fix busco call for annotate

nextgenusfs · Dec 29, 2019 · d6b4aa4 · d6b4aa4
1 parent b2315c9
commit d6b4aa4
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Showing 2 changed files with 7 additions and 8 deletions.
diff --git a/funannotate/annotate.py b/funannotate/annotate.py
@@ -33,7 +33,7 @@ def MEROPSBlast(input, cpus, evalue, tmpdir, output, diamond=True):
         cmd = ['blastp', '-db', blastdb, '-outfmt', '5', '-out', blast_tmp, '-num_threads', str(cpus),
                '-max_target_seqs', '1', '-evalue', str(evalue), '-query', input]
     if not os.path.isfile(blast_tmp):
-        lib.runSubprocess(cmd, '.', lib.log)
+        lib.runSubprocess4(cmd, '.', lib.log)
     # parse results
     with open(output, 'w') as out:
         with open(blast_tmp, 'r') as results:
@@ -62,7 +62,7 @@ def SwissProtBlast(input, cpus, evalue, tmpdir, GeneDict, diamond=True):
         cmd = ['blastp', '-db', blastdb, '-outfmt', '5', '-out', blast_tmp, '-num_threads', str(cpus),
                '-max_target_seqs', '1', '-evalue', str(evalue), '-query', input]
     if not lib.checkannotations(blast_tmp):
-        lib.runSubprocess(cmd, '.', lib.log)
+        lib.runSubprocess4(cmd, '.', lib.log)
     # parse results
     counter = 0
     total = 0
@@ -293,8 +293,6 @@ def __init__(self, prog):
         '--antismash', help='antiSMASH results in genbank format')
     parser.add_argument('--force', action='store_true',
                         help='Over-write output folder')
-    parser.add_argument('--AUGUSTUS_CONFIG_PATH',
-                        help='Path to Augustus config directory, $AUGUSTUS_CONFIG_PATH')
     parser.add_argument('--phobius', help='Phobius results')
     parser.add_argument('--eggnog', help='EggNog Mapper annotations')
     parser.add_argument('--busco_db', default='dikarya',

diff --git a/funannotate/aux_scripts/funannotate-BUSCO2.py b/funannotate/aux_scripts/funannotate-BUSCO2.py
@@ -2967,7 +2967,7 @@ def _parse_args():
     optional.add_argument('--stopCodon', default='False', dest='stopCodon', choices=['True', 'False'],
                           help='stop codon option for augustus, --stopCodonExcludedFromCDS=')
 
-    required.add_argument('--local_augustus', required=True, dest='local_augustus',
+    optional.add_argument('--local_augustus', required=False, dest='local_augustus',
                           help='local augustus folder')                          
 
     optional.add_argument('--augustus_parameters', required=False, default='', dest='augustus_parameters',
@@ -3178,8 +3178,10 @@ def _define_parameters(args):
         except IOError:
             _logger.error('Impossible to read the fasta file %s ' % args['in'])
             raise SystemExit
-
-    augustus_config_path = args['local_augustus']
+    if 'local_augustus' in args:
+        augustus_config_path = args['local_augustus']
+    else:
+        augustus_config_path = os.environ["AUGUSTUS_CONFIG_PATH"]
     try:
         if augustus_config_path[-1] != '/':
             augustus_config_path += '/'
@@ -3269,7 +3271,6 @@ def main(show_thread=False):
         _check_path_exist(args['in'])
         _check_path_exist(args['clade'])
         params = _define_parameters(args)
-        print(params)
         _set_rerun_busco_command(params)
 
         _logger.info('To reproduce this run: %s' % _rerun_cmd)