From d59b7ec5913a00ee83c7d3461e105d7f6b221502 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Fri, 16 Dec 2011 12:54:21 -0500
Subject: [PATCH] Add Maximal Information-based Nonparametric Exploration
 (MINE) tool.

---
 tool_conf.xml.sample        |  1 +
 tools/stats/MINE.xml        | 82 +++++++++++++++++++++++++++++++++++
 tools/stats/mine_wrapper.py | 85 +++++++++++++++++++++++++++++++++++++
 3 files changed, 168 insertions(+)
 create mode 100644 tools/stats/MINE.xml
 create mode 100644 tools/stats/mine_wrapper.py

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 5405c591cb7..2e038351e73 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -149,6 +149,7 @@
     <tool file="stats/plot_from_lda.xml" />
     <tool file="regVariation/t_test_two_samples.xml" />
     <tool file="regVariation/compute_q_values.xml" />
+    <tool file="stats/MINE.xml" />
     
     <label text="GFF" id="gff" />
     <tool file="stats/count_gff_features.xml" />
diff --git a/tools/stats/MINE.xml b/tools/stats/MINE.xml
new file mode 100644
index 00000000000..7f8666b28ec
--- /dev/null
+++ b/tools/stats/MINE.xml
@@ -0,0 +1,82 @@
+<tool id="maximal_information_based_nonparametric_exploration" name="MINE" version="0.0.1">
+  <description>- Maximal Information-based Nonparametric Exploration</description>
+  <requirements>
+      <requirement type="package" version="1.0">MINE</requirement>
+  </requirements>
+  <command interpreter="python">mine_wrapper.py
+    --jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/mine/MINE.jar" 
+    
+    --infile "${input_file}"
+    
+    #if str( $master_variable_type.master_variable_type_selector ) in [ 'allPairs', 'adjacentPairs' ]:
+      --master_variable "${master_variable_type.master_variable_type_selector}"
+    #else:
+        --master_variable "${master_variable_type.master_variable}"
+    #end if
+    
+    --cv "${cv}"
+    
+    --exp "${exp}"
+    
+    --c "${c}"
+    
+    ##--gc ##skip
+    
+    
+    #if str( $master_variable_type.master_variable_type_selector ) != 'allPairs' and $master_variable_type.permute:
+      --permute
+    #end if
+    
+    --output_results "${output_results}"
+    
+    --output_log "${output_log}"
+  </command>
+  <inputs>
+    <param name="input_file" type="data" format="csv" label="CSV file" />
+    
+    <conditional name="master_variable_type">
+      <param name="master_variable_type_selector" type="select" label="Choose the master variable type">
+        <option value="allPairs">allPairs</option>
+        <option value="adjacentPairs">adjacentPairs</option>
+        <option value="compare_against_ith" selected="True">compare against i-th</option>
+      </param>
+      <when value="compare_against_ith">
+        <param type="integer" value="0" name="master_variable" />
+        <param type="boolean" truevalue="--permute" false_value="" name="permute" checked="False" />
+      </when>
+      <when value="adjacentPairs">
+        <param type="boolean" truevalue="--permute" false_value="" name="permute" checked="False" />
+      </when>
+    </conditional>
+    
+    <param type="float" value="0" name="cv" />
+    
+    <param type="float" value="0.6" name="exp" />
+    
+    <param type="float" value="15" name="c" />
+    
+  </inputs>
+  <outputs>
+    <data format="csv" name="output_results" label="${tool.name} on ${on_string} (Results)" />
+    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
+  </outputs>
+  <tests>
+      <!-- TODO -->
+  </tests>
+  <help>
+**What it does**
+
+Applies the Maximal Information-based Nonparametric Exploration strategy to an input dataset.
+
+See http://www.exploredata.net/ for more information.
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `David N. Reshef, Yakir A. Reshef, Hilary K. Finucane5, Sharon R. Grossman, Gilean McVean, Peter J. Turnbaugh, Eric S. Lander, Michael Mitzenmacher, Pardis C. Sabeti Detecting Novel Associations in Large Data Sets. Science. 2011 Dec. &lt;http://www.sciencemag.org/content/334/6062/1518&gt;`_
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
+  </help>
+</tool>
diff --git a/tools/stats/mine_wrapper.py b/tools/stats/mine_wrapper.py
new file mode 100644
index 00000000000..4e8b30b0dd3
--- /dev/null
+++ b/tools/stats/mine_wrapper.py
@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+"""
+A wrapper script for running the MINE.jar commands.
+"""
+
+import sys, optparse, os, tempfile, subprocess, shutil
+
+CHUNK_SIZE = 2**20 #1mb
+
+BASE_NAME = "galaxy_mime_file.txt"
+JOB_ID = "galaxy_mine"
+
+def cleanup_before_exit( tmp_dir ):
+    if tmp_dir and os.path.exists( tmp_dir ):
+        print os.listdir( tmp_dir )
+        shutil.rmtree( tmp_dir )
+
+def open_file_from_option( filename, mode = 'rb' ):
+    if filename:
+        return open( filename, mode = mode )
+    return None
+
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-j', '--jar', dest='jar', action='store', type="string", help='Location of JAR file' )
+    parser.add_option( '-i', '--infile', dest='infile', action='store', type="string", help='infile' )
+    parser.add_option( '-m', '--master_variable', dest='master_variable', action='store', type="string", help='master_variable' )
+    parser.add_option( '-v', '--cv', dest='cv', action='store', type="string", help='cv' )
+    parser.add_option( '-e', '--exp', dest='exp', action='store', type="string", help='exp' )
+    parser.add_option( '-c', '--c', dest='c', action='store', type="string", help='c' )
+    parser.add_option( '-p', '--permute', dest='permute', action='store_true', default=False, help='permute' )
+    parser.add_option( '-o', '--output_results', dest='output_results', action='store', type="string", help='output_results' )
+    parser.add_option( '-l', '--output_log', dest='output_log', action='store', type="string", help='output_log' )
+    parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' )
+    parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' )
+    (options, args) = parser.parse_args()
+    
+    tmp_dir = tempfile.mkdtemp( prefix='tmp-MINE-' )
+    tmp_input_name = os.path.join( tmp_dir, BASE_NAME )
+    if options.permute:
+        permute = "-permute"
+    else:
+        permute = ""
+    
+    os.symlink( options.infile, tmp_input_name )
+    
+    cmd = 'java -jar "%s" "%s" %s -cv%s -exp%s -c%s %s "%s"' % ( options.jar, tmp_input_name, options.master_variable, options.cv, options.exp, options.c, permute, JOB_ID )
+    print cmd
+    
+    #set up stdout and stderr output options
+    stdout = open_file_from_option( options.stdout, mode = 'wb' )
+    stderr = open_file_from_option( options.stderr, mode = 'wb' )
+    #if no stderr file is specified, we'll use our own
+    if stderr is None:
+        stderr = tempfile.NamedTemporaryFile( prefix="MINE-stderr-", dir=tmp_dir )
+    
+    proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
+    return_code = proc.wait()
+    
+    if return_code:
+        stderr_target = sys.stderr
+    else:
+        stderr_target = sys.stdout
+    stderr.flush()
+    stderr.seek(0)
+    while True:
+        chunk = stderr.read( CHUNK_SIZE )
+        if chunk:
+            stderr_target.write( chunk )
+        else:
+            break
+    stderr.close()
+    
+    print os.listdir( tmp_dir )
+    
+    shutil.move( '%s,%s,Results.csv' % ( tmp_input_name, JOB_ID ), options.output_results )
+    shutil.move( '%s,%s,Status.csv' % ( tmp_input_name, JOB_ID ), options.output_log )
+    
+    cleanup_before_exit( tmp_dir )
+
+if __name__=="__main__": __main__()