From 4c2bbded5295d9969c23dc221261d7e4befefeaa Mon Sep 17 00:00:00 2001
From: Jon Palmer <nextgenusfs@gmail.com>
Date: Sun, 25 Feb 2024 14:08:57 -0800
Subject: [PATCH] fix biopython GC change in recent versions #1000

---
 funannotate/library.py | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/funannotate/library.py b/funannotate/library.py
index 9dc7b81..7df3688 100755
--- a/funannotate/library.py
+++ b/funannotate/library.py
@@ -2740,7 +2740,15 @@ def dict2nucleotides2(input, prots, trans, cdstrans):
 
 
 def simpleFastaStats(fasta):
-    from Bio.SeqUtils import GC
+    try:
+        from Bio.SeqUtils import gc_fraction
+
+        def GC(sequence):
+            return 100 * gc_fraction(sequence, ambiguous="ignore")
+
+    except ImportError:
+        # Older versions have this:
+        from Bio.SeqUtils import GC
     from Bio.SeqIO.FastaIO import SimpleFastaParser
 
     contigs = []
@@ -9184,7 +9192,15 @@ def splitFASTA(input, outputdir):
 
 
 def genomeStats(input):
-    from Bio.SeqUtils import GC
+    try:
+        from Bio.SeqUtils import gc_fraction
+
+        def GC(sequence):
+            return 100 * gc_fraction(sequence, ambiguous="ignore")
+
+    except ImportError:
+        # Older versions have this:
+        from Bio.SeqUtils import GC
 
     lengths = []
     GeeCee = []