|
Commit message:
Upload ctat tools. |
|
added:
ctat_abundance_estimation_to_matrix.py ctat_abundance_estimation_to_matrix.xml ctat_trinity_tool_wrapper.py test-data/Sp_ds.RSEM.genes.results test-data/Sp_hs.RSEM.genes.results |
| b |
| diff -r 000000000000 -r 5eca0c75b178 ctat_abundance_estimation_to_matrix.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_abundance_estimation_to_matrix.py Tue Jul 17 11:47:32 2018 -0400 |
| [ |
| @@ -0,0 +1,40 @@ +#!/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]) + "/ctat_trinity_tool_wrapper.py " + " util/abundance_estimates_to_matrix.pl --gene_trans_map none --est_method RSEM --cross_sample_norm TMM " + " ".join(label_list) + +run_command(cmd) + +sys.exit(0) + |
| b |
| diff -r 000000000000 -r 5eca0c75b178 ctat_abundance_estimation_to_matrix.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_abundance_estimation_to_matrix.xml Tue Jul 17 11:47:32 2018 -0400 |
| [ |
| @@ -0,0 +1,101 @@ +<tool id="ctat_abundance_estimation_to_matrix" name="ctat_abundance_estimation_to_matrix" version="1.0.0" profile="17.05"> + + <description>Join RSEM estimates from multiple samples into a single matrix</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" version="2.6.6">trinity</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + python $__tool_directory__/ctat_abundance_estimation_to_matrix.py +#for $q in $RSEM_samples +${q.file} "${q.column_label}" +#end for + ]]> + + </command> + <inputs> + + <repeat name="RSEM_samples" title="RSEM abundance estimates for samples"> + <param name="file" label="Add file" type="data" format="txt"/> + <param name="column_label" label="column label" type="text" /> + </repeat> + + </inputs> + <outputs> + <data format="tabular" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="RSEM.isoform.counts.matrix"/> + <data format="tabular" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="RSEM.isoform.TMM.EXPR.matrix"/> +</outputs> + <tests> +<test> + <repeat name="RSEM_samples"> + <param name="file" value="Sp_ds.RSEM.genes.results" /> + <param name="column_label" value="Sp_ds" /> + </repeat> + <repeat name="RSEM_samples"> + <param name="file" value="Sp_hs.RSEM.genes.results" /> + <param name="column_label" value="Sp_hs" /> + </repeat> + + <output name="counts_matrix" > + <assert_contents> + <has_line_matching expression=".+" /> + <has_line line="	Sp_ds	Sp_hs" /> + <has_n_columns n="3" /> + <has_line_matching expression="TRINITY_DN.+" /> + </assert_contents> + </output> + <output name="tmm_expr_matrix" > + <assert_contents> + <has_line_matching expression=".+" /> + <has_line line="	Sp_ds	Sp_hs" /> + <has_n_columns n="3" /> + <has_line_matching expression="TRINITY_DN.+" /> + </assert_contents> + </output> + </test> + <!-- The following test has not been tested to see if it works. +<test> + <repeat name="RSEM_samples"> + <param name="file" value="Sp_ds.RSEM.isoforms.results" /> + <param name="column_label" value="Sp_ds" /> + </repeat> + <repeat name="RSEM_samples"> + <param name="file" value="Sp_hs.RSEM.isoforms.results" /> + <param name="column_label" value="Sp_hs" /> + </repeat> + + <output name="counts_matrix" > + <assert_contents> + <has_line_matching expression=".+" /> + </assert_contents> + </output> + <output name="tmm_expr_matrix" > + <assert_contents> + <has_line_matching expression=".+" /> + </assert_contents> + </output> + </test> + --> + </tests> + <help> +.. class:: infomark + +This step will join the RSEM-computed gene or isoform fragment counts into a matrix file, which will be used to run edgeR and identify differentially expressed transcripts in next few steps. Execution of this will generate a counts matrix file with a name 'abundance_estimation_to_matrix: counts_matrix'. + +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> |
| b |
| diff -r 000000000000 -r 5eca0c75b178 ctat_trinity_tool_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_trinity_tool_wrapper.py Tue Jul 17 11:47:32 2018 -0400 |
| [ |
| @@ -0,0 +1,123 @@ +#!/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 +print sys.version + +assert sys.version_info[:2] >= ( 2, 4 ) + +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. + # 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 just 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) + + +# 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 + +# Add TrinityPath and its utils to the PATH environment variable. +# print "Initially the PATH env variable is:\n\t{:s}".format(os.environ['PATH']) +os.environ['PATH'] = os.environ['PATH'] + ":{:s}:{:s}".format(TRINITY_BASE_DIR,TRINITY_BASE_DIR+"/util") +# print "Now the PATH env variable is:\n\t{:s}".format(os.environ['PATH']) + + +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" ) + print "The TRINITY_BASE_DIR is:\n\t{:s}".format(TRINITY_BASE_DIR) + print "The PATH env variable is:\n\t{:s}".format(os.environ['PATH']) + + args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]); + + cmdline = " ".join(args) + + print "The command being invoked is:\n\t{:s}".format(cmdline) + + + 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__() |
| b |
| diff -r 000000000000 -r 5eca0c75b178 test-data/Sp_ds.RSEM.genes.results --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Sp_ds.RSEM.genes.results Tue Jul 17 11:47:32 2018 -0400 |
| b |
| b'@@ -0,0 +1,353 @@\n+gene_id\ttranscript_id(s)\tlength\teffective_length\texpected_count\tTPM\tFPKM\n+TRINITY_DN100_c0_g1\tTRINITY_DN100_c0_g1_i1\t223.00\t7.26\t1.00\t1618.59\t1457.32\n+TRINITY_DN100_c0_g2\tTRINITY_DN100_c0_g2_i1\t794.00\t529.51\t13.00\t288.49\t259.75\n+TRINITY_DN101_c0_g1\tTRINITY_DN101_c0_g1_i1\t1450.00\t1185.51\t64.00\t634.36\t571.16\n+TRINITY_DN101_c0_g2\tTRINITY_DN101_c0_g2_i1\t271.00\t28.48\t0.00\t0.00\t0.00\n+TRINITY_DN101_c0_g3\tTRINITY_DN101_c0_g3_i1\t793.00\t528.51\t30.00\t667.01\t600.55\n+TRINITY_DN102_c0_g1\tTRINITY_DN102_c0_g1_i1\t217.00\t5.65\t2.00\t4156.55\t3742.39\n+TRINITY_DN104_c0_g1\tTRINITY_DN104_c0_g1_i1\t326.00\t67.47\t1.00\t174.16\t156.81\n+TRINITY_DN104_c0_g2\tTRINITY_DN104_c0_g2_i1\t385.00\t120.79\t3.00\t291.84\t262.76\n+TRINITY_DN105_c0_g1\tTRINITY_DN105_c0_g1_i1\t569.00\t304.51\t7.00\t270.12\t243.21\n+TRINITY_DN105_c0_g2\tTRINITY_DN105_c0_g2_i1\t1004.00\t739.51\t16.00\t254.24\t228.91\n+TRINITY_DN106_c0_g1\tTRINITY_DN106_c0_g1_i1\t818.00\t553.51\t29.00\t615.65\t554.31\n+TRINITY_DN107_c0_g1\tTRINITY_DN107_c0_g1_i1\t564.00\t299.51\t13.00\t510.03\t459.21\n+TRINITY_DN108_c0_g1\tTRINITY_DN108_c0_g1_i1\t300.00\t47.43\t1.00\t247.77\t223.08\n+TRINITY_DN108_c0_g2\tTRINITY_DN108_c0_g2_i1\t735.00\t470.51\t8.00\t199.79\t179.89\n+TRINITY_DN109_c0_g1\tTRINITY_DN109_c0_g1_i1,TRINITY_DN109_c0_g1_i2\t1120.33\t855.84\t55.00\t755.15\t679.91\n+TRINITY_DN10_c0_g1\tTRINITY_DN10_c0_g1_i1\t735.00\t470.51\t97.00\t2422.51\t2181.14\n+TRINITY_DN110_c0_g1\tTRINITY_DN110_c0_g1_i1\t1194.00\t929.51\t644.00\t8141.33\t7330.14\n+TRINITY_DN111_c0_g1\tTRINITY_DN111_c0_g1_i1\t263.00\t23.97\t6.00\t2941.61\t2648.52\n+TRINITY_DN111_c0_g2\tTRINITY_DN111_c0_g2_i1\t371.00\t107.34\t13.00\t1423.20\t1281.39\n+TRINITY_DN112_c0_g1\tTRINITY_DN112_c0_g1_i1\t370.00\t106.39\t2.00\t220.90\t198.89\n+TRINITY_DN113_c0_g1\tTRINITY_DN113_c0_g1_i1\t503.00\t238.51\t12.00\t591.20\t532.30\n+TRINITY_DN115_c0_g1\tTRINITY_DN115_c0_g1_i1\t989.00\t724.51\t28.00\t454.13\t408.88\n+TRINITY_DN115_c0_g2\tTRINITY_DN115_c0_g2_i1\t513.00\t248.51\t9.00\t425.56\t383.16\n+TRINITY_DN116_c0_g1\tTRINITY_DN116_c0_g1_i1\t354.00\t91.62\t2.00\t256.51\t230.95\n+TRINITY_DN116_c0_g2\tTRINITY_DN116_c0_g2_i1\t260.00\t22.37\t2.00\t1050.69\t946.00\n+TRINITY_DN116_c0_g3\tTRINITY_DN116_c0_g3_i1\t219.00\t6.16\t1.00\t1907.25\t1717.21\n+TRINITY_DN117_c0_g1\tTRINITY_DN117_c0_g1_i1\t208.00\t3.71\t0.00\t0.00\t0.00\n+TRINITY_DN117_c0_g2\tTRINITY_DN117_c0_g2_i1\t235.00\t11.19\t0.00\t0.00\t0.00\n+TRINITY_DN117_c0_g3\tTRINITY_DN117_c0_g3_i1\t345.00\t83.60\t4.00\t562.20\t506.19\n+TRINITY_DN117_c0_g4\tTRINITY_DN117_c0_g4_i1\t276.00\t31.46\t1.00\t373.50\t336.29\n+TRINITY_DN117_c0_g5\tTRINITY_DN117_c0_g5_i1\t560.00\t295.51\t9.00\t357.88\t322.22\n+TRINITY_DN118_c0_g1\tTRINITY_DN118_c0_g1_i1\t450.00\t185.51\t7.00\t443.40\t399.22\n+TRINITY_DN118_c0_g2\tTRINITY_DN118_c0_g2_i1\t242.00\t13.93\t2.00\t1687.41\t1519.28\n+TRINITY_DN118_c0_g3\tTRINITY_DN118_c0_g3_i1\t207.00\t3.53\t0.00\t0.00\t0.00\n+TRINITY_DN118_c0_g4\tTRINITY_DN118_c0_g4_i1\t228.00\t8.78\t0.00\t0.00\t0.00\n+TRINITY_DN118_c0_g5\tTRINITY_DN118_c0_g5_i1\t303.00\t49.60\t2.00\t473.79\t426.59\n+TRINITY_DN119_c0_g1\tTRINITY_DN119_c0_g1_i1\t316.00\t59.46\t0.00\t0.00\t0.00\n+TRINITY_DN119_c0_g2\tTRINITY_DN119_c0_g2_i1\t529.00\t264.51\t5.00\t222.12\t199.99\n+TRINITY_DN119_c0_g3\tTRINITY_DN119_c0_g3_i1\t403.00\t138.57\t0.00\t0.00\t0.00\n+TRINITY_DN11_c0_g1\tTRINITY_DN11_c0_g1_i1\t311.00\t55.59\t6.00\t1268.37\t1142.00\n+TRINITY_DN120_c0_g1\tTRINITY_DN120_c0_g1_i1\t245.00\t15.19\t1.00\t773.34\t696.28\n+TRINITY_DN120_c0_g2\tTRINITY_DN120_c0_g2_i1\t310.00\t54.82\t0.00\t0.00\t0.00\n+TRINITY_DN120_c0_g3\tTRINITY_DN120_c0_g3_i1\t976.00\t711.51\t20.00\t330.30\t297.39\n+TRINITY_DN121_c0_g1\tTRINITY_DN121_c0_g1_i1\t1780.00\t1515.51\t196.00\t1519.71\t1368.29\n+TRINITY_DN122_c0_g1\tTRINITY_DN122_c0_g1_i1\t1415.00\t1150.51\t32.00\t326.83\t294.27\n+TRINITY_DN122_c0_g2\tTRINITY_DN122_c0_g2_i1\t459.00\t194.51\t6.00\t362.47\t326.35\n+TRINITY_DN123_c0_g1\tTRINITY_DN123_c0_g1_i1\t203.00\t2.87\t0.00\t0.00\t0.00\n+TRINITY_DN123_c0_g2\tTRINITY_DN123_c0_g2_i1\t302.00\t48.87\t4.00\t961.74\t865.91\n+TRINITY_DN124_c0_g1\tTRINITY_DN124_c0_g1_i1\t519.00\t254.51\t19.00\t877.23\t789.82\n+TRINITY_DN124_c0_g2\tTRINITY_DN124_c0_g2_i1\t377.00\t113.05\t13.00\t1351.26\t1216.63\n+TRINITY_DN124_c0_g3\tTRINITY_DN124_c0_g3_i1\t1509.00\t1'..b'DN67_c0_g1_i1\t270.00\t27.90\t2.00\t842.45\t758.51\n+TRINITY_DN68_c0_g1\tTRINITY_DN68_c0_g1_i1\t829.00\t564.51\t50.00\t1040.79\t937.08\n+TRINITY_DN69_c0_g1\tTRINITY_DN69_c0_g1_i1\t381.00\t116.90\t5.00\t502.58\t452.50\n+TRINITY_DN70_c0_g1\tTRINITY_DN70_c0_g1_i1\t216.00\t5.41\t0.00\t0.00\t0.00\n+TRINITY_DN70_c0_g2\tTRINITY_DN70_c0_g2_i1\t496.00\t231.51\t9.00\t456.81\t411.29\n+TRINITY_DN71_c0_g1\tTRINITY_DN71_c0_g1_i1\t247.00\t16.07\t0.00\t0.00\t0.00\n+TRINITY_DN71_c0_g2\tTRINITY_DN71_c0_g2_i1\t1598.00\t1333.51\t191.00\t1683.06\t1515.37\n+TRINITY_DN72_c0_g1\tTRINITY_DN72_c0_g1_i1\t348.00\t86.25\t7.00\t953.68\t858.65\n+TRINITY_DN74_c0_g1\tTRINITY_DN74_c0_g1_i1\t965.00\t700.51\t25.00\t419.36\t377.58\n+TRINITY_DN75_c0_g1\tTRINITY_DN75_c0_g1_i1\t266.00\t25.62\t2.00\t917.31\t825.91\n+TRINITY_DN75_c0_g2\tTRINITY_DN75_c0_g2_i1\t202.00\t2.72\t0.00\t0.00\t0.00\n+TRINITY_DN76_c0_g1\tTRINITY_DN76_c0_g1_i1\t525.00\t260.51\t14.00\t631.49\t568.57\n+TRINITY_DN76_c0_g2\tTRINITY_DN76_c0_g2_i1\t379.00\t114.97\t4.00\t408.82\t368.08\n+TRINITY_DN76_c0_g3\tTRINITY_DN76_c0_g3_i1\t1516.00\t1251.51\t55.00\t516.41\t464.95\n+TRINITY_DN77_c0_g1\tTRINITY_DN77_c0_g1_i1\t220.00\t6.43\t0.00\t0.00\t0.00\n+TRINITY_DN77_c0_g2\tTRINITY_DN77_c0_g2_i1\t265.00\t25.06\t0.00\t0.00\t0.00\n+TRINITY_DN78_c0_g1\tTRINITY_DN78_c0_g1_i1\t207.00\t3.53\t0.00\t0.00\t0.00\n+TRINITY_DN78_c0_g2\tTRINITY_DN78_c0_g2_i1\t1720.00\t1455.51\t77.00\t621.64\t559.70\n+TRINITY_DN78_c0_g3\tTRINITY_DN78_c0_g3_i1\t721.00\t456.51\t17.00\t437.58\t393.98\n+TRINITY_DN79_c0_g1\tTRINITY_DN79_c0_g1_i1\t587.00\t322.51\t7.00\t255.05\t229.63\n+TRINITY_DN80_c0_g1\tTRINITY_DN80_c0_g1_i1\t319.00\t61.82\t1.00\t190.07\t171.14\n+TRINITY_DN81_c0_g1\tTRINITY_DN81_c0_g1_i1\t1289.00\t1024.51\t143.00\t1640.15\t1476.73\n+TRINITY_DN81_c0_g2\tTRINITY_DN81_c0_g2_i1\t1182.00\t917.51\t115.00\t1472.82\t1326.07\n+TRINITY_DN82_c0_g1\tTRINITY_DN82_c0_g1_i1\t1440.00\t1175.51\t86.00\t859.68\t774.02\n+TRINITY_DN83_c0_g1\tTRINITY_DN83_c0_g1_i1\t212.00\t4.51\t0.00\t0.00\t0.00\n+TRINITY_DN83_c0_g2\tTRINITY_DN83_c0_g2_i1\t281.00\t34.57\t2.00\t679.92\t612.17\n+TRINITY_DN84_c0_g1\tTRINITY_DN84_c0_g1_i1\t362.00\t98.93\t1.00\t118.78\t106.95\n+TRINITY_DN85_c0_g1\tTRINITY_DN85_c0_g1_i1\t626.00\t361.51\t23.00\t747.60\t673.11\n+TRINITY_DN85_c0_g2\tTRINITY_DN85_c0_g2_i1\t1045.00\t780.51\t46.00\t692.54\t623.53\n+TRINITY_DN86_c0_g1\tTRINITY_DN86_c0_g1_i1\t298.00\t46.00\t0.00\t0.00\t0.00\n+TRINITY_DN86_c0_g2\tTRINITY_DN86_c0_g2_i1\t332.00\t72.44\t1.00\t162.21\t146.05\n+TRINITY_DN86_c0_g3\tTRINITY_DN86_c0_g3_i1\t285.00\t37.13\t1.00\t316.44\t284.91\n+TRINITY_DN87_c0_g1\tTRINITY_DN87_c0_g1_i1\t267.00\t26.18\t2.00\t897.64\t808.20\n+TRINITY_DN89_c0_g1\tTRINITY_DN89_c0_g1_i1\t259.00\t21.85\t0.00\t0.00\t0.00\n+TRINITY_DN89_c0_g2\tTRINITY_DN89_c0_g2_i1\t797.00\t532.51\t15.00\t331.00\t298.02\n+TRINITY_DN89_c0_g3\tTRINITY_DN89_c0_g3_i1\t232.00\t10.12\t0.00\t0.00\t0.00\n+TRINITY_DN8_c0_g1\tTRINITY_DN8_c0_g1_i1\t2016.00\t1751.51\t587.00\t3938.12\t3545.73\n+TRINITY_DN90_c0_g1\tTRINITY_DN90_c0_g1_i1\t456.00\t191.51\t5.00\t306.79\t276.22\n+TRINITY_DN91_c0_g1\tTRINITY_DN91_c0_g1_i1\t1374.00\t1109.51\t40.00\t423.64\t381.43\n+TRINITY_DN92_c0_g1\tTRINITY_DN92_c0_g1_i1\t1030.00\t765.51\t1154.00\t17714.07\t15949.07\n+TRINITY_DN93_c0_g1\tTRINITY_DN93_c0_g1_i1\t237.00\t11.94\t0.00\t0.00\t0.00\n+TRINITY_DN93_c0_g2\tTRINITY_DN93_c0_g2_i1\t249.00\t16.97\t0.00\t0.00\t0.00\n+TRINITY_DN93_c0_g3\tTRINITY_DN93_c0_g3_i1\t660.00\t395.51\t18.00\t534.78\t481.50\n+TRINITY_DN94_c0_g1\tTRINITY_DN94_c0_g1_i1\t381.00\t116.90\t3.00\t301.55\t271.50\n+TRINITY_DN95_c0_g1\tTRINITY_DN95_c0_g1_i1\t407.00\t142.55\t4.00\t329.73\t296.87\n+TRINITY_DN95_c0_g2\tTRINITY_DN95_c0_g2_i1\t614.00\t349.51\t16.00\t537.93\t484.33\n+TRINITY_DN95_c0_g3\tTRINITY_DN95_c0_g3_i1\t264.00\t24.51\t2.00\t958.73\t863.21\n+TRINITY_DN96_c0_g1\tTRINITY_DN96_c0_g1_i1\t652.00\t387.51\t29.00\t879.38\t791.76\n+TRINITY_DN97_c0_g1\tTRINITY_DN97_c0_g1_i1\t500.00\t235.51\t31.00\t1546.73\t1392.62\n+TRINITY_DN97_c0_g2\tTRINITY_DN97_c0_g2_i1\t1352.00\t1087.51\t82.00\t886.02\t797.74\n+TRINITY_DN98_c0_g1\tTRINITY_DN98_c0_g1_i1\t499.00\t234.51\t10.00\t501.07\t451.15\n+TRINITY_DN99_c0_g1\tTRINITY_DN99_c0_g1_i1\t960.00\t695.51\t32.00\t540.64\t486.77\n+TRINITY_DN99_c0_g2\tTRINITY_DN99_c0_g2_i1\t201.00\t2.58\t0.00\t0.00\t0.00\n+TRINITY_DN9_c0_g1\tTRINITY_DN9_c0_g1_i1\t270.00\t27.90\t1.00\t421.22\t379.25\n' |
| b |
| diff -r 000000000000 -r 5eca0c75b178 test-data/Sp_hs.RSEM.genes.results --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Sp_hs.RSEM.genes.results Tue Jul 17 11:47:32 2018 -0400 |
| b |
| b'@@ -0,0 +1,353 @@\n+gene_id\ttranscript_id(s)\tlength\teffective_length\texpected_count\tTPM\tFPKM\n+TRINITY_DN100_c0_g1\tTRINITY_DN100_c0_g1_i1\t223.00\t3.02\t1.00\t3639.81\t3284.97\n+TRINITY_DN100_c0_g2\tTRINITY_DN100_c0_g2_i1\t794.00\t513.05\t21.00\t449.31\t405.51\n+TRINITY_DN101_c0_g1\tTRINITY_DN101_c0_g1_i1\t1450.00\t1169.05\t56.00\t525.82\t474.56\n+TRINITY_DN101_c0_g2\tTRINITY_DN101_c0_g2_i1\t271.00\t19.35\t0.00\t0.00\t0.00\n+TRINITY_DN101_c0_g3\tTRINITY_DN101_c0_g3_i1\t793.00\t512.05\t19.00\t407.31\t367.60\n+TRINITY_DN102_c0_g1\tTRINITY_DN102_c0_g1_i1\t217.00\t2.11\t0.00\t0.00\t0.00\n+TRINITY_DN104_c0_g1\tTRINITY_DN104_c0_g1_i1\t326.00\t54.66\t5.00\t1004.09\t906.20\n+TRINITY_DN104_c0_g2\tTRINITY_DN104_c0_g2_i1\t385.00\t105.12\t9.00\t939.81\t848.19\n+TRINITY_DN105_c0_g1\tTRINITY_DN105_c0_g1_i1\t569.00\t288.05\t8.00\t304.87\t275.15\n+TRINITY_DN105_c0_g2\tTRINITY_DN105_c0_g2_i1\t1004.00\t723.05\t26.00\t394.72\t356.24\n+TRINITY_DN106_c0_g1\tTRINITY_DN106_c0_g1_i1\t818.00\t537.05\t19.00\t388.35\t350.49\n+TRINITY_DN107_c0_g1\tTRINITY_DN107_c0_g1_i1\t564.00\t283.05\t7.00\t271.47\t245.01\n+TRINITY_DN108_c0_g1\tTRINITY_DN108_c0_g1_i1\t300.00\t36.21\t0.00\t0.00\t0.00\n+TRINITY_DN108_c0_g2\tTRINITY_DN108_c0_g2_i1\t735.00\t454.05\t18.00\t435.17\t392.74\n+TRINITY_DN109_c0_g1\tTRINITY_DN109_c0_g1_i1,TRINITY_DN109_c0_g1_i2\t1117.82\t836.86\t212.00\t2780.78\t2509.68\n+TRINITY_DN10_c0_g1\tTRINITY_DN10_c0_g1_i1\t735.00\t454.05\t36.00\t870.34\t785.49\n+TRINITY_DN110_c0_g1\tTRINITY_DN110_c0_g1_i1\t1194.00\t913.05\t227.00\t2729.09\t2463.03\n+TRINITY_DN111_c0_g1\tTRINITY_DN111_c0_g1_i1\t263.00\t15.51\t0.00\t0.00\t0.00\n+TRINITY_DN111_c0_g2\tTRINITY_DN111_c0_g2_i1\t371.00\t92.23\t0.00\t0.00\t0.00\n+TRINITY_DN112_c0_g1\tTRINITY_DN112_c0_g1_i1\t370.00\t91.33\t1.00\t120.20\t108.48\n+TRINITY_DN113_c0_g1\tTRINITY_DN113_c0_g1_i1\t503.00\t222.05\t6.00\t296.61\t267.70\n+TRINITY_DN115_c0_g1\tTRINITY_DN115_c0_g1_i1\t989.00\t708.05\t25.00\t387.58\t349.80\n+TRINITY_DN115_c0_g2\tTRINITY_DN115_c0_g2_i1\t513.00\t232.05\t4.00\t189.22\t170.77\n+TRINITY_DN116_c0_g1\tTRINITY_DN116_c0_g1_i1\t354.00\t77.32\t1.00\t141.97\t128.13\n+TRINITY_DN116_c0_g2\tTRINITY_DN116_c0_g2_i1\t260.00\t14.18\t0.00\t0.00\t0.00\n+TRINITY_DN116_c0_g3\tTRINITY_DN116_c0_g3_i1\t219.00\t2.38\t0.00\t0.00\t0.00\n+TRINITY_DN117_c0_g1\tTRINITY_DN117_c0_g1_i1\t208.00\t1.24\t0.00\t0.00\t0.00\n+TRINITY_DN117_c0_g2\tTRINITY_DN117_c0_g2_i1\t235.00\t5.61\t2.00\t3914.29\t3532.69\n+TRINITY_DN117_c0_g3\tTRINITY_DN117_c0_g3_i1\t345.00\t69.76\t2.00\t314.69\t284.01\n+TRINITY_DN117_c0_g4\tTRINITY_DN117_c0_g4_i1\t276.00\t21.95\t1.00\t500.14\t451.38\n+TRINITY_DN117_c0_g5\tTRINITY_DN117_c0_g5_i1\t560.00\t279.05\t11.00\t432.71\t390.53\n+TRINITY_DN118_c0_g1\tTRINITY_DN118_c0_g1_i1\t450.00\t169.05\t4.00\t259.73\t234.41\n+TRINITY_DN118_c0_g2\tTRINITY_DN118_c0_g2_i1\t242.00\t7.58\t0.00\t0.00\t0.00\n+TRINITY_DN118_c0_g3\tTRINITY_DN118_c0_g3_i1\t207.00\t1.18\t0.00\t0.00\t0.00\n+TRINITY_DN118_c0_g4\tTRINITY_DN118_c0_g4_i1\t228.00\t3.97\t0.00\t0.00\t0.00\n+TRINITY_DN118_c0_g5\tTRINITY_DN118_c0_g5_i1\t303.00\t38.19\t0.00\t0.00\t0.00\n+TRINITY_DN119_c0_g1\tTRINITY_DN119_c0_g1_i1\t316.00\t47.23\t4.00\t929.65\t839.02\n+TRINITY_DN119_c0_g2\tTRINITY_DN119_c0_g2_i1\t529.00\t248.05\t12.00\t531.04\t479.27\n+TRINITY_DN119_c0_g3\tTRINITY_DN119_c0_g3_i1\t403.00\t122.36\t1.00\t89.71\t80.97\n+TRINITY_DN11_c0_g1\tTRINITY_DN11_c0_g1_i1\t311.00\t43.67\t10.00\t2513.77\t2268.70\n+TRINITY_DN120_c0_g1\tTRINITY_DN120_c0_g1_i1\t245.00\t8.53\t0.00\t0.00\t0.00\n+TRINITY_DN120_c0_g2\tTRINITY_DN120_c0_g2_i1\t310.00\t42.97\t1.00\t255.47\t230.57\n+TRINITY_DN120_c0_g3\tTRINITY_DN120_c0_g3_i1\t976.00\t695.05\t15.00\t236.90\t213.80\n+TRINITY_DN121_c0_g1\tTRINITY_DN121_c0_g1_i1\t1780.00\t1499.05\t234.00\t1713.50\t1546.46\n+TRINITY_DN122_c0_g1\tTRINITY_DN122_c0_g1_i1\t1415.00\t1134.05\t16.00\t154.87\t139.77\n+TRINITY_DN122_c0_g2\tTRINITY_DN122_c0_g2_i1\t459.00\t178.05\t1.00\t61.65\t55.64\n+TRINITY_DN123_c0_g1\tTRINITY_DN123_c0_g1_i1\t203.00\t0.00\t0.00\t0.00\t0.00\n+TRINITY_DN123_c0_g2\tTRINITY_DN123_c0_g2_i1\t302.00\t37.53\t0.00\t0.00\t0.00\n+TRINITY_DN124_c0_g1\tTRINITY_DN124_c0_g1_i1\t519.00\t238.05\t7.00\t322.79\t291.32\n+TRINITY_DN124_c0_g2\tTRINITY_DN124_c0_g2_i1\t377.00\t97.68\t4.00\t449.49\t405.67\n+TRINITY_DN124_c0_g3\tTRINITY_DN124_c0_g3_i1\t1509.00\t1228.05\t28.00\t250.28\t225.88\n+TRINITY_DN124_c0'..b'RINITY_DN67_c0_g1_i1\t270.00\t18.85\t0.00\t0.00\t0.00\n+TRINITY_DN68_c0_g1\tTRINITY_DN68_c0_g1_i1\t829.00\t548.05\t15.00\t300.44\t271.15\n+TRINITY_DN69_c0_g1\tTRINITY_DN69_c0_g1_i1\t381.00\t101.38\t4.00\t433.10\t390.88\n+TRINITY_DN70_c0_g1\tTRINITY_DN70_c0_g1_i1\t216.00\t1.99\t0.00\t0.00\t0.00\n+TRINITY_DN70_c0_g2\tTRINITY_DN70_c0_g2_i1\t496.00\t215.05\t3.00\t153.13\t138.20\n+TRINITY_DN71_c0_g1\tTRINITY_DN71_c0_g1_i1\t247.00\t9.19\t0.00\t0.00\t0.00\n+TRINITY_DN71_c0_g2\tTRINITY_DN71_c0_g2_i1\t1598.00\t1317.05\t342.00\t2850.42\t2572.54\n+TRINITY_DN72_c0_g1\tTRINITY_DN72_c0_g1_i1\t348.00\t72.26\t1.00\t151.92\t137.11\n+TRINITY_DN74_c0_g1\tTRINITY_DN74_c0_g1_i1\t965.00\t684.05\t17.00\t272.80\t246.21\n+TRINITY_DN75_c0_g1\tTRINITY_DN75_c0_g1_i1\t266.00\t16.90\t0.00\t0.00\t0.00\n+TRINITY_DN75_c0_g2\tTRINITY_DN75_c0_g2_i1\t202.00\t0.00\t0.00\t0.00\t0.00\n+TRINITY_DN76_c0_g1\tTRINITY_DN76_c0_g1_i1\t525.00\t244.05\t3.00\t134.94\t121.78\n+TRINITY_DN76_c0_g2\tTRINITY_DN76_c0_g2_i1\t379.00\t99.53\t1.00\t110.29\t99.54\n+TRINITY_DN76_c0_g3\tTRINITY_DN76_c0_g3_i1\t1516.00\t1235.05\t31.00\t275.53\t248.67\n+TRINITY_DN77_c0_g1\tTRINITY_DN77_c0_g1_i1\t220.00\t2.53\t1.00\t4339.65\t3916.58\n+TRINITY_DN77_c0_g2\tTRINITY_DN77_c0_g2_i1\t265.00\t16.43\t2.00\t1336.19\t1205.92\n+TRINITY_DN78_c0_g1\tTRINITY_DN78_c0_g1_i1\t207.00\t1.18\t0.00\t0.00\t0.00\n+TRINITY_DN78_c0_g2\tTRINITY_DN78_c0_g2_i1\t1720.00\t1439.05\t59.00\t450.05\t406.18\n+TRINITY_DN78_c0_g3\tTRINITY_DN78_c0_g3_i1\t721.00\t440.05\t13.00\t324.29\t292.67\n+TRINITY_DN79_c0_g1\tTRINITY_DN79_c0_g1_i1\t587.00\t306.05\t12.00\t430.41\t388.45\n+TRINITY_DN80_c0_g1\tTRINITY_DN80_c0_g1_i1\t319.00\t49.42\t1.00\t222.12\t200.47\n+TRINITY_DN81_c0_g1\tTRINITY_DN81_c0_g1_i1\t1289.00\t1008.05\t63.00\t686.03\t619.15\n+TRINITY_DN81_c0_g2\tTRINITY_DN81_c0_g2_i1\t1182.00\t901.05\t50.00\t609.13\t549.74\n+TRINITY_DN82_c0_g1\tTRINITY_DN82_c0_g1_i1\t1440.00\t1159.05\t57.00\t539.83\t487.20\n+TRINITY_DN83_c0_g1\tTRINITY_DN83_c0_g1_i1\t212.00\t1.56\t0.00\t0.00\t0.00\n+TRINITY_DN83_c0_g2\tTRINITY_DN83_c0_g2_i1\t281.00\t24.68\t0.00\t0.00\t0.00\n+TRINITY_DN84_c0_g1\tTRINITY_DN84_c0_g1_i1\t362.00\t84.23\t1.00\t130.32\t117.62\n+TRINITY_DN85_c0_g1\tTRINITY_DN85_c0_g1_i1\t626.00\t345.05\t17.00\t540.82\t488.10\n+TRINITY_DN85_c0_g2\tTRINITY_DN85_c0_g2_i1\t1045.00\t764.05\t40.00\t574.68\t518.65\n+TRINITY_DN86_c0_g1\tTRINITY_DN86_c0_g1_i1\t298.00\t34.91\t2.00\t628.80\t567.50\n+TRINITY_DN86_c0_g2\tTRINITY_DN86_c0_g2_i1\t332.00\t59.30\t3.00\t555.33\t501.19\n+TRINITY_DN86_c0_g3\tTRINITY_DN86_c0_g3_i1\t285.00\t26.95\t2.00\t814.50\t735.10\n+TRINITY_DN87_c0_g1\tTRINITY_DN87_c0_g1_i1\t267.00\t17.38\t1.00\t631.61\t570.04\n+TRINITY_DN89_c0_g1\tTRINITY_DN89_c0_g1_i1\t259.00\t13.76\t1.00\t797.91\t720.12\n+TRINITY_DN89_c0_g2\tTRINITY_DN89_c0_g2_i1\t797.00\t516.05\t8.00\t170.17\t153.58\n+TRINITY_DN89_c0_g3\tTRINITY_DN89_c0_g3_i1\t232.00\t4.87\t0.00\t0.00\t0.00\n+TRINITY_DN8_c0_g1\tTRINITY_DN8_c0_g1_i1\t2016.00\t1735.05\t923.00\t5839.49\t5270.20\n+TRINITY_DN90_c0_g1\tTRINITY_DN90_c0_g1_i1\t456.00\t175.05\t9.00\t564.37\t509.35\n+TRINITY_DN91_c0_g1\tTRINITY_DN91_c0_g1_i1\t1374.00\t1093.05\t92.00\t923.92\t833.85\n+TRINITY_DN92_c0_g1\tTRINITY_DN92_c0_g1_i1\t1030.00\t749.05\t355.00\t5202.40\t4695.22\n+TRINITY_DN93_c0_g1\tTRINITY_DN93_c0_g1_i1\t237.00\t6.14\t1.00\t1787.86\t1613.57\n+TRINITY_DN93_c0_g2\tTRINITY_DN93_c0_g2_i1\t249.00\t9.89\t0.00\t0.00\t0.00\n+TRINITY_DN93_c0_g3\tTRINITY_DN93_c0_g3_i1\t660.00\t379.05\t7.00\t202.72\t182.95\n+TRINITY_DN94_c0_g1\tTRINITY_DN94_c0_g1_i1\t381.00\t101.38\t4.00\t433.10\t390.88\n+TRINITY_DN95_c0_g1\tTRINITY_DN95_c0_g1_i1\t407.00\t126.27\t6.00\t521.60\t470.75\n+TRINITY_DN95_c0_g2\tTRINITY_DN95_c0_g2_i1\t614.00\t333.05\t9.00\t296.63\t267.72\n+TRINITY_DN95_c0_g3\tTRINITY_DN95_c0_g3_i1\t264.00\t15.97\t2.00\t1375.06\t1241.01\n+TRINITY_DN96_c0_g1\tTRINITY_DN96_c0_g1_i1\t652.00\t371.05\t16.00\t473.34\t427.20\n+TRINITY_DN97_c0_g1\tTRINITY_DN97_c0_g1_i1\t500.00\t219.05\t8.00\t400.90\t361.82\n+TRINITY_DN97_c0_g2\tTRINITY_DN97_c0_g2_i1\t1352.00\t1071.05\t30.00\t307.47\t277.49\n+TRINITY_DN98_c0_g1\tTRINITY_DN98_c0_g1_i1\t499.00\t218.05\t6.00\t302.05\t272.61\n+TRINITY_DN99_c0_g1\tTRINITY_DN99_c0_g1_i1\t960.00\t679.05\t19.00\t307.14\t277.20\n+TRINITY_DN99_c0_g2\tTRINITY_DN99_c0_g2_i1\t201.00\t0.00\t0.00\t0.00\t0.00\n+TRINITY_DN9_c0_g1\tTRINITY_DN9_c0_g1_i1\t270.00\t18.85\t1.00\t582.36\t525.59\n' |