Merge pull request #2 from BIONF/master

deactivate fas config output

Author: HannahBioI

fdog/libs/addtaxon.py

@@ -103,7 +103,7 @@ def create_genome(args):
     ### load fasta seq
     in_seq = SeqIO.to_dict((SeqIO.parse(open(faIn), 'fasta')))
     if not os.path.exists(genome_path):
-            Path(genome_path).mkdir(parents = True, exist_ok = True)
+        Path(genome_path).mkdir(parents = True, exist_ok = True)
     genome_file = '%s/%s.fa' % (genome_path, spec_name)
     if (not os.path.exists(os.path.abspath(genome_file))) or (os.stat(genome_file).st_size == 0) or force:
         f = open(genome_file, 'w')

fdog/libs/fas.py

@@ -78,7 +78,7 @@ def calc_pairwise_fas(seed_json, query_json, seqName, hmmpath):
     general_fn.check_file_exist(seed_json)
     general_fn.check_file_exist(query_json)
 
-    fas_cmd = 'fas.run -s %s -q %s' % (seed_json, query_json)
+    fas_cmd = 'fas.run -s %s -q %s --no_config' % (seed_json, query_json)
     fas_cmd = '%s -a %s/%s --raw --tsv --domain --cpus 1 -o %s/%s' \
                 % (fas_cmd, hmmpath, seqName, hmmpath, seqName)
     try:

fdog/libs/preparation.py

@@ -192,7 +192,6 @@ def identify_seed_id(seqFile, refspec, corepath, debug, silentOff):
         sys.exit()
     for hit in blast_out['hits']:
         if blast_out['hits'][hit]['align_len'] == blast_out['query_len']:
-            print("BEST BLAST HIT")
             return(hit)
         elif abs(int(blast_out['hits'][hit]['align_len']) - int(blast_out['query_len'])) < 10:
             output_fn.print_stdout(silentOff, 'WARNING: Found seed sequence shorter/longer than input!')

setup.py

@@ -26,7 +26,7 @@
 
 setup(
     name="fdog",
-    version="0.1.23",
+    version="0.1.24",
     python_requires='>=3.7.0',
     description="Feature-aware Directed OrtholoG search tool",
     long_description=long_description,