busco: handling augustus versions properly, default is 3.2.3

quast_libs/qutils.py

@@ -688,39 +688,46 @@ def relpath(path, start=curdir):
     return join(*rel_list)
 
 
-def get_path_to_program(program, dirpath=None, min_version=None, recommend_version=None):
+def get_path_to_program(program, dirpath=None, min_version=None, recommend_version=None, max_allowed_version=None):
     """
     returns the path to an executable or None if it can't be found
     """
-    OLD_VERSION = 0
+    INCOMPATIBLE_VERSION = 0
     CORRECT_VERSION = 1
     NOT_RECOMMENDED_VERSION = 2
 
     def is_exe(fpath):
         if os.path.isfile(fpath) and os.access(fpath, os.X_OK):
-            version_check = check_version(fpath, min_version, recommend_version)
-            if version_check != OLD_VERSION:
+            version_check = check_version(fpath, min_version, recommend_version, max_allowed_version)
+            if version_check != INCOMPATIBLE_VERSION:
                 if version_check == NOT_RECOMMENDED_VERSION:
-                    logger.warning('Version of installed %s differs from its version in QUAST package (%s). '
+                    logger.warning('Version of installed %s differs from its version in the QUAST package (%s). '
                                    'Please make sure that you use an actual version of software.' % (program, recommend_version))
                 return True
+        return False
 
-    def check_version(fpath, min_version, recommend_version=None):
-        if not min_version: return CORRECT_VERSION
+    def check_version(fpath, min_version, recommend_version=None, max_allowed_version=None):
+        if not min_version:
+            return CORRECT_VERSION
         p = subprocess.Popen([fpath, '--version'], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
         stdout, stderr = p.communicate()
         version_pattern = re.compile('(?P<major_version>\d+)\.(?P<minor_version>\d+)')
         v = version_pattern.search(str(stdout))
         if not v.group('major_version') or not v.group('minor_version'):
-            return OLD_VERSION
-        version, minor_version = map(int, min_version.split('.'))
-        rec_version, rec_minor_version = map(int, recommend_version.split('.'))
+            return INCOMPATIBLE_VERSION
+        version, minor_version = map(int, min_version.split('.')[:2])
         if int(v.group('major_version')) == version and int(v.group('minor_version')) >= minor_version:
-            if not recommend_version or (int(v.group('major_version')) == rec_version and int(v.group('minor_version')) == rec_minor_version):
-                return CORRECT_VERSION
-            else:
-                return NOT_RECOMMENDED_VERSION
-        else: return OLD_VERSION
+            if max_allowed_version is not None:
+                max_version, max_minor_version = map(int, max_allowed_version.split('.')[:2])
+                if int(v.group('major_version')) > max_version or int(v.group('minor_version')) > max_minor_version:
+                    return INCOMPATIBLE_VERSION
+            if recommend_version is not None:
+                rec_version, rec_minor_version = map(int, recommend_version.split('.')[:2])
+                if int(v.group('major_version')) != rec_version or int(v.group('minor_version')) != rec_minor_version:
+                    return NOT_RECOMMENDED_VERSION
+            return CORRECT_VERSION
+        else:
+            return INCOMPATIBLE_VERSION
 
     if dirpath:
         exe_file = os.path.join(dirpath, program)

quast_libs/run_busco.py

@@ -20,7 +20,8 @@
 
 logger = get_logger(qconfig.LOGGER_DEFAULT_NAME)
 
-augustus_version = '3.3.3'
+augustus_version = '3.2.3'
+augustus_max_allowed_version = '3.3'
 augustus_url = 'http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-' + augustus_version + '.tar.gz'
 bacteria_db_url = 'https://busco-archive.ezlab.org/v3/datasets/bacteria_odb9.tar.gz'
 fungi_db_url = 'https://busco-archive.ezlab.org/v3/datasets/fungi_odb9.tar.gz'
@@ -116,7 +117,9 @@ def __check_preinstalled_augustus_completeness(dirpath):
             return True
         return False
 
-    preinstalled_augustus = qutils.get_path_to_program('augustus')
+    preinstalled_augustus = qutils.get_path_to_program('augustus', min_version=augustus_version,
+                                                       recommend_version=augustus_version,
+                                                       max_allowed_version=augustus_max_allowed_version)
     if preinstalled_augustus is not None:
         preinstalled_augustus_dirpath = os.path.dirname(os.path.dirname(preinstalled_augustus))
         if __check_preinstalled_augustus_completeness(preinstalled_augustus_dirpath):
@@ -235,6 +238,7 @@ def do(contigs_fpaths, output_dir, logger):
         return
 
     config_fpath = make_config(output_dir, tmp_dir, busco_threads, clade_dirpath, augustus_dirpath)
+    logger.info('  running BUSCO with augustus from ' + augustus_dirpath)
     logger.info('Logs and results will be saved under ' + output_dir + '...')
 
     os.environ['BUSCO_CONFIG_FILE'] = config_fpath
@@ -281,6 +285,8 @@ def do(contigs_fpaths, output_dir, logger):
                        '  3. Problem with BUSCO dependencies, most likely Augustus. Check that the binaries in ' + augustus_dirpath + '/bin/ are working properly.\n'
                        '     If something is wrong with Augustus, you may try to install it yourself '
                              '(https://github.com/Gaius-Augustus/Augustus or `conda install -c bioconda augustus`) and make sure "augustus" binary is in PATH.\n'
+                       '     Please install the PROPER VERSION of Augustus, we tested BUSCO with augustus-' + augustus_version +
+                             ', it may also work with augustus-' + augustus_max_allowed_version + ', the newer/older versions are not supported.\n'
                        '  4. Some other problem with BUSCO. Check the logs (you may need to rerun QUAST with --debug to see all intermediate files).\n'
                        '     If you cannot solve the problem yourself, post an issue at https://github.com/ablab/quast/issues or write to [email protected]')
     if not qconfig.debug: