Circular import in gisaid_utils.py

[ArtPoon]

art@Wernstrom covizu % python3 covizu/utils/gisaid_utils.py -h
Traceback (most recent call last):
  File "/Users/art/git/covizu/covizu/utils/gisaid_utils.py", line 12, in <module>
    from covizu.minimap2 import minimap2, encode_diffs
  File "/usr/local/lib/python3.9/site-packages/covizu-0.3-py3.9.egg/covizu/minimap2.py", line 9, in <module>
    from covizu.utils import gisaid_utils
  File "/usr/local/lib/python3.9/site-packages/covizu-0.3-py3.9.egg/covizu/utils/gisaid_utils.py", line 12, in <module>
    from covizu.minimap2 import minimap2, encode_diffs
ImportError: cannot import name 'minimap2' from partially initialized module 'covizu.minimap2' (most likely due to a circular import) (/usr/local/lib/python3.9/site-packages/covizu-0.3-py3.9.egg/covizu/minimap2.py)

[ArtPoon]

Patched this with the following:

diff --git a/covizu/minimap2.py b/covizu/minimap2.py
index 9219eba..0034cc9 100644
--- a/covizu/minimap2.py
+++ b/covizu/minimap2.py
@@ -7,6 +7,7 @@ import json

 import covizu
 from covizu.utils import gisaid_utils
+#from covizu.utils.gisaid_utils import filter_problematic

 def apply_cigar(seq, rpos, cigar):
diff --git a/covizu/utils/gisaid_utils.py b/covizu/utils/gisaid_utils.py
index 5651b55..7c0b4fd 100644
--- a/covizu/utils/gisaid_utils.py
+++ b/covizu/utils/gisaid_utils.py
@@ -9,7 +9,8 @@ from datetime import datetime
 import getpass

 import covizu
-from covizu.minimap2 import minimap2, encode_diffs
+from covizu import minimap2
+#from covizu.minimap2 import minimap2, encode_diffs
 from covizu.utils.seq_utils import *
 from covizu.utils.progress_utils import Callback

@@ -132,9 +133,9 @@ def extract_features(batcher, ref_file, binpath='minimap2', nthread=3, minlen=29
         reflen = len(convert_fasta(handle)[0][1])

     for fasta, batch in batcher:
-        mm2 = minimap2(fasta, ref_file, stream=True, path=binpath, nthread=nthread,
+        mm2 = minimap2.minimap2(fasta, ref_file, stream=True, path=binpath, nthread=nthread,
                        minlen=minlen)
-        result = list(encode_diffs(mm2, reflen=reflen))
+        result = list(minimap2.encode_diffs(mm2, reflen=reflen))
         for row, record in zip(result, batch):
             # reconcile minimap2 output with GISAID record
             qname, diffs, missing = row

[ArtPoon]

Unit test suite should have caught this. We need to make sure this gets run with every PR. Also need to incorporate the above patch into dev.

[ArtPoon]

Close, deal with this when we work on #389