parse_tree now uses config

workflow/notebooks/config.py

@@ -0,0 +1,71 @@
+# Config
+
+import pandas as pd
+
+
+# ------------------------------------------------------------------------
+# VARIABLES
+# ------------------------------------------------------------------------
+
+# Pandas
+# pd.set_option("display.max_rows", None, "display.max_columns", None)
+pd.set_option("display.max_rows", 10, "display.max_columns", None)
+
+# Branch Support Thresholds (from IQTREE docs)
+ALRT_THRESH = 80
+UFBOOT_THRESH = 95
+
+# Significant digits for writing newick files
+BRANCH_LEN_SIG_DIG = 12
+
+# Data parsing
+NO_DATA_CHAR = "NA"
+
+# How to color branch supports
+LOW_COL = "black"
+HIGH_COL = "red"
+TERM_COL = "grey"
+
+# Nextstrain / augur / auspice
+JSON_INDENT = 2
+
+
+# ------------------------------------------------------------------------
+# Functions
+# ------------------------------------------------------------------------
+
+# This code is from the biopython Phylo module
+def get_x_positions(tree):
+    """Create a mapping of each clade to its horizontal position.
+    Dict of {clade: x-coord}
+    """
+    depths = tree.depths()
+    # If there are no branch lengths, assume unit branch lengths
+    if not max(depths.values()):
+        depths = tree.depths(unit_branch_lengths=True)
+    return depths
+
+
+# This code is from the biopython Phylo module
+def get_y_positions(tree):
+    """Create a mapping of each clade to its vertical position.
+    Dict of {clade: y-coord}.
+    Coordinates are negative, and integers for tips.
+    """
+    maxheight = tree.count_terminals()
+    # Rows are defined by the tips
+    heights = {
+        tip: maxheight - i for i, tip in enumerate(reversed(tree.get_terminals()))
+    }
+
+    # Internal nodes: place at midpoint of children
+    def calc_row(clade):
+        for subclade in clade:
+            if subclade not in heights:
+                calc_row(subclade)
+        # Closure over heights
+        heights[clade] = (heights[clade.clades[0]] + heights[clade.clades[-1]]) / 2.0
+
+    if tree.root.clades:
+        calc_row(tree.root)
+    return heights