Essentiality files are outputed and unit tests adjusted.

albatradis/BlockInsertions.py

@@ -128,6 +128,7 @@ def essentiality(self, plotfile_objects, plotfile, filetype):
         if self.verbose:
             print("Essentiality:\t" + filetype + "\t" + e.output_filename)
 
+
         return pe
 
     def run_essentiality(self, plotfile_objects):
@@ -171,12 +172,13 @@ def generate_logfc_plot(self, analysis_type, essentiality_files):
         mid = int(len(files) / 2)
 
         t = TradisComparison(files[:mid], files[mid:], self.verbose, self.minimum_block, only_ess_files[:mid],
-                             only_ess_files[mid:])
+                             only_ess_files[mid:], analysis_type, self.prefix)
         t.run()
         p = PlotLog(t.output_filename, self.genome_length, self.minimum_logfc, self.pvalue, self.qvalue,
                     self.minimum_logcpm, self.window_size, self.span_gaps, self.report_decreased_insertions,
                     annotation_files[0])
         p.construct_plot_file()
+
         renamed_csv_file = os.path.join(self.prefix, analysis_type + ".csv")
         renamed_plot_file = os.path.join(self.prefix, analysis_type + ".plot")
 
@@ -185,6 +187,7 @@ def generate_logfc_plot(self, analysis_type, essentiality_files):
         os.remove(t.output_filename)
         os.remove(p.output_filename)
 
+
         if self.verbose:
             print("Comparison:\t" + renamed_csv_file)
             print("Plot log:\t" + renamed_plot_file)

albatradis/TradisComparison.py

@@ -2,6 +2,7 @@
 from tempfile import mkstemp
 import os
 import csv
+import shutil
 
 
 class GeneEssentiality:
@@ -24,14 +25,16 @@ def status(self):
 
 class TradisComparison:
     def __init__(self, condition_files, control_files, verbose, minimum_block, only_ess_files_condition,
-                 only_ess_files_control, exec="tradis_comparison.R"):
+                 only_ess_files_control, analysis_type, prefix,  exec="tradis_comparison.R"):
         self.condition_files = condition_files
         self.control_files = control_files
         self.exec = exec
         self.verbose = verbose
         self.minimum_block = minimum_block
         self.only_ess_files_condition = only_ess_files_condition
         self.only_ess_files_control = only_ess_files_control
+        self.analysis_type = analysis_type
+        self.prefix = prefix
 
         fd, self.output_filename = mkstemp()
         fd, self.conditions_fofn = mkstemp()
@@ -65,6 +68,12 @@ def all_gene_essentiality(self, input_filename):
             for e in ess_gene_names:
                 if e in genes_ess:
                     genes_ess[e].control += 1
+
+        condition_name = os.path.join(self.prefix, self.analysis_type + "_condition_essen.ess")
+        shutil.copy(self.only_ess_files_condition[0], condition_name)
+        control_name = os.path.join(self.prefix, self.analysis_type + "_control_essen.ess")
+        shutil.copy(self.only_ess_files_control[0], control_name)
+
         return genes_ess
 
     def create_fofn(self):

albatradis/TradisEssentiality.py

@@ -23,7 +23,7 @@ def run(self):
 
 		self.replace_comma_tabs(self.tabfile +".all.csv", self.output_filename)
 		shutil.copy(self.tabfile +".essen.csv", self.essential_filename)
-		
+
 		if self.verbose:
 			print("all.csv\t" + self.output_filename)
 			print("essen.csv\t" + self.essential_filename)
@@ -32,7 +32,7 @@ def run(self):
 		os.remove(self.tabfile +".essen.csv")
 		os.remove(self.tabfile +".ambig.csv")
 		os.remove(self.tabfile +".QC_and_changepoint_plots.pdf")
-		os.remove(self.tabfile )
+		os.remove(self.tabfile)
 
 		return self
 

albatradis/tests/AlbaTraDIS_test.py

@@ -70,18 +70,3 @@ def test_small_use_annotation(self):
 		self.assertTrue(t.run())
 		self.assertTrue(os.path.exists('testoutput'))
 		shutil.rmtree("testoutput")
-
-	# def test_example_toy(self):
-	# 	case = os.path.join(example_dir, '025mgLTricRep1.insert_site_plot_short.gz')
-	# 	control = os.path.join(example_dir, 'controlLBrep1.insert_site_plot_short.gz')
-	# 	emblfile = os.path.join(example_dir, 'reference_BW25113_short.embl')
-	# 	out_dir = (os.path.join(base_dir, 'albatradis_output:/work'))
-	#
-	# 	cmd = " ".join(
-	# 		['docker run --rm  -v', out_dir, 'quadraminstitute/albatradis:latest albatradis -v -a ', emblfile, case, control])
-	#
-	# 	subprocess.call(cmd, shell=True)
-	#
-	# 	self.assertTrue(os.path.exists(os.path.join(base_dir, 'albatradis_output/output')))
-	# 	self.assertTrue(os.path.exists(os.path.join(base_dir, 'albatradis_output/output/gene_report.csv')))
-	# 	shutil.rmtree(os.path.join(base_dir,'albatradis_output'))

albatradis/tests/PresenceAbsence_test.py

@@ -40,5 +40,5 @@ def test_valid_file(self):
 		self.assertTrue(nj_tree)
 		self.assertTrue(filecmp.cmp(exp_lfc, all_outputfile))
 
-		#sshutil.rmtree('testoutput')
+		shutil.rmtree('testoutput')
 

albatradis/tests/ScatterPlot_test.py

@@ -1,7 +1,5 @@
 import unittest
 import os
-import logging
-import filecmp
 from albatradis.ScatterPlot import ScatterPlot
 
 test_modules_dir = os.path.dirname(os.path.realpath(__file__))
@@ -19,3 +17,6 @@ def test_valid(self):
 		self.assertTrue(s.create_linear_plot())
 		self.assertTrue(s.create_abs_scatter_plot())
 
+		os.remove("scattertest_absscatter.png")
+		os.remove("scattertest_linear.png")
+		os.remove("scattertest_scatter.png")