From 99c20ba0fcb6fc4707c404975a62ea3741f12b93 Mon Sep 17 00:00:00 2001
From: Natalie Catlett <ncatlett@selventa.com>
Date: Mon, 3 Mar 2014 16:01:41 -0500
Subject: [PATCH] added script to write gene-orthology .bel file

---
 datasets.py  | 19 ++++++++----
 orthology.py | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 97 insertions(+), 5 deletions(-)
 create mode 100755 orthology.py

diff --git a/datasets.py b/datasets.py
index d3942b2..f4752c8 100644
--- a/datasets.py
+++ b/datasets.py
@@ -32,14 +32,19 @@ class OrthologyData(DataSet):
 	def __init__(self, dictionary={},  prefix='use-index-term-prefix'):
 		super().__init__(dictionary, prefix)
 	
+	def get_values(self):
+		for term_id in self._dict:
+			yield term_id
+
 	def get_orthologs(self, term_id):
 		orthologs = set()
 		mapping = self._dict.get(term_id)
 		mouse_orthologs = mapping.get('mouse_ortholog_id').split('|')
 		orthologs.update(mouse_orthologs)
-		human_orthologs = mapping.get('human_ortholog_id').split('|')
-		human_orthologs = {'HGNC:' + ortho for ortho in human_orthologs}
-		orthologs.update(human_orthologs)
+		if mapping.get('human_ortholog_id') is not '':
+			human_orthologs = mapping.get('human_ortholog_id').split('|')
+			human_orthologs = {'HGNC:' + ortho for ortho in human_orthologs}
+			orthologs.update(human_orthologs)
 		return orthologs
 
 	def __str__(self):
@@ -293,8 +298,12 @@ def get_values(self):
 
 	def get_label(self, term_id):
 		''' Return preferred label associated with term id. '''
-		label = self._dict.get(term_id).get('Symbol')
-		return label
+		mapping = self._dict.get(term_id)
+		if mapping is None:
+			return None
+		else:
+			label = mapping.get('Symbol')
+			return label
 
 	def get_encoding(self, term_id):
 		mapping = self._dict.get(term_id)
diff --git a/orthology.py b/orthology.py
new file mode 100755
index 0000000..3277646
--- /dev/null
+++ b/orthology.py
@@ -0,0 +1,83 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+import argparse
+import os
+import pickle
+import time
+import datasets
+import bel_functions
+from collections import defaultdict
+
+if __name__=='__main__':	
+	# command line arguments - directory for pickled data objects
+	parser = argparse.ArgumentParser(description="""Generate BEL orthology file
+	from pickled data objects.""")
+
+	parser.add_argument("-n", required=True, metavar="DIRECTORY",
+					help="directory to store the new namespace equivalence data")
+	args = parser.parse_args()
+	if os.path.exists(args.n):
+		os.chdir(args.n)
+	else:
+		print('data directory {0} not found!'.format(args.n))
+
+	data_list = ['rgd', 'hgnc', 'rgd_ortho', 'mgi']
+	data_dict = {}
+	for files in os.listdir("."):
+		if files.endswith("parsed_data.pickle"):
+			with open(files,'rb') as f:
+				d = pickle.load(f)
+				if str(d) in data_list:
+					data_dict[str(d)] = d
+	for data in data_list:
+		if data not in data_dict.keys():
+			print('missing required dependency {0}!'.format(data))
+
+	hgnc_ortho_statements = set()
+	for term_id in data_dict.get('hgnc').get_values():
+		term_label = data_dict.get('hgnc').get_label(term_id)
+		hgnc_term = bel_functions.bel_term(term_label, 'HGNC', 'g')
+		orthos = data_dict.get('hgnc').get_orthologs(term_id)
+		if orthos is not None:
+			for o in orthos:
+				if len(o.split(':')) == 2:
+					prefix, value = o.split(':')
+					if prefix == 'RGD':
+						o_label = data_dict.get('rgd').get_label(value)
+					if prefix == 'MGI':
+						o_label = data_dict.get('mgi').get_label(value)
+					if o_label is None:
+						print('WARNING - missing label for {0}, {1}'.format(prefix, value))
+						continue
+					ortho_term = bel_functions.bel_term(o_label, prefix, 'g')
+					hgnc_ortho_statements.add('{0} orthologous {1}'.format(hgnc_term, ortho_term)) 
+			
+	rgd_ortho_statements = set()	
+	for term_id in data_dict.get('rgd_ortho').get_values():
+		term_label = data_dict.get('rgd').get_label(term_id)
+		rgd_term = bel_functions.bel_term(term_label, 'RGD', 'g')
+		orthos = data_dict.get('rgd_ortho').get_orthologs(term_id)
+		if orthos is not None:
+			for o in orthos:
+				prefix = ''
+				if len(o.split(':')) == 2:
+					prefix, value = o.split(':')
+					if prefix == 'HGNC':
+						o_label = data_dict.get('hgnc').get_label(value)
+					if prefix == 'MGI':
+						o_label = data_dict.get('mgi').get_label(value)
+					if o_label is None:
+						print('WARNING - {2} missing label for {0}, {1}'.format(prefix, value, rgd_term))
+						continue
+					ortho_term = bel_functions.bel_term(o_label, prefix, 'g')
+					rgd_ortho_statements.add('{0} orthologous {1}'.format(rgd_term, ortho_term)) 
+
+	with open('gene-orthology.bel', 'w') as ortho:
+		ortho.write('SET Citation = {"Online Resource", "HUGO Gene Nomenclature Committee data download", "ftp://ftp.ebi.ac.uk/pub/databases/genenames/hgnc_complete_set.txt.gz"}\n')
+		for s in sorted(hgnc_ortho_statements):
+			ortho.write(s + '\n')
+		ortho.write('\n')
+		ortho.write('SET Citation = {"Online Resource","RGD Orthology FTP file", "ftp://rgd.mcw.edu/pub/data_release/RGD_ORTHOLOGS.txt"}\n')
+		for s in sorted(rgd_ortho_statements):
+			ortho.write(s + '\n')