__main__.py

#!/usr/bin/env python

from src import ResultFileHandler, GeneFileHandler
import sys

result_format = sys.argv[1]
mapping_path = sys.argv[2]
out_path = sys.argv[3]

if result_format == 'gene_lists':
	background_path = sys.argv[4]
	diff_path = sys.argv[5]
	GeneFileHandler(
		mapping_path,
		out_path,
		background_file=background_path,
		diff_file=diff_path
	).perform_test()
elif result_format == 'gene_lists_directional':
	background_path = sys.argv[4]
	up_path = sys.argv[5]
	down_path = sys.argv[6]
	GeneFileHandler(
		mapping_path,
		out_path,
		background_file=background_path,
		up_file=up_path,
		down_file=down_path
	).perform_test()
else:
	data_paths = [sys.argv[4]] if len(sys.argv) == 5 else sys.argv[4:-1]
	min_prop = sys.argv[-1]
	if result_format == 'sleuth':
		ResultFileHandler(mapping_path, out_path).perform_test(
			data_paths,
			target_field='target_id',
			lrt_sig_field='qval.LRT',
			interaction_sig_field='interaction_qval',
			main_effect_sig_field='main_effect_qval',
			wt_sig_field='qval.WT',
			change_field='b',
			sep='\t',
			alpha=0.05,
			min_prop=min_prop
		)
	elif result_format == 'sleuth_interactions':
		ResultFileHandler(mapping_path, out_path).perform_test(
			data_paths,
			target_field='target_id',
			lrt_sig_field='interaction_qval',
			change_field='b',
			sep='\t',
			alpha=0.05,
			min_prop=min_prop
		)
	elif result_format == 'limma':
		ResultFileHandler(mapping_path, out_path).perform_test(
			data_paths,
			target_field='GeneID',
			lrt_sig_field='adj.P.Val',
			change_field='logFC',
			min_prop=min_prop
		)
	elif result_format == 'wgcna':
		print('ok')
		ResultFileHandler(mapping_path, out_path).perform_test(
			data_paths,
			target_field="gene",
			lrt_sig_field=sys.argv[5],
			change_field="sign",
			min_prop=1
		)
	elif result_format == 'deseq2':
		print('ok')
		ResultFileHandler(mapping_path, out_path).perform_test(
			data_paths,
			target_field="GeneID",
			lrt_sig_field="padj",
			change_field="log2FoldChange",
			min_prop=1
		)
	elif result_format == 'correlations':
		print('ok')
		ResultFileHandler(mapping_path, out_path).perform_test(
			data_paths,
			target_field="GeneID",
			lrt_sig_field="q.val",
			change_field="correlation",
			min_prop=1
		)