clipkit 2.2.2__tar.gz → 2.2.4__tar.gz

{clipkit-2.2.2 → clipkit-2.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: clipkit
-Version: 2.2.2
+Version: 2.2.4
 Summary: Alignment trimming software for phylogenetics.
 Home-page: https://github.com/jlsteenwyk/clipkit
 Author: Jacob L. Steenwyk

{clipkit-2.2.2 → clipkit-2.2.4}/clipkit/parser.py

@@ -80,8 +80,8 @@ def create_parser() -> ArgumentParser:
                                                     (default: 0.9)
 
         -gc, --gap_characters <string_of_gap_chars> specifies gap characters used in input file
-                                                    (default for aa: "-?*XxNn"
-                                                     default for nt: "-?*Xx")
+                                                    (default for aa: Xx-?*
+                                                     default for nt: XxNn-?*)
 
         -if, --input_file_format <file_format>      specifies input file format
                                                     (default: auto-detect)    
@@ -126,10 +126,10 @@ def create_parser() -> ArgumentParser:
             iteration of trimming that uses smart-gap.
 
         Gap characters
-            Specifies gap characters used in the input file. All gap characters
-            should have a quotes (single or double) surrounding them. For example,
+            Specifies gap characters used in the input file. For example,
             "NnXx-?" would specify that "N", "n", "X", "x", "-", and "?" are
-            gap characters.
+            gap characters. Note, the first gap character cannot be "-" because
+            the parser will interpret the gaps list as a new argument.
 
         Sequence type
             Specifies the type of sequences in the input file. Valid options

clipkit-2.2.4/clipkit/settings.py

@@ -0,0 +1,2 @@
+DEFAULT_AA_GAP_CHARS = ["-", "?", "*", "X", "x"]
+DEFAULT_NT_GAP_CHARS = ["-", "?", "*", "X", "x", "N", "n"]

clipkit-2.2.4/clipkit/version.py

@@ -0,0 +1 @@
+__version__ = "2.2.4"

{clipkit-2.2.2 → clipkit-2.2.4}/clipkit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: clipkit
-Version: 2.2.2
+Version: 2.2.4
 Summary: Alignment trimming software for phylogenetics.
 Home-page: https://github.com/jlsteenwyk/clipkit
 Author: Jacob L. Steenwyk

clipkit-2.2.2/clipkit/settings.py

@@ -1,2 +0,0 @@
-DEFAULT_AA_GAP_CHARS = ["-", "?", "*"]
-DEFAULT_NT_GAP_CHARS = ["-", "?", "*", "X", "x"]

clipkit-2.2.2/clipkit/version.py

@@ -1 +0,0 @@
-__version__ = "2.2.2"