blosum - npm Package Compare versions

Comparing version 1.1.0 to 1.1.1

PKG-INFO

 Metadata-Version: 2.1
 Name: blosum
-Version: 1.1.0
+Version: 1.1.1
 Summary: A simple BLOSUM toolbox without dependencies.
@@ -39,3 +39,3 @@ Home-page: https://github.com/not-a-feature/blosum
         ### Default BLOSUM 
-        This package comes with the most commonly used BLOSUM matrices built in.
+        This package provides with the commonly used BLOSUM matrices.
         You can choose from BLOSUM 45, 50, 62, 80 and 90.
@@ -60,3 +60,4 @@
         ```
-        # One Header Line
+        # Comments should start with #
+        # Each value should be seperated by one or many whitespace
            A  R  N  D
@@ -63,0 +64,0 @@ A  5 -2 -1 -2

README.md

@@ -32,3 +32,3 @@ ![blosum](https://github.com/not-a-feature/blosum/raw/main/blosum.png)
 ### Default BLOSUM 
-This package comes with the most commonly used BLOSUM matrices built in.
+This package provides with the commonly used BLOSUM matrices.
 You can choose from BLOSUM 45, 50, 62, 80 and 90.
@@ -53,3 +53,4 @@
 ```
-# One Header Line
+# Comments should start with #
+# Each value should be seperated by one or many whitespace
    A  R  N  D
@@ -56,0 +57,0 @@ A  5 -2 -1 -2

setup.cfg

 [metadata]
 name = blosum
-version = 1.1.0
+version = 1.1.1
 description = A simple BLOSUM toolbox without dependencies.
@@ -5,0 +5,0 @@ long_description = file: README.md

src/blosum.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: blosum
-Version: 1.1.0
+Version: 1.1.1
 Summary: A simple BLOSUM toolbox without dependencies.
@@ -39,3 +39,3 @@ Home-page: https://github.com/not-a-feature/blosum
         ### Default BLOSUM 
-        This package comes with the most commonly used BLOSUM matrices built in.
+        This package provides with the commonly used BLOSUM matrices.
         You can choose from BLOSUM 45, 50, 62, 80 and 90.
@@ -60,3 +60,4 @@
         ```
-        # One Header Line
+        # Comments should start with #
+        # Each value should be seperated by one or many whitespace
            A  R  N  D
@@ -63,0 +64,0 @@ A  5 -2 -1 -2

src/blosum/_blosum.py

@@ -30,3 +30,2 @@ """
             https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM62
-
         """
@@ -63,26 +62,28 @@
 
-        # Skip header line
-        content = content[1:]
+        blosumDict = {}
 
-        # Extract labels
-        labels = content[0]
-        labelslist = labels.split()
+        header = True
+        for line in content:
+            line = line.strip()
 
-        # Check if quadratic
-        if not len(labelslist) == len(content)-1:
-            raise EOFError("Blosum file is not quadratic.")
+            # Skip comments starting with #
+            if line.startswith("#"):
+                continue
 
-        # Check if all AA are covered
-        if not len(labelslist) == 25:
-            warn(UserWarning("Blosum matrix may not cover all amino-acids"))
+            linelist = line.split()
 
-        # Skip label line
-        content = content[1:]
+            # Extract labels only once
+            if header:
+                labelslist = linelist
+                header = False
 
-        blosumDict = {}
-        # For each line
-        for line in content:
-            linelist = line.split()
-            if len(linelist) < 0:
-                break
+                # Check if all AA are covered
+                if not len(labelslist) == 25:
+                    warn(UserWarning("Blosum matrix may not cover all amino-acids"))
+                continue
+
+            if not len(linelist) == len(labelslist) + 1:
+                # Check if line has as may entries as labels
+                raise EOFError("Blosum file is missing values.")
+
             # Add Line/Label combination to dict
@@ -92,2 +93,5 @@ for index, lab in enumerate(labelslist, start=1):
 
+        # Check quadratic
+        if not len(blosumDict) == len(labelslist)**2:
+            raise EOFError("Blosum file is not quadratic.")
         self.matrix = blosumDict
@@ -94,0 +98,0 @@

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Improved metrics

Total package byte prevSize

94263

0.47%

Lines of code

562

0.54%