.network fixes and opening up GlycoDraw

build/lib/glycowork/motif/analysis.py

@@ -876,7 +876,7 @@ def get_jtk(df, timepoints, replicates, periods, interval, motifs = False, featu
     df.replace(0, np.nan, inplace = True)
     df = mf.fit_transform(df)
     if motifs:
-        df = quantify_motifs(pd.DataFrame(df.iloc[:, 1:], df.iloc[:, 0].values.tolist()), feature_set).T
+        df = quantify_motifs(df.iloc[:, 1:], df.iloc[:, 0].values.tolist(), feature_set).T
     res = df.apply(jtkx, param_dic = param_dic, axis = 1)
     JTK_BHQ = pd.DataFrame(sm.stats.multipletests(res[0], method = 'fdr_bh')[1])
     Results = pd.concat([res.iloc[:, 0], JTK_BHQ, res.iloc[:, 1:]], axis = 1)

build/lib/glycowork/motif/draw.py

@@ -6,11 +6,9 @@
 import copy
 
 try:
-  import cairosvg
   import drawsvg as draw
 except ImportError:
   raise ImportError("<draw dependencies missing; did you do 'pip install glycowork[draw]'?>")
-import networkx as nx
 import numpy as np
 import sys
 import re
@@ -2147,7 +2145,11 @@ def calculate_degree(y1, y2, x1, x2):
         with open(filepath, 'w') as f:
           f.write(data)
       elif 'pdf' in filepath:
-        cairosvg.svg2pdf(bytestring = data, write_to = filepath)
+        try:
+          from cairosvg import svg2pdf
+          svg2pdf(bytestring = data, write_to = filepath)
+        except ImportError:
+          raise ImportError("You're missing some draw dependencies. Either use .svg or head to https://bojarlab.github.io/glycowork/examples.html#glycodraw-code-snippets to learn more.")
   return d2
 
 
@@ -2244,11 +2246,15 @@ def annotate_figure(svg_input, scale_range = (25, 80), compact = False, glycan_s
   svg_tmp += '</svg>'
 
   if filepath:
+    try:
+      from cairosvg import svg2pdf, svg2svg, svg2png
       if filepath.split('.')[-1] == 'pdf':
-        cairosvg.svg2pdf(bytestring = svg_tmp, write_to = filepath, dpi = 300)
+        svg2pdf(bytestring = svg_tmp, write_to = filepath, dpi = 300)
       elif filepath.split('.')[-1] == 'svg':
-        cairosvg.svg2svg(bytestring = svg_tmp, write_to = filepath, dpi = 300)
+        svg2svg(bytestring = svg_tmp, write_to = filepath, dpi = 300)
       elif filepath.split('.')[-1] == 'png':
-        cairosvg.svg2png(bytestring = svg_tmp, write_to = filepath, dpi = 300) 
+        svg2png(bytestring = svg_tmp, write_to = filepath, dpi = 300)
+    except ImportError:
+      raise ImportError("You're missing some draw dependencies. Either don't use filepath or head to https://bojarlab.github.io/glycowork/examples.html#glycodraw-code-snippets to learn more.")
   else:
-      return svg_tmp
+    return svg_tmp

build/lib/glycowork/motif/processing.py

@@ -200,8 +200,11 @@ def choose_correct_isoform(glycans, reverse = False):
   | :-
   | Returns the correct isomer as a string (if reverse=False; otherwise it returns a list of strings)
   """
+  glycans = list(set(glycans))
   if len(glycans) == 1:
     return glycans[0]
+  if not any(['[' in g for g in glycans]):
+    return [] if reverse else glycans
   floaty = False
   if '{' in glycans[0]:
     floaty = glycans[0][:glycans[0].rindex('}')+1]

glycowork/motif/analysis.py

@@ -876,7 +876,7 @@ def get_jtk(df, timepoints, replicates, periods, interval, motifs = False, featu
     df.replace(0, np.nan, inplace = True)
     df = mf.fit_transform(df)
     if motifs:
-        df = quantify_motifs(pd.DataFrame(df.iloc[:, 1:], df.iloc[:, 0].values.tolist()), feature_set).T
+        df = quantify_motifs(df.iloc[:, 1:], df.iloc[:, 0].values.tolist(), feature_set).T
     res = df.apply(jtkx, param_dic = param_dic, axis = 1)
     JTK_BHQ = pd.DataFrame(sm.stats.multipletests(res[0], method = 'fdr_bh')[1])
     Results = pd.concat([res.iloc[:, 0], JTK_BHQ, res.iloc[:, 1:]], axis = 1)

glycowork/motif/draw.py

@@ -6,11 +6,9 @@
 import copy
 
 try:
-  import cairosvg
   import drawsvg as draw
 except ImportError:
   raise ImportError("<draw dependencies missing; did you do 'pip install glycowork[draw]'?>")
-import networkx as nx
 import numpy as np
 import sys
 import re
@@ -2147,7 +2145,11 @@ def calculate_degree(y1, y2, x1, x2):
         with open(filepath, 'w') as f:
           f.write(data)
       elif 'pdf' in filepath:
-        cairosvg.svg2pdf(bytestring = data, write_to = filepath)
+        try:
+          from cairosvg import svg2pdf
+          svg2pdf(bytestring = data, write_to = filepath)
+        except ImportError:
+          raise ImportError("You're missing some draw dependencies. Either use .svg or head to https://bojarlab.github.io/glycowork/examples.html#glycodraw-code-snippets to learn more.")
   return d2
 
 
@@ -2244,11 +2246,15 @@ def annotate_figure(svg_input, scale_range = (25, 80), compact = False, glycan_s
   svg_tmp += '</svg>'
 
   if filepath:
+    try:
+      from cairosvg import svg2pdf, svg2svg, svg2png
       if filepath.split('.')[-1] == 'pdf':
-        cairosvg.svg2pdf(bytestring = svg_tmp, write_to = filepath, dpi = 300)
+        svg2pdf(bytestring = svg_tmp, write_to = filepath, dpi = 300)
       elif filepath.split('.')[-1] == 'svg':
-        cairosvg.svg2svg(bytestring = svg_tmp, write_to = filepath, dpi = 300)
+        svg2svg(bytestring = svg_tmp, write_to = filepath, dpi = 300)
       elif filepath.split('.')[-1] == 'png':
-        cairosvg.svg2png(bytestring = svg_tmp, write_to = filepath, dpi = 300) 
+        svg2png(bytestring = svg_tmp, write_to = filepath, dpi = 300)
+    except ImportError:
+      raise ImportError("You're missing some draw dependencies. Either don't use filepath or head to https://bojarlab.github.io/glycowork/examples.html#glycodraw-code-snippets to learn more.")
   else:
-      return svg_tmp
+    return svg_tmp

glycowork/motif/processing.py

@@ -200,8 +200,11 @@ def choose_correct_isoform(glycans, reverse = False):
   | :-
   | Returns the correct isomer as a string (if reverse=False; otherwise it returns a list of strings)
   """
+  glycans = list(set(glycans))
   if len(glycans) == 1:
     return glycans[0]
+  if not any(['[' in g for g in glycans]):
+    return [] if reverse else glycans
   floaty = False
   if '{' in glycans[0]:
     floaty = glycans[0][:glycans[0].rindex('}')+1]

glycowork/network/biosynthesis.py

@@ -754,7 +754,8 @@ def construct_network(glycans, libr = None, allowed_ptms = allowed_ptms,
   if len(isomeric_graphs) > 0:
     isomeric_nodes = [[virtual_nodes[virtual_graphs.index(k[0])],
                        virtual_nodes[virtual_graphs.index(k[1])]] for k in isomeric_graphs]
-    network.remove_nodes_from([choose_correct_isoform(k, reverse = True)[0] for k in isomeric_nodes])
+    isomeric_nodes = [choose_correct_isoform(k, reverse = True) for k in isomeric_nodes if len(set(k)) > 1]
+    network.remove_nodes_from([n[0] for n in isomeric_nodes if n])
   network.remove_edges_from(nx.selfloop_edges(network))
   # Make network directed
   network = prune_directed_edges(network.to_directed())

glycowork/network/evolution.py

@@ -208,7 +208,7 @@ def get_communities(graph_list, label_list = None):
   comm_list = [community_louvain.best_partition(g) for g in graph_list]
   if label_list is None:
     label_list = list(range(len(comm_list)))
-  final_comm_dict = []
+  final_comm_dict = {}
   # Label the communities by species name and running number to distinguish them afterwards
   for comm_dict, label in zip(comm_list, label_list):
     updated_dict = {