Mercurial > repos > trinity_ctat > ctat_analyze_differential_expression
changeset 0:2ca97cd84ce3 draft default tip
Upload ctat tools.
| author | trinity_ctat |
|---|---|
| date | Tue, 17 Jul 2018 11:49:33 -0400 |
| parents | |
| children | |
| files | ctat_analyze_differential_expression.py ctat_analyze_differential_expression.xml test-data/Sp.TMM.EXPR.matrix test-data/Sp.edgeR.tar.gz |
| diffstat | 4 files changed, 552 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_analyze_differential_expression.py Tue Jul 17 11:49:33 2018 -0400 @@ -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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_analyze_differential_expression.xml Tue Jul 17 11:49:33 2018 -0400 @@ -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>
--- /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 @@ -0,0 +1,353 @@ + Sp_ds Sp_hs +TRINITY_DN126_c0_g2 208.413 663.692 +TRINITY_DN173_c0_g3 229.681 359.359 +TRINITY_DN16_c0_g1 3576.565 814.603 +TRINITY_DN107_c0_g1 428.409 323.191 +TRINITY_DN165_c0_g1 503.376 658.359 +TRINITY_DN192_c0_g1 39126.126 19142.811 +TRINITY_DN9_c0_g1 353.811 693.312 +TRINITY_DN85_c0_g2 581.711 684.169 +TRINITY_DN175_c0_g2 1744.797 0.000 +TRINITY_DN170_c0_g2 0.000 0.000 +TRINITY_DN226_c0_g1 26319.359 8886.950 +TRINITY_DN135_c0_g2 404.134 200.734 +TRINITY_DN176_c0_g3 316.584 120.017 +TRINITY_DN80_c0_g1 159.653 264.439 +TRINITY_DN119_c0_g2 186.574 632.215 +TRINITY_DN134_c0_g1 354.869 190.269 +TRINITY_DN150_c0_g1 1375.774 2962.222 +TRINITY_DN149_c0_g2 531.548 366.669 +TRINITY_DN188_c0_g1 7070.931 30112.711 +TRINITY_DN122_c0_g1 274.527 184.376 +TRINITY_DN118_c0_g2 1417.370 0.000 +TRINITY_DN173_c0_g1 0.000 2330.019 +TRINITY_DN219_c0_g1 1643.145 1160.152 +TRINITY_DN141_c0_g2 368.939 544.176 +TRINITY_DN81_c0_g1 1377.673 816.734 +TRINITY_DN178_c0_g4 168.220 280.987 +TRINITY_DN117_c0_g1 0.000 0.000 +TRINITY_DN125_c0_g1 478.966 0.000 +TRINITY_DN158_c0_g2 567.684 392.718 +TRINITY_DN128_c1_g1 28463.880 171.388 +TRINITY_DN177_c1_g1 0.000 3469.241 +TRINITY_DN180_c0_g2 383.613 811.686 +TRINITY_DN32_c0_g1 1167.261 1122.091 +TRINITY_DN113_c0_g1 496.589 353.121 +TRINITY_DN201_c0_g1 499.159 325.013 +TRINITY_DN60_c0_g2 0.000 0.000 +TRINITY_DN50_c0_g1 95606.418 24142.635 +TRINITY_DN112_c0_g1 185.549 143.101 +TRINITY_DN87_c0_g1 753.988 751.946 +TRINITY_DN179_c0_g1 292.124 237.557 +TRINITY_DN170_c0_g4 2125.765 991.693 +TRINITY_DN74_c0_g1 352.249 324.774 +TRINITY_DN199_c0_g1 16504.791 313.512 +TRINITY_DN89_c0_g2 278.029 202.591 +TRINITY_DN49_c0_g1 406.150 412.766 +TRINITY_DN116_c0_g2 882.546 0.000 +TRINITY_DN215_c0_g1 8281.072 6884.290 +TRINITY_DN129_c0_g1 1043.097 2058.318 +TRINITY_DN143_c0_g1 447.904 137.648 +TRINITY_DN176_c0_g2 476.480 147.422 +TRINITY_DN162_c0_g1 257.164 476.506 +TRINITY_DN77_c0_g1 0.000 5166.450 +TRINITY_DN84_c0_g1 99.771 155.149 +TRINITY_DN104_c0_g1 146.289 1195.391 +TRINITY_DN18_c0_g1 402.655 818.520 +TRINITY_DN102_c0_g1 3491.367 0.000 +TRINITY_DN183_c0_g2 772.367 1652.695 +TRINITY_DN10_c0_g1 2034.830 1036.159 +TRINITY_DN158_c0_g3 560.804 517.782 +TRINITY_DN36_c0_g1 375.558 319.572 +TRINITY_DN104_c0_g2 245.136 1118.865 +TRINITY_DN144_c0_g3 0.000 0.000 +TRINITY_DN152_c0_g1 1210.922 106.802 +TRINITY_DN97_c0_g1 1299.203 477.280 +TRINITY_DN53_c0_g1 649.446 328.227 +TRINITY_DN140_c0_g1 633.940 0.000 +TRINITY_DN75_c0_g1 770.511 0.000 +TRINITY_DN195_c0_g1 786.495 1157.152 +TRINITY_DN128_c0_g1 6202.362 48712.107 +TRINITY_DN24_c0_g1 313.728 0.000 +TRINITY_DN149_c0_g1 153.689 506.115 +TRINITY_DN178_c0_g2 461.512 633.203 +TRINITY_DN24_c0_g2 739.491 165.364 +TRINITY_DN174_c0_g4 445.678 431.350 +TRINITY_DN68_c0_g1 874.230 357.680 +TRINITY_DN25_c0_g1 438.278 389.741 +TRINITY_DN227_c0_g1 537.814 941.667 +TRINITY_DN176_c0_g1 130.178 418.457 +TRINITY_DN194_c0_g1 0.000 0.000 +TRINITY_DN213_c0_g1 777.172 1416.602 +TRINITY_DN211_c0_g1 3179.781 5736.531 +TRINITY_DN127_c0_g1 450.601 425.707 +TRINITY_DN108_c0_g2 167.817 518.080 +TRINITY_DN162_c0_g6 0.000 2381.342 +TRINITY_DN4_c0_g1 1173.451 1671.767 +TRINITY_DN207_c0_g1 793.761 1501.713 +TRINITY_DN172_c0_g1 106.676 167.173 +TRINITY_DN178_c0_g3 386.503 0.000 +TRINITY_DN35_c0_g1 6061.063 11700.571 +TRINITY_DN11_c0_g1 1065.390 2992.699 +TRINITY_DN38_c0_g1 755.097 431.850 +TRINITY_DN85_c0_g1 627.960 643.858 +TRINITY_DN197_c0_g1 775.080 1034.588 +TRINITY_DN162_c0_g4 415.759 339.704 +TRINITY_DN206_c0_g1 1620.121 518.246 +TRINITY_DN143_c0_g5 239.979 0.000 +TRINITY_DN186_c0_g1 117333.607 291664.823 +TRINITY_DN145_c0_g1 193.839 226.056 +TRINITY_DN120_c0_g3 277.441 282.035 +TRINITY_DN212_c0_g1 1037.100 911.107 +TRINITY_DN117_c0_g5 300.608 515.151 +TRINITY_DN30_c0_g1 0.000 0.000 +TRINITY_DN216_c0_g1 21841.441 2669.484 +TRINITY_DN180_c0_g1 421.286 0.000 +TRINITY_DN133_c0_g2 498.168 0.000 +TRINITY_DN13_c0_g1 4310.285 27106.714 +TRINITY_DN146_c0_g2 406.679 480.697 +TRINITY_DN162_c0_g5 346.587 0.000 +TRINITY_DN91_c0_g1 355.844 1099.947 +TRINITY_DN75_c0_g2 0.000 0.000 +TRINITY_DN69_c0_g1 422.151 515.615 +TRINITY_DN183_c0_g1 654.368 508.293 +TRINITY_DN205_c0_g1 14959.873 476.566 +TRINITY_DN157_c0_g1 561.611 289.035 +TRINITY_DN132_c0_g1 0.000 0.000 +TRINITY_DN191_c0_g1 634.125 3756.538 +TRINITY_DN106_c0_g1 517.126 462.339 +TRINITY_DN224_c0_g1 528.239 465.708 +TRINITY_DN31_c0_g1 2080.054 1060.350 +TRINITY_DN79_c0_g1 214.234 512.413 +TRINITY_DN149_c0_g5 522.401 0.000 +TRINITY_DN144_c0_g2 319.095 242.128 +TRINITY_DN47_c0_g1 1293.080 913.416 +TRINITY_DN20_c0_g2 474.867 600.059 +TRINITY_DN93_c0_g1 0.000 2128.487 +TRINITY_DN203_c0_g1 583.030 1079.244 +TRINITY_DN221_c0_g1 8879.524 85908.722 +TRINITY_DN116_c0_g1 215.460 169.018 +TRINITY_DN53_c0_g2 879.093 1120.984 +TRINITY_DN99_c0_g2 0.000 0.000 +TRINITY_DN71_c0_g2 1413.716 3393.488 +TRINITY_DN81_c0_g2 1237.121 725.183 +TRINITY_DN5_c0_g1 980.696 1855.619 +TRINITY_DN163_c0_g1 0.000 0.000 +TRINITY_DN19_c0_g1 29165.278 107059.123 +TRINITY_DN15_c0_g1 1374.599 2003.696 +TRINITY_DN124_c0_g4 622.836 257.915 +TRINITY_DN230_c0_g1 11667.737 755.124 +TRINITY_DN184_c0_g1 1436.781 1275.656 +TRINITY_DN160_c0_g1 0.000 1876.525 +TRINITY_DN60_c0_g1 3785.608 3226.732 +TRINITY_DN26_c0_g1 130.346 393.003 +TRINITY_DN174_c0_g5 197.619 241.426 +TRINITY_DN168_c0_g1 516.328 208.972 +TRINITY_DN111_c0_g2 1195.442 0.000 +TRINITY_DN220_c0_g1 0.000 0.000 +TRINITY_DN222_c0_g1 27210.732 208.294 +TRINITY_DN167_c0_g3 420.001 182.328 +TRINITY_DN97_c0_g2 744.228 366.050 +TRINITY_DN155_c0_g1 393.802 0.000 +TRINITY_DN178_c0_g5 261.927 133.779 +TRINITY_DN155_c0_g3 975.093 1767.604 +TRINITY_DN175_c0_g3 289.075 434.124 +TRINITY_DN51_c0_g1 240.894 724.968 +TRINITY_DN168_c0_g2 316.466 112.147 +TRINITY_DN167_c0_g2 343.681 501.448 +TRINITY_DN111_c0_g1 2470.857 0.000 +TRINITY_DN146_c0_g1 238.534 350.656 +TRINITY_DN193_c0_g1 225.271 562.212 +TRINITY_DN123_c0_g2 807.830 0.000 +TRINITY_DN108_c0_g1 208.119 0.000 +TRINITY_DN202_c0_g1 1215.912 726.540 +TRINITY_DN156_c0_g1 572.178 160.470 +TRINITY_DN229_c0_g1 1858.991 1537.369 +TRINITY_DN94_c0_g1 253.292 515.615 +TRINITY_DN33_c0_g1 1363.864 1426.900 +TRINITY_DN135_c0_g3 0.000 1951.218 +TRINITY_DN175_c0_g1 305.001 158.435 +TRINITY_DN110_c0_g1 6838.453 3249.042 +TRINITY_DN198_c0_g1 768.957 681.538 +TRINITY_DN161_c0_g2 0.000 0.000 +TRINITY_DN136_c0_g1 186.473 406.028 +TRINITY_DN174_c0_g3 497.975 0.000 +TRINITY_DN185_c0_g1 426.746 296.619 +TRINITY_DN116_c0_g3 1602.028 0.000 +TRINITY_DN127_c0_g2 2855.545 2118.248 +TRINITY_DN171_c0_g1 0.000 0.000 +TRINITY_DN214_c0_g1 623.794 165.411 +TRINITY_DN8_c0_g1 3307.893 6952.042 +TRINITY_DN63_c0_g1 2838.578 3766.884 +TRINITY_DN71_c0_g1 0.000 0.000 +TRINITY_DN120_c0_g2 0.000 304.143 +TRINITY_DN143_c0_g6 203.449 101.135 +TRINITY_DN118_c0_g3 0.000 0.000 +TRINITY_DN92_c0_g1 14879.244 6193.573 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