Converting to tabs.

B-UMMI · Jul 11, 2024 · 3be2401 · 3be2401
1 parent e8e1f0e
commit 3be2401
Show file tree

Hide file tree

Showing 16 changed files with 5,094 additions and 5,094 deletions.
diff --git a/CHEWBBACA/utils/chewiens_requests.py b/CHEWBBACA/utils/chewiens_requests.py
diff --git a/CHEWBBACA/utils/constants.py b/CHEWBBACA/utils/constants.py
diff --git a/CHEWBBACA/utils/distance_matrix.py b/CHEWBBACA/utils/distance_matrix.py
diff --git a/CHEWBBACA/utils/fasttree_wrapper.py b/CHEWBBACA/utils/fasttree_wrapper.py
@@ -16,22 +16,22 @@
 
 
 def call_fasttree(alignment_file, tree_file):
-    """Compute a phylogenetic tree based on MSA data.
-
-    Parameters
-    ----------
-    alignment_file : str
-        Path to a file with a MSA.
-    tree_file : str
-        Path to the output tree file in Newick format.
-    """
-    proc = subprocess.Popen(['FastTree', '-fastest', '-nosupport',
-                             '-noml', '-out', tree_file, alignment_file],
-                            stdout=subprocess.PIPE,
-                            stderr=subprocess.PIPE)
-
-    # Read the stdout from FastTree
-    stdout = proc.stdout.readlines()
-    stderr = proc.stderr.readlines()
-
-    return [stdout, stderr]
+	"""Compute a phylogenetic tree based on MSA data.
+
+	Parameters
+	----------
+	alignment_file : str
+		Path to a file with a MSA.
+	tree_file : str
+		Path to the output tree file in Newick format.
+	"""
+	proc = subprocess.Popen(['FastTree', '-fastest', '-nosupport',
+							 '-noml', '-out', tree_file, alignment_file],
+							stdout=subprocess.PIPE,
+							stderr=subprocess.PIPE)
+
+	# Read the stdout from FastTree
+	stdout = proc.stdout.readlines()
+	stderr = proc.stderr.readlines()
+
+	return [stdout, stderr]