push @atiweb changes in #384 and copy/delete in annotate for logfile

Author: Jon Palmer

funannotate/annotate.py

@@ -1402,8 +1402,9 @@ def __init__(self, prog):
     if os.path.isfile(log_name):
         if not os.path.isdir(os.path.join(outputdir, 'logfiles')):
             os.makedirs(os.path.join(outputdir, 'logfiles'))
-        os.rename(log_name, os.path.join(
+        shutil.copyfile(log_name, os.path.join(
             outputdir, 'logfiles', 'funannotate-annotate.log'))
+        os.remove(log_name)
 
 
 if __name__ == "__main__":

funannotate/compare.py

@@ -7,6 +7,7 @@
 import subprocess
 import shutil
 import argparse
+import io
 from datetime import datetime
 from goatools import obo_parser
 from Bio import SeqIO
@@ -373,13 +374,13 @@ def __init__(self, prog):
         pfam_desc.append(PFAM.get(i))
     pfamdf2['descriptions'] = pfam_desc
     # write to file
-    pfamdf2.to_csv(os.path.join(args.out, 'pfam', 'pfam.results.csv'))
+    pfamdf2.to_csv(os.path.join(args.out, 'pfam', 'pfam.results.csv'), encoding='utf-8')
     pfamdf2.reset_index(inplace=True)
     pfamdf2.rename(columns={'index': 'PFAM'}, inplace=True)
     pfamdf2['PFAM'] = '<a target="_blank" href="http://pfam.xfam.org/family/' + \
         pfamdf2['PFAM'].astype(str)+'">'+pfamdf2['PFAM']+'</a>'
     # create html output
-    with open(os.path.join(args.out, 'pfam.html'), 'w') as output:
+    with io.open(os.path.join(args.out, 'pfam.html'), 'w', encoding='utf-8') as output:
         pd.set_option('display.max_colwidth', -1)
         output.write(lib.HEADER)
         output.write(lib.PFAM)

funannotate/library.py

@@ -7041,6 +7041,7 @@ def dictFlipLookup(input, lookup):
                 result = k+': '+lookup.get(k)
             else:
                 result = k+': No description'
+            result = result.encode('utf-8')
             for i in v:
                 if i in outDict:
                     outDict[i].append(str(result))