Added auto-optional scale factor reporting (1249e3f3) · Commits · Chaos / Cutandrun

bin/lib/reports.py

+10 −4

Original line number	Diff line number	Diff line
		@@ -99,10 +99,15 @@ class Reports:

		self.metadata_noctrl_table = pd.read_csv(self.meta_path, sep=',')
		self.metadata_table = pd.read_csv(self.meta_ctrl_path, sep=',')

		self.duplicate_info = False
		if 'dedup_percent_duplication' in self.metadata_table.columns:
		self.duplicate_info = True

		self.scale_factor_info = False
		if 'scale_factor' in self.metadata_table.columns:
		self.scale_factor_info = True

		# Make new perctenage alignment columns
		self.metadata_table['target_alignment_rate'] = self.metadata_table.loc[:, ('bt2_total_aligned_target')] / self.metadata_table.loc[:, ('bt2_total_reads_target')] * 100
		self.metadata_table['spikein_alignment_rate'] = self.metadata_table.loc[:, ('bt2_total_aligned_spikein')] / self.metadata_table.loc[:, ('bt2_total_reads_spikein')] * 100
		@@ -303,6 +308,7 @@ class Reports:
		data["04_replicate_heatmap"] = data5

		# Plot section 6
		if self.scale_factor_info == True:
		multi_plot, data6 = self.scale_factor_summary()
		plots["05_01_scale_factor"] = multi_plot[0]
		plots["05_02_frag_count"] = multi_plot[1]