Update print statements to make it clear when is a warning for debugg…

…ing, update tests inline with changes, clean up some old files and update version number
cov-lineages · May 29, 2021 · 20c4f7c · 20c4f7c
1 parent bb7847b
commit 20c4f7c
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Showing 11 changed files with 54 additions and 382 deletions.
diff --git a/environment.yml b/environment.yml
@@ -6,7 +6,7 @@ channels:
   - defaults
 dependencies:
   - wget
-  - biopython
+  - biopython>=1.74
   - minimap2
   - pip
   - python>=3.6

diff --git a/scorpio/__init__.py b/scorpio/__init__.py
@@ -1,2 +1,2 @@
 _program = "scorpio"
-__version__ = "0.2"
+__version__ = "0.3"
diff --git a/scorpio/command.py b/scorpio/command.py
diff --git a/scorpio/scripts/__init__.py b/scorpio/scripts/__init__.py
diff --git a/scorpio/scripts/extract_definitions.py b/scorpio/scripts/extract_definitions.py
@@ -7,7 +7,7 @@
 from Bio.Seq import Seq
 from operator import itemgetter
 
-from type_constellations import load_feature_coordinates
+from .type_constellations import load_feature_coordinates
 
 def parse_args():
     parser = argparse.ArgumentParser(description="""Pick a representative sample for each unique sequence""",

diff --git a/scorpio/scripts/scorpio.smk b/scorpio/scripts/scorpio.smk
diff --git a/scorpio/scripts/scorpiofunks.py b/scorpio/scripts/scorpiofunks.py