added support for virtualenv based installs

.gitignore

@@ -2,3 +2,6 @@
 *.pyc
 splicing_0.1.tar.gz
 pysplicing-0.1.tar.gz
+env/*
+build/*
+misopy/test-output/*

Makefile

@@ -1,6 +1,9 @@
 
 all: Pythonpackage
 
+virtualenv: Pythonpackage
+	./install.sh
+
 ########################################################
 
 RSRC=$(wildcard src/*.c) $(wildcard src/*.h) $(wildcard src/*.pmt)

install.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+VIRTUALENV=`which virtualenv-2.7`
+if [ "$VIRTUALENV" == "" ]; then
+    VIRTUALENV=`which virtualenv-2.6`
+fi
+if [ "$VIRTUALENV" == "" ]; then
+    VIRTUALENV=`which virtualenv`
+fi
+if [ "$VIRTUALENV" == "" ]; then
+    echo "Missing virtualenv!"
+    exit 1
+fi
+
+if [ ! -e env ]; then 
+    echo "Initializing virtualenv folder (env)"
+    $VIRTUALENV env
+fi
+. env/bin/activate
+python setup.py install --prefix env
+pip install numpy
+pip install -r requirements.txt
+
+#
+# If you're on a Mac, and matplotlib won't install, try this:
+# LDFLAGS="-L/usr/X11/lib" CFLAGS="-I/usr/X11/include -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng15" pip install matplotlib

miso

@@ -0,0 +1,44 @@
+#!/bin/bash
+function usage() {
+    echo "Usage: $(basename $0) command args..."
+    echo ""
+    echo "Valid commands: exon_utils"
+    echo "                filter_events"
+    echo "                index_gff"
+    echo "                module_availability"
+    echo "                pe_utils"
+    echo "                plot"
+    echo "                run_events_analysis"
+    echo "                run"
+    echo "                sam_to_bam"
+    echo ""
+    exit 1
+}
+REAL=`python -c 'import os,sys;print os.path.realpath(sys.argv[1])' "$0"`
+DIR=`dirname "$REAL"`
+. $DIR/env/bin/activate
+
+
+if [ ! "$1" ]; then
+    usage
+fi
+
+cmd="$1"
+shift
+
+export MISO_SHELL_EXEC="$0"
+
+if [ "$cmd" == "run" ]; then
+    python $DIR/env/bin/run_miso.py "$@"
+elif [ -e "$DIR/env/bin/$cmd.py" ]; then
+    python "$DIR/env/bin/$cmd.py" "$@"
+elif [ -e "$DIR/env/bin/$cmd" ]; then
+    python "$DIR/env/bin/$cmd" "$@"
+elif [ -e "$cmd" ]; then
+    # this is for hard-coded commands, such as used in the cluster code
+    # or to run test-scripts
+    python "$cmd" "$@"
+else
+    echo "Unknown command: $cmd"
+    usage
+fi

misopy/run_events_analysis.py

@@ -47,8 +47,8 @@ def compute_all_genes_psi(gff_dir, bam_filename, read_len, output_dir,
     all_miso_cmds = []
 
     for gene_id, gff_index_filename in gene_ids_to_gff_index.iteritems():
-        miso_cmd = "python %s --compute-gene-psi \"%s\" \"%s\" %s %s --read-len %d " \
-                   %(miso_run, gene_id, gff_index_filename, bam_filename, output_dir,
+        miso_cmd = "%s %s --compute-gene-psi \"%s\" \"%s\" %s %s --read-len %d " \
+                   %(Settings.get_miso_exec(), miso_run, gene_id, gff_index_filename, bam_filename, output_dir,
                      read_len)
         if paired_end != None:
             # Run in paired-end mode
@@ -183,8 +183,9 @@ def compute_psi(sample_filenames, output_dir, event_type, read_len, overhang_len
 	events_filename = events.output_file(results_output_dir, sample_label)
 
 	# Run MISO on them
-	miso_cmd = 'python %s --compute-two-iso-psi %s %s --event-type %s --read-len %d --overhang-len %d ' \
-                   %(os.path.join(miso_path, 'run_miso.py'),
+	miso_cmd = '%s %s --compute-two-iso-psi %s %s --event-type %s --read-len %d --overhang-len %d ' \
+                   %(Settings.get_miso_exec(), 
+                     os.path.join(miso_path, 'run_miso.py'),
                      events_filename,
                      results_output_dir,
                      event_type,

misopy/run_miso.py

@@ -148,8 +148,9 @@ def run_two_iso_on_cluster(miso_path, events_filename, event_type, psi_outdir,
 	num_jobs_per_batch = len(event_batch)
 	print "Processing a batch of size %d events" %(num_jobs_per_batch)
 	for event_name in event_batch:
-	    miso_event_cmd = 'python %s --run-two-iso-event \"%s\" %s %s --event-type %s --read-len %d --overhang-len %d' \
-			     %(os.path.join(miso_path, 'run_miso.py'),
+	    miso_event_cmd = '%s %s --run-two-iso-event \"%s\" %s %s --event-type %s --read-len %d --overhang-len %d' \
+			     %(Settings.get_miso_exec(),
+                   os.path.join(miso_path, 'run_miso.py'),
 			       event_name,
 			       events_filename,
 			       psi_outdir,
@@ -181,7 +182,7 @@ def get_curr_script_cmd():
     Get the invocation of the current script (with its command line arguments) as a
     full command for use in a script.
     """
-    return 'python ' + get_current_args()
+    return '%s %s' % (Settings.get_miso_exec(), get_current_args())
 
 def strip_option(cmd, option):
     """

misopy/settings.py

@@ -1,10 +1,12 @@
 ##
 ## Settings with relevant directories
 ##
+
 import misopy
 from misopy.parse_csv import *
 import ConfigParser
 import os
+import sys
 
 miso_path = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))
 
@@ -141,6 +143,12 @@ def get_filters(cls, event_type):
     @classmethod
     def get(cls):
         return cls.global_settings
+
+    @classmethod
+    def get_miso_exec(cls):
+        if 'MISO_SHELL_EXEC' in os.environ:
+            return os.environ['MISO_SHELL_EXEC']
+        return sys.executable
 
 
 def load_settings(settings_filename):

misopy/test_cluster.py

@@ -4,6 +4,7 @@
 ##
 import unittest
 import os
+from misopy.settings import Settings
 
 class TestCluster(unittest.TestCase):
     """
@@ -13,8 +14,8 @@ def setUp(self):
         # Find out the current directory
         self.miso_path = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))
         self.tests_data_dir = os.path.join(self.miso_path, "test-data")
-        self.events_analysis_cmd = "python %s " %(os.path.join(self.miso_path,
-                                                               "run_events_analysis.py"))
+        self.events_analysis_cmd = "%s %s " % (Settings.get_miso_exec(),
+                                              os.path.join(self.miso_path, "run_events_analysis.py"))
         self.tests_output_dir = os.path.join(self.miso_path, "test-output")
         self.test_sam_filename = os.path.join(self.tests_data_dir,
                                               "sam-data",
@@ -69,7 +70,7 @@ def test_cluster_gene_psi(self):
         # First index the GFF of interest
         gff_filename = os.path.join(self.gff_events_dir, "mm9", "genes", "Atp2b1.mm9.gff")
         gff_index_dir = os.path.join(self.gff_events_dir, "mm9", "indexed")
-        index_cmd = "python %s --index %s %s" %(self.index_gff_script,
+        index_cmd = "%s %s --index %s %s" %(Settings.get_miso_exec(), self.index_gff_script,
                                                 gff_filename,
                                                 gff_index_dir)
 
@@ -92,4 +93,5 @@ def test_cluster_gene_psi(self):
 
 
 if __name__ == '__main__':
+    Settings.load()
     unittest.main()

misopy/test_miso.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 import unittest
 import os
+from misopy.settings import Settings
 
 class TestMISO(unittest.TestCase):
     """
@@ -10,8 +11,9 @@ def setUp(self):
         # Find out the current directory
         self.miso_path = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))
         self.tests_data_dir = os.path.join(self.miso_path, "test-data")
-        self.events_analysis_cmd = "python %s " %(os.path.join(self.miso_path,
-                                                               "run_events_analysis.py"))
+        self.events_analysis_cmd = "%s %s" % (Settings.get_miso_exec(),
+                                              os.path.join(self.miso_path,
+                                              "run_events_analysis.py"))
         self.tests_output_dir = os.path.join(self.miso_path, "test-output")
         self.test_sam_filename = os.path.join(self.tests_data_dir,
                                               "sam-data",
@@ -29,9 +31,10 @@ def test_a_sam_to_bam(self):
 
         print "Testing conversion of SAM to BAM..."
         output_dir = os.path.join(self.tests_output_dir, "sam-output")
-        sam_to_bam_cmd = "python %s --convert %s %s" %(self.sam_to_bam_script,
-                                                       self.test_sam_filename,
-                                                       output_dir)
+        sam_to_bam_cmd = "%s %s --convert %s %s" % (Settings.get_miso_exec(),
+                                                    self.sam_to_bam_script,
+                                                    self.test_sam_filename,
+                                                    output_dir)
         print "Executing: %s" %(sam_to_bam_cmd)
         os.system(sam_to_bam_cmd)
 
@@ -58,9 +61,10 @@ def test_z_gene_psi(self):
         gff_filename = os.path.join(self.gff_events_dir, "mm9", "genes", "Atp2b1.mm9.gff")
         gff_index_dir = os.path.join(self.gff_events_dir, "mm9", "genes", "Atp2b1", "indexed")
         print "Testing GFF indexing of: %s" %(gff_filename)
-        index_cmd = "python %s --index %s %s" %(self.index_gff_script,
-                                                gff_filename,
-                                                gff_index_dir)
+        index_cmd = "%s %s --index %s %s" % (Settings.get_miso_exec(),
+                                             self.index_gff_script,
+                                             gff_filename,
+                                             gff_index_dir)
 
         print "Executing: %s" %(index_cmd)
         os.system(index_cmd)

requirements.txt

@@ -0,0 +1,5 @@
+numpy
+scipy
+simplejson
+pysam
+matplotlib