def generate_logfc_plot(self, analysis_type, essentiality_files):
files = [
getattr(essentiality_files[plotfile],
analysis_type).tradis_essentiality_filename
for plotfile in self.plotfiles
]
only_ess_files = [
getattr(essentiality_files[plotfile],
analysis_type).only_essential_filename
for plotfile in self.plotfiles
]
annotation_files = [
essentiality_files[plotfile].embl_filename
for plotfile in self.plotfiles
]
mid = int(len(files) / 2)
t = TradisComparison(files[:mid], files[mid:], self.verbose,
self.minimum_block, 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")
shutil.copy(t.output_filename, renamed_csv_file)
shutil.copy(p.output_filename, renamed_plot_file)
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)
return renamed_plot_file
def test_span_gaps_block_at_end_neg(self):
p = PlotLog('x', 20, 2, 0.05, 1, 4, 1, True, None)
l = p.span_block_gaps([0,0,0,-9,-9,-9,0,0,0,0,0,-8,-8,-8,-8,0,0,-7,-7,-7])
self.assertEqual([0,0,0,-9,-9,-9,0,0,0,0,0,-8,-8,-8,-8,-2,-2,-7,-7,-7],l )
def test_span_gaps_nomerge_neg(self):
p = PlotLog('x', 20, 2, 0.05, 1, 4, 1, True, None)
l = p.span_block_gaps([0,0,0,-9,-9,-9,0,0,0,0,0,-8,-8,-8,-8,0,0,0,0,0])
self.assertEqual([0,0,0,-9,-9,-9,0,0,0,0,0,-8,-8,-8,-8,0,0,0,0,0],l )
def test_span_gaps_block_at_end(self):
p = PlotLog('x', 20, 2, 0.05, 1, 4, 1, True, None)
l = p.span_block_gaps([0,0,0,9,9,9,0,0,0,0,0,8,8,8,8,0,0,7,7,7])
self.assertEqual([0,0,0,9,9,9,0,0,0,0,0,8,8,8,8,2,2,7,7,7],l )
def test_span_gaps_merge(self):
p = PlotLog('x', 20, 2, 0.05, 1, 4, 1, True, None)
l = p.span_block_gaps([0,0,0,9,9,9,9,0,0,0,0,8,8,8,8,0,0,0,0,0])
self.assertEqual([0,0,0,9,9,9,9,2,2,2,2,8,8,8,8,0,0,0,0,0],l )
