Merge pull request #367 from SysBioChalmers/feat/reaction-names

feat: add reaction names from KEGG

code/curateReactionNames.py

@@ -0,0 +1,68 @@
+"""Fetch Human-GEM reaction names from KEGG
+Original file is located at
+    https://colab.research.google.com/drive/17X0Qx0H4pwjZjLLWHnpp5ac2daH9hOxs
+"""
+
+import requests
+import re
+import yaml
+import pandas
+
+"""Get all the KEGG reactions via their API, and save the result to a file."""
+
+KEGG_REACTIONS = 'kegg_reactions.txt'
+HG_YAML = '../model/Human-GEM.yml'
+F_YAML = '../model/curated-Human-GEM.yml'
+
+with open(KEGG_REACTIONS,'w') as f:
+  r = requests.get('http://rest.kegg.jp/list/reaction/')
+  f.write(r.text)
+
+"""Extract the KEGG reactions as key-value pairs."""
+
+raw_reactions = open(KEGG_REACTIONS, 'r')
+raw_reaction_lines = raw_reactions.readlines()
+
+reaction_id = re.compile('(?:^rn\:)(R\d+)')
+reaction_name = re.compile('(?:\t)([^;]+)(?:;)')
+kegg_reactions = {}
+for line in raw_reaction_lines:
+  try:
+    kegg_reactions[reaction_id.search(line).group(1)] = reaction_name.search(line).group(1)
+  except:
+    kegg_reactions[reaction_id.search(line).group(1)] = ''
+# print(kegg_reactions[])
+
+"""Fetch Human-GEM reactions from the TSV annotation."""
+
+hg_annotation = pandas.read_csv('../model/reactions.tsv', sep='\t', index_col=0)
+
+""" Traverse the YAML, and for each line that looks like a reaction definition, extract the reaction identifier, and get the matching KEGG id. Then, change the next line that contains the reaction name to the name provided by KEGG."""
+
+with open(HG_YAML, 'r') as inputf:
+  with open(F_YAML, 'w') as outputf:
+    count = 0
+    count_blank = 0
+    while True:
+      reaction_id = re.compile('(?:^      - id: ")(MAR\d+)')
+      reaction_name = re.compile('(?:^      - name: ")()("$)')
+      try:
+        line = inputf.readline()
+        r_id = reaction_id.search(line).group(1)
+        outputf.write(line)
+        line = inputf.readline()
+        r_name = reaction_name.search(line).group(1)
+        kegg_id = hg_annotation.loc[r_id]['rxnKEGGID']
+        if kegg_id and r_name == "":
+            if kegg_reactions[kegg_id] == "":
+                count_blank = count_blank + 1
+            else:
+                line = '      - name: "' + kegg_reactions[kegg_id] + '"\n'
+                count = count + 1
+      except:
+        None
+      outputf.write(line)
+      if not line:
+        break
+    print('Reaction names adopted from KEGG: ' + str(count))
+    print('Blank names also blank in KEGG: ' + str(count_blank))