From 288b05d2770dab8b6c2d59aff35ca68e481f4a8d Mon Sep 17 00:00:00 2001
From: zhangrengang <zhangrenang@ori-gene.cn>
Date: Thu, 24 Oct 2024 13:53:47 +0800
Subject: [PATCH] fix bug; support Proteinortho6

---
 README.md        |  1 +
 soi/colors.py    | 18 +++++++++++++-----
 soi/evaluator.py |  2 +-
 soi/mcscan.py    |  4 +++-
 4 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 15affaa..3ed0dfe 100644
--- a/README.md
+++ b/README.md
@@ -396,6 +396,7 @@ Tetracendron_sinense|Tesin01G0062600    Trochodendron_aralioides|evm.TU.group9.7
 
 #### Orthology format ####
 The outputs from [OrthoFinder2](https://github.com/davidemms/OrthoFinder), OrthoMCL, 
+[Proteinortho6](https://gitlab.com/paulklemm_PHD/proteinortho), 
 [Broccoli](https://github.com/rderelle/Broccoli), [SonicParanoid2](https://gitlab.com/salvo981/sonicparanoid2) are supported:
 ```
 # OrthoFinder2 output directory like:
diff --git a/soi/colors.py b/soi/colors.py
index 5133e9d..bbd79c6 100644
--- a/soi/colors.py
+++ b/soi/colors.py
@@ -2,6 +2,7 @@
 #from reportlab.lib import colors
 import numpy as np
 from matplotlib import cm
+from matplotlib import colors
 import matplotlib
 
 COLORS_HEX = ['#f9c00c', '#00b9f1', '#7200da', '#f9320c', '#00b8a9', "#F4A460", '#009999', '#00C02E',
@@ -20,8 +21,9 @@ def __init__(self, colors_hex=None):
 		self.colors_hex = colors_hex
 	@property
 	def colors_rgb(self):
-		colors_lst = [colors.HexColor(v) for v in self.colors_hex]
-		return [','.join(map(str, v.bitmap_rgb())) for v in colors_lst]
+#		colors_lst = [colors.HexColor(v) for v in self.colors_hex]
+#		return [','.join(map(str, v.bitmap_rgb())) for v in colors_lst]
+		return [hex2rgb(v) for v in self.colors_hex]
 	@property 
 	def colors_r(self):
 		return 'c({})'.format(','.join(map(repr, self.colors_hex)))
@@ -30,6 +32,11 @@ def __str__(self):
 	def __repr__(self):
 		return str(self.colors_hex)
 
+def hex2rgb(Hex):
+	rgb = colors.to_rgb(Hex)
+	rgb255 = ','.join(map(str, [int(v*255) for v in rgb]))
+	return rgb255
+
 class Colors:
 	def __init__(self, n):
 		self.n = n
@@ -48,9 +55,10 @@ def to_hex(self):
 		colors_hex = [matplotlib.colors.to_hex(c) for c in self.colors]
 		return colors_hex
 	def to_rgb(self):
-		colors_hex = self.to_hex()
-		colors_lst = [colors.HexColor(v) for v in colors_hex]
-		colors_rgb = [','.join(map(str, v.bitmap_rgb())) for v in colors_lst]
+#		colors_hex = self.to_hex()
+#		colors_lst = [colors.HexColor(v) for v in colors_hex]
+#		colors_rgb = [','.join(map(str, v.bitmap_rgb())) for v in colors_lst]
+		colors_rgb = [hex2rgb(v) for v in self.colors]
 		return colors_rgb
 
 
diff --git a/soi/evaluator.py b/soi/evaluator.py
index c351507..1a297c3 100644
--- a/soi/evaluator.py
+++ b/soi/evaluator.py
@@ -106,7 +106,7 @@ def plot_eval(d_rcs, outfig, legend_fontsize=9):
 	ncols = n // 30 + 1
 	ax0.set_xlim(0,1)
 	ax0.set_ylim(0,1)
-	ax0.legend(loc=(-1.5, 0),fancybox=False, frameon=False, ncols=ncols)
+	ax0.legend(loc=(-1.5, 0),fancybox=False, frameon=False, ncols=ncols)	#
 	ax0.xaxis.set_tick_params(length=0)
 	ax0.spines['right'].set_color('none')
 	ax0.spines['top'].set_color('none')
diff --git a/soi/mcscan.py b/soi/mcscan.py
index b4426ff..cb9740f 100644
--- a/soi/mcscan.py
+++ b/soi/mcscan.py
@@ -1127,7 +1127,7 @@ def slim_tandem(tandem, pairs, outPairs):
 		pair.write(outPairs)
 	
 def split_pair(line, sep=None, parser=None):
-	pair = tuple(line.rstrip().split(sep, 1))
+	pair = tuple(line.rstrip().split(sep)) # 1
 	return parser(*pair)
 	
 class CommonPair(object):
@@ -1186,6 +1186,8 @@ def __iter__(self):
 	def _parse(self):
 		for line in open(self.pairs):
 			line = lazy_decode(line)
+			if line.startswith('#'): # comments
+				continue
 			yield split_pair(line, self.sep, self.parser)
 	def graph(self):
 		G = nx.Graph()