From 2741809bd28447048b9e79eb333f81dc2c8555ee Mon Sep 17 00:00:00 2001
From: isabelrem <42750792+isabelrem@users.noreply.github.com>
Date: Thu, 9 May 2024 14:11:37 +0100
Subject: [PATCH] Update fh.py

Removed notes to self. Added note in PRS(object) docstring that notes the paper this class was based on originally used build 37 genomic coordinates for the SNPs, whereas the v2.0.0 version of this script uses build 38 genomic coordinates.
---
 fh.py | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/fh.py b/fh.py
index 75e2d9e..1f04578 100755
--- a/fh.py
+++ b/fh.py
@@ -14,6 +14,7 @@ class PRS(object):
 	"""
 	Class to easily calculate Polygenic Risk Score for FH.
 	see Talmund et al 2013
+ 	NOTE: Talmund et al use build 37 genomic coordinates. This script uses build 38 genomic coordinates. 
 
 	Attributes
 	----------
@@ -39,57 +40,57 @@ class PRS(object):
 	
 	"""
 	SCORES = {
-	"1:55038977": { #rs2479409 (PCSK9) build 38
+	"1:55038977": { #rs2479409 (PCSK9)
 		"GG":0.104,
 		"GA":0.052,
 		"AA":0
 	}, 
-	"1:109275684":{ #rs629301 (CELSR2) build 38
+	"1:109275684":{ #rs629301 (CELSR2)
 		"GG":0,
 		"GT":0.15,
 		"TT":0.3
 	}, 
-	"2:21041028":{ #rs1367117 (APOB) build 38
+	"2:21041028":{ #rs1367117 (APOB)
 		"GG":0,
 		"GA":0.1,
 		"AA":0.2
 	}, 
-	"2:43845437":{ #rs4299376 (ABCG8) build 38
+	"2:43845437":{ #rs4299376 (ABCG8)
 		"GG":0.142,
 		"GT":0.071,
 		"TT":0
 	}, 
-	"6:16127176":{ #rs3757354 (MYLIP) build 38
+	"6:16127176":{ #rs3757354 (MYLIP)
 		"CC":0.074,
 		"CT":0.037,
 		"TT":0
 	}, 
-	"6:26092913":{ #rs1800562 (HFE) build 38
+	"6:26092913":{ #rs1800562 (HFE)
 		"GG":0.114,
 		"GA":0.057,
 		"AA":0
 	}, 
-	"6:160157828":{ #rs1564348 (SLC22A1) build 38
+	"6:160157828":{ #rs1564348 (SLC22A1)
 		"TT":0.028,
 		"TC":0.014,
 		"CC":0
 	},
-	"11:126374057":{ #rs11220462 (ST3GAL4) build 38
+	"11:126374057":{ #rs11220462 (ST3GAL4)
 		"GG":0,
 		"GA":0.05,
 		"AA":0.1
 	}, 
-	"14:24414681":{ #rs8017377 (NYNRIN) build 38
+	"14:24414681":{ #rs8017377 (NYNRIN)
 		"GG":0,
 		"GA":0.029,
 		"AA":0.058
 	},
-	"19:11091630":{ #rs6511720 (LDLR) build 38
+	"19:11091630":{ #rs6511720 (LDLR)
 		"GG":0.36,
 		"GT":0.18,
 		"TT":0
 	},
-	"19:44908684,19:44908822":{ #rs429358,rs7412 build 38
+	"19:44908684,19:44908822":{ #rs429358,rs7412
 		"TTTT":-0.9,
 		"TCTT":-0.4,
 		"TTCT":-0.4,