abutils - npm Package Compare versions

Comparing version 0.4.13 to 0.4.14

abutils.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: abutils
-Version: 0.4.13
+Version: 0.4.14
 Summary: Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
@@ -5,0 +5,0 @@ Home-page: https://github.com/briney/abutils

abutils/tools/phylo.py

@@ -38,3 +38,4 @@ #!/usr/bin/env python
 import matplotlib.pyplot as plt
-from abstar.core.germline import get_imgt_germlines
+
+# from abstar.core.germline import get_imgt_germlines
 from Bio import Phylo
@@ -260,3 +261,3 @@ from matplotlib import markers
                 return
-            germ = get_imgt_germlines(self.germ_db, "V", gene=top_v)
+            # germ = get_imgt_germlines(self.germ_db, "V", gene=top_v)
             self._root = self._get_top_germline_v()
@@ -927,2 +928,4 @@ elif isinstance(self._root, str):
         """
+        from abstar.core.germline import get_imgt_germlines
+
         v_counts = Counter([s.get("v_call", None) for s in self.sequences])
@@ -929,0 +932,0 @@ top_v = v_counts.most_common()[0][0]

abutils/utils/phylogeny.py

@@ -29,4 +29,2 @@ #!/usr/bin/env python
 import colorsys
-from collections import Counter
-from copy import copy, deepcopy
 import itertools
@@ -43,22 +41,20 @@ import math
 import tempfile
+from collections import Counter
+from copy import copy, deepcopy
 from typing import Optional
 
+import abstar
+import ete3
+import matplotlib.pyplot as plt
 import numpy as np
+import pandas as pd
 import scipy
-import pandas as pd
+import seaborn as sns
 
+# from abstar.core.germline import get_imgt_germlines
+from Bio import AlignIO, Phylo
+from matplotlib.colors import ListedColormap
 from scipy.ndimage import gaussian_filter1d
 from scipy.special import rel_entr
 
-import matplotlib.pyplot as plt
-from matplotlib.colors import ListedColormap
-import seaborn as sns
-
-import ete3
-
-from Bio import AlignIO, Phylo
-
-import abstar
-from abstar.core.germline import get_imgt_germlines
-
 from ..core.pair import Pair
@@ -68,3 +64,3 @@ from ..core.sequence import Sequence
 from .cluster import cluster
-from .color import hex_to_rgb, get_cmap
+from .color import get_cmap, hex_to_rgb
 from .decorators import lazy_property
@@ -100,8 +96,8 @@ from .pipeline import make_dir
     aln : str
-        Path to a multiple sequence alignment file, in FASTA format, or a 
+        Path to a multiple sequence alignment file, in FASTA format, or a
         FASTA-formatted multiple sequence alignment string. Required.
 
     tree_file : str
-        Path to the tree file which will be output by FastTree. If the parent 
-        directory does not exist, it will be created. If not provided, the output 
+        Path to the tree file which will be output by FastTree. If the parent
+        directory does not exist, it will be created. If not provided, the output
         (a Newick-formatted tree file) will be returned as a ``str``.
@@ -115,3 +111,3 @@
     fasttree_bin : str, optional
-        Path to the desired FastTree binary. Default is to use the version of 
+        Path to the desired FastTree binary. Default is to use the version of
         FastTree that is bundled with ``abutils``.
@@ -125,3 +121,3 @@
 
-    
+
     Returns
@@ -214,3 +210,8 @@ -------
 
-def igphyml(input_file: str = None, tree_file: str = None, root: str = None, verbose: bool = False) -> str:
+def igphyml(
+    input_file: str = None,
+    tree_file: str = None,
+    root: str = None,
+    verbose: bool = False,
+) -> str:
     """
@@ -220,3 +221,3 @@ Computes a phylogenetic tree using IgPhyML.
     .. note::
-        
+
         IgPhyML must be installed. It can be downloaded from https://github.com/kbhoehn/IgPhyML.
@@ -232,3 +233,3 @@
 
-        verbose (bool): If `True`, prints the standard output and standard error for each IgPhyML run. 
+        verbose (bool): If `True`, prints the standard output and standard error for each IgPhyML run.
             Default is `False`.
@@ -395,2 +396,4 @@ """
 
+    from abstar.core.germline import get_imgt_germlines
+
     if project_dir is None:
@@ -397,0 +400,0 @@ print("\nERROR: project_dir is required\n")

abutils/version.py

@@ -6,2 +6,2 @@ # Store the version here so:
 
-__version__ = "0.4.13"
+__version__ = "0.4.14"

PKG-INFO

 Metadata-Version: 2.1
 Name: abutils
-Version: 0.4.13
+Version: 0.4.14
 Summary: Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
@@ -5,0 +5,0 @@ Home-page: https://github.com/briney/abutils

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