python - ValueError: invalid literal for int() with base 10: '6_0'

Question

I've got error in executing the python script provided by CAFE

resultfile.cafe were generated by CAFE cafe cafetutorial_run.sh

(python27) [XX@XX DIR]$ python cafetutorial_report_analysis.py -in resultfile.cafe -o summary_run
    =======================================================================
            CAFE Report File Analysis
            01.22.2021 | 10:14:46
    ---------
    Parsing format information...
    
---------
Initializing output structures...

---------
Counting changes per branch...
                                                                                                                                          [*-------------------------------------------------] 0.135% complete.Traceback (most recent call last):
  File "/new_data/SOFTWARE/phylogenetics/CAFE_python_scripts/cafetutorial_report_analysis.py", line 371, in <module>
    results_main, node_fams_main = cra(inlines_main, results_main, node_fams_main, linestart_main, ancfilename, sorted_nodes, 1);
  File "/new_data/SOFTWARE/phylogenetics/CAFE_python_scripts/cafetutorial_report_analysis.py", line 192, in cra
    curcount = int(tlinfo[tlnode][4]);
ValueError: invalid literal for int() with base 10: '6_0'

Here is part of the python script:

   131  #######################
   132  def cra(inlines, results, node_fams, linestart, afilename, s_nodes, v):
   133          numbars = 0;
   134          donepercent = [];
   135          i = 0;
   136          acount = 0;
   137          afile = open(afilename, "a");
   138  
   139          for inline in inlines:
   140          # Each line of the report file is read.
   141                  if v == 1:
   142                          numbars, donepercent = cafecore.loadingBar(i, len(inlines), donepercent, numbars);
   143                  i = i + 1;
   144  
   145                  if i <= linestart:
   146                          continue;
   147                  # If the line is a CAFE info line, skip it.
   148  
   149                  inline = inline.strip().split("");
   150                  famid = inline[0];
   151                  famtree = inline[1];
   152                  nodeformat = inline[3].replace("),(", ") (");
   153                  # Parsing the information for the current family.
   154  
   155                  outline = famid + "";
   156                  outlist = [0 for n in s_nodes];
   157                  # Prep for the anc states file.
   158  
   159                  nodes = formatLineParse(nodeformat);
   160  
   161                  tlinfo, newfamtree = cafecore.treeParseNew(famtree, 1);
   162                  # Reading the tree and adding my node labels.
   163  
   164                  for tlnode in tlinfo:
   165                          if tlinfo[tlnode][3] == 'root':
   166                                  tlinfo[tlnode].append(famtree[famtree.rfind("_")+1:]);
   167                          elif tlinfo[tlnode][3] == 'tip':
   168                                  tlinfo[tlnode].append(tlnode[tlnode.index("_")+1:]);
   169                          else:
   170                                  tlinfo[tlnode][4] = tlinfo[tlnode][4][1:];
   171                  # Gene counts for each node are read as support values for internal nodes, but must
   172                  # have the underscore removed. Tip and root node counts are added here as well.
   173  
   174                  tlinfo = nodeRelabel(tlinfo);
   175                  # Removes the gene counts from the tip node labels.
   176  
   177                  if i == (linestart + 1):
   178                          maps = nodeMap(tinfo, tlinfo);
   179                  # If this is the first family, we need to build our maps from my node ids to CAFE's.
   180  
   181                  for tlnode in tlinfo:
   182                  # For each node in the current gene family tree, we make our counts.
   183  
   184                          if tlinfo[tlnode][3] == 'root':
   185                                  continue;
   186                          # No count is made at the root of the tree.
   187  
   188                          curanc = tlinfo[tlnode][1];
   189                          curmap = maps[tlnode];
   190                          # Get the ancestor and the map of the current node.
   191  
   192                          curcount = int(tlinfo[tlnode][4]);
   193                          anccount = int(tlinfo[curanc][4]);
   194                          # Get the gene counts of the current node and the ancestor.
   195  
   196                          outlist[s_nodes.index(curmap)] = str(curcount);
   197                          # Save the count of the current node to be sent to the anc states file.
   198  
   199                          diff = curcount - anccount;
   200                          # Calculate the difference in gene count.
   201  
   202                          typeflag = 0;
   203                          # typeflag tells whether an expansion or contraction has occurred.
   204  
   205                          if curcount > anccount:
   206                                  typeflag = 1;
   207                                  results[curmap][0] += 1;
   208                                  results[curmap][1] += diff;
   209  
   210                                  if r_opt == 0:
   211                                          node_fams[curmap][0].append(famid + "[+" + str(diff) + "]");
   212  
   213                                          if famid not in node_fams['total']:
   214                                                  node_fams['total'].append(famid);
   215                          # If the difference in gene count between the current node and the ancestor is positive, an
   216                          # expansion has occurred. This makes the appropriate counts.
   217  
   218                          elif curcount < anccount:
   219                                  typeflag = 2
   220                                  results[curmap][3] += 1;
   221                                  results[curmap][4] += abs(diff);
   222  
   223                                  if curcount == 0 and anccount != 0:
   224                                          results[curmap][5] += 1;
   225  
   226                                  if r_opt == 0:
   227                                          node_fams[curmap][1].append(famid + "[" + str(diff) + "]");
   228  
   229                                          if famid not in node_fams['total']:
   230                                                  node_fams['total'].append(famid);
   231                          # If the difference in gene count between the current node and the ancestor is negative, a
   232                          # contraction has occurred. This makes the appropriate counts. It also checks for family losses
   233                          # along that branch by seeing if the current node has transitioned to a count of 0.
   234  
   235                          elif curcount == anccount:
   236                                  results[curmap][2] += 1;
   237                          # Otherwise, the counts at the current node and the ancestor are the same and no change has occurred.

question from:https://stackoverflow.com/questions/65838672/valueerror-invalid-literal-for-int-with-base-10-6-0

Answer 1

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