From 23b813f4a001e9a3b7da9242c7558d9ad3da8db6 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 1 Mar 2022 17:26:40 +0100
Subject: [PATCH] Encode confidence in ConSurf values
Requires a container with latest ConSurf deps
---
var3d/seq_anno.py | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/var3d/seq_anno.py b/var3d/seq_anno.py
index 3c11bcc..a67e548 100644
--- a/var3d/seq_anno.py
+++ b/var3d/seq_anno.py
@@ -25,8 +25,11 @@ class ConsurfSeqAnno(SeqAnno):
The code is not opensource but kindly provided by the Ben-Tal group
and wrapped into a Singularity container by us.
- The returned annotations correspond to the Consurf conservation scores in
- range [1-9]
+ ConSurf conservation scores are in range [1-9]. However, the returned values
+ additionally encode confidence. A score is considered non-confident if less
+ than 6 non-gaped homologue sequences have been found at that location or if
+ the ConSurf internal confidence interval is >= 4. Non-confident scores are
+ multiplied by -1. So a non-confident score of 8 would be represented as -8.
:param seq_db: Path to sequence db that can be read by Jackhmmer, i.e. a big
fat fasta file. Typically uniref90
@@ -108,7 +111,10 @@ class ConsurfSeqAnno(SeqAnno):
with open(result_json, "r") as fh:
result = json.load(fh)
- return self.MapAnno(sequence, result["COLOR"], seq_range)
+ color = result["COLOR"]
+ confidence = result["CONFIDENCE"]
+ scores = [a if b else -a for a,b in zip(color, confidence)]
+ return self.MapAnno(sequence, scores, seq_range)
class EntropySeqAnno(SeqAnno):
--
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