Major improvements in visualization

KOs now converted to EC numbers directly to the maps
No more gray outline boxes
Exception for loading metabolic map improved

kegg_charter.py

@@ -7,9 +7,9 @@
 from io import StringIO
 from matplotlib import colors, cm
 import argparse, pandas as pd, numpy as np, os, pathlib, PIL, re, sys, subprocess
-import matplotlib.pyplot as plt
+import matplotlib.pyplot as plt, traceback
 
-__version__ = "0.1.0"
+__version__ = "0.1.1"
 
 class KEGGCharter:
 
@@ -506,6 +506,7 @@ def main(self):
                         differential_no_kos.append(metabolic_map)
                 plt.close()
             except Exception as e:
+                print(traceback.format_exc())
                 print('[{}/{}] Representation of pathway [{}] has failed!'.format(
                         str(i), str(len(metabolic_maps)), metabolic_map))
                 print(e)

kegg_pathway_map.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 from Bio.KEGG.KGML import KGML_parser, KGML_pathway
-from Bio.KEGG.REST import kegg_get
+from Bio.KEGG.REST import kegg_get, kegg_link
 from Bio.Graphics.KGML_vis import KGMLCanvas
 from matplotlib import colors, cm
 
@@ -86,7 +86,7 @@ def set_pathway(self, data, pathway_ID, ko_column, ec_column):
         self.ko_boxes = dict()
         for i in range(len(self.pathway.orthologs)):
             self.set_bgcolor(self.pathway.orthologs[i], "#ffffff")              # set all boxes to white
-            self.set_fgcolor(self.pathway.orthologs[i], "#ffffff")              # ditto
+            #self.set_fgcolor(self.pathway.orthologs[i], "#ffffff")             # This might be helpful in the future, if an additional layer of marking is needed
             orthologs_in_box = [ide[3:] for ide in self.pathway.orthologs[i].name.split()]  # 'ko:K16157 ko:K16158 ko:K16159' -> ['K16157', 'K16158', 'K16159']
             for ortholog in orthologs_in_box:
                 if ortholog not in self.ko_boxes.keys():
@@ -95,15 +95,16 @@ def set_pathway(self, data, pathway_ID, ko_column, ec_column):
             ko.append(self.pathway.orthologs[i].graphics[0].name.rstrip("."))   # 'K16157...' -> 'K16157'
 
         # Set text in boxes to EC numbers
-        data = data[data[ec_column].notnull()][[ko_column, ec_column]]
-        ko_to_ec = {data.iloc[i][ko_column]:data.iloc[i][ec_column]
-                    for i in range(len(data))}                                  # {'K16157':'ec:1.14.13.25'}
         for ortholog_rec in self.pathway.orthologs:
-            ko = ortholog_rec.graphics[0].name.strip(".")
-            if ko in ko_to_ec.keys():
-                ortholog_rec.graphics[0].name = ko_to_ec[ko]
+            ecs = list()
+            kos = ortholog_rec.name.split()
+            for ko in kos:
+                lines = kegg_link("enzyme", ko).read().split('\n')
+                ecs += [line.split('\t')[1] for line in lines if len(line) > 0]
+            if len(ecs) > 0:
+                ortholog_rec.graphics[0].name = max(set(ecs), key = ecs.count).upper()
             else:
-                ortholog_rec.graphics[0].name = ko
+                ortholog_rec.graphics[0].name = kos[0][3:]
 
     ############################################################################
     ####                    Graphical Manipulation                          ####

meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "keggcharter" %}
-{% set version = "0.1.0" %}
+{% set version = "0.1.1" %}
 {% set sha256 = "905268158c74058228faca2b34d44eae8f84b23bfa5dee49285635cf59684d7f" %}
 
 package: