333.607\t291664.823\n+TRINITY_DN145_c0_g1\t193.839\t226.056\n+TRINITY_DN120_c0_g3\t277.441\t282.035\n+TRINITY_DN212_c0_g1\t1037.100\t911.107\n+TRINITY_DN117_c0_g5\t300.608\t515.151\n+TRINITY_DN30_c0_g1\t0.000\t0.000\n+TRINITY_DN216_c0_g1\t21841.441\t2669.484\n+TRINITY_DN180_c0_g1\t421.286\t0.000\n+TRINITY_DN133_c0_g2\t498.168\t0.000\n+TRINITY_DN13_c0_g1\t4310.285\t27106.714\n+TRINITY_DN146_c0_g2\t406.679\t480.697\n+TRINITY_DN162_c0_g5\t34'..b'0\t4660.049\n+TRINITY_DN124_c0_g3\t737.584\t297.964\n+TRINITY_DN40_c0_g1\t548.978\t511.270\n+TRINITY_DN86_c0_g2\t136.251\t661.133\n+TRINITY_DN167_c0_g1\t418.321\t212.639\n+TRINITY_DN95_c0_g1\t276.963\t620.976\n+TRINITY_DN76_c0_g3\t433.768\t328.025\n+TRINITY_DN209_c0_g1\t313.728\t0.000\n+TRINITY_DN228_c0_g1\t16954.653\t6175.024\n+TRINITY_DN86_c0_g1\t0.000\t748.600\n+TRINITY_DN72_c0_g1\t801.060\t180.864\n+TRINITY_DN165_c0_g2\t1745.679\t0.000\n+TRINITY_DN146_c0_g4\t402.328\t333.715\n+TRINITY_DN179_c0_g3\t438.110\t152.339\n+TRINITY_DN154_c0_g1\t557.822\t0.000\n+TRINITY_DN54_c0_g1\t258.550\t262.403\n+TRINITY_DN115_c0_g1\t381.454\t461.423\n+TRINITY_DN152_c0_g2\t1101.029\t544.450\n+T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