Tiny fixes regarding BUSCO downloading and running (better error messages; do not run on Python 2.6 and earlier)

Author: alexeigurevich

quast.py

@@ -220,9 +220,9 @@ def main(args):
         if qconfig.platform_name == 'macosx':
             logger.main_info("")
             logger.warning("BUSCO can be run on Linux only")
-        elif sys.version[0:3] == '2.5':
+        elif sys.version[0:3] < '2.7':
             logger.main_info("")
-            logger.warning("BUSCO does not support Python versions earlier than 2.6.")
+            logger.warning("BUSCO does not support Python versions earlier than 2.7.")
         else:
             from quast_libs import run_busco
             run_busco.do(contigs_fpaths, os.path.join(output_dirpath, qconfig.busco_dirname), logger)

quast_libs/qutils.py

@@ -997,7 +997,9 @@ def download_file(url, fpath, tool_name, move_file=True):
             _, exc_value, _ = sys.exc_info()
             logger.error(
                 'Failed downloading %s (url: %s), QUAST functionality will be limited! '
-                'Exception caught: %s' % (tool_name, url, exc_value))
+                'Exception caught: %s\n'
+                'You can try to download the file manually, place it in %s and restart QUAST'
+                % (tool_name, url, exc_value, fpath))
             return None
         if move_file:
             shutil.move(fpath + '.download', fpath)

quast_libs/ra_utils/misc.py

@@ -62,16 +62,14 @@ def get_gridss_fpath():
 
 
 def download_unpack_compressed_tar(name, download_url, downloaded_fpath, final_dirpath, logger, ext='gz'):
-    if download_file(download_url, downloaded_fpath, name, move_file=False):
-        unpack_tar(downloaded_fpath + '.download', final_dirpath, ext=ext)
+    if download_file(download_url, downloaded_fpath, name, move_file=True):
+        unpack_tar(downloaded_fpath, final_dirpath, ext=ext)
         logger.main_info('  Done')
-    else:
-        logger.main_info('  Failed downloading %s from %s!' % (name, download_url))
-        return False
+        return True
+    return False
 
 
 def unpack_tar(fpath, dst_dirpath, ext='bz2'):
-    shutil.move(fpath, fpath)
     import tarfile
     tar = tarfile.open(fpath, "r:" + ext)
     tar.extractall(dst_dirpath)

tc_tests/test_busco.py

@@ -9,6 +9,10 @@
     print('Busco can be run on Linux only')
     sys.exit(0)
 
+if sys.version[:3] < '2.7':
+    print('BUSCO does not support Python versions earlier than 2.7')
+    sys.exit(0)
+
 name = os.path.basename(__file__)[5:-3]
 contigs = [meta_contigs_1, meta_contigs_2]