fixed output filename for muscle5

Author: trvinh

fdog/libs/addtaxon.py

@@ -158,14 +158,16 @@ def create_genome(args):
         if len(id_dict) > 0:
             mapping_file = '%s.mapping' % genome_file
             with open(mapping_file, 'w') as mp:
-                for o,n in id_dict.items():
-                    mp.write('%s\t%s\n' % (o,n))
+                for id in in_seq:
+                    if id in id_dict:
+                        mp.write(f'{id}\t{id_dict[id]}\n')
+                    else:
+                        mp.write(f'{id}\t{id}\n')
             if pipe == 1:
                 print('\033[94mWARNING: Sequence IDs contain pipe(s). They will be replaced by "_"!\033[0m')
             if long_id == 'yes':
-                print('\033[94mWARNING: Some headers longer than 80 characters have been automatically shortened. Please check the %s.mapping file for details!\033[0m' % genome_file)
-            if pipe == 1:
-                print('\033[94mWARNING: Please check the %s file for details!\033[0m' % mapping_file)
+                print('\033[94mWARNING: Some headers longer than 80 characters have been automatically shortened.\033[0m')
+            print('\033[94mPlease check the %s file for details!\033[0m' % mapping_file)
     else:
         print(genome_path + '/' + spec_name + '.fa already exists!')
     return(genome_file)

fdog/libs/alignment.py

@@ -67,7 +67,9 @@ def do_align(aligner, fa_file):
     input_fa = SeqIO.to_dict((SeqIO.parse(open(fa_file), 'fasta')))
     if len(input_fa) == 1:
         return(input_fa)
-    out_file = fa_file.replace('@', '_')
+    # parse output file name (otherwise cause troubles for muscle_v5)
+    out_file = fa_file.split('/')[-1].replace('@', '_')
+    # check muscle version
     if aligner == 'muscle':
         if get_muscle_version(aligner) == 'v3':
             if fasta_fn.check_long_seq(fa_file) == 1:
@@ -76,7 +78,7 @@ def do_align(aligner, fa_file):
                 aligner = 'muscle_v3'
         else:
             aligner = 'muscle_v5'
-
+    # create alignment command and run
     align_cline = ''
     if aligner == 'muscle_v3':
         align_cline = 'muscle -in %s' % fa_file

setup.py

@@ -26,7 +26,7 @@
 
 setup(
     name="fdog",
-    version="0.1.13",
+    version="0.1.14",
     python_requires='>=3.7.0',
     description="Feature-aware Directed OrtholoG search tool",
     long_description=long_description,