From 5255692b7f712ddcd7e4e6ccaae49b27c16f6a64 Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Wed, 21 Feb 2018 16:21:42 +0100
Subject: [PATCH] Close SeqIO
---
src/dgenies/lib/functions.py | 3 ++-
src/dgenies/lib/paf.py | 1 +
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/src/dgenies/lib/functions.py b/src/dgenies/lib/functions.py
index e3bd5a7..a33cc25 100644
--- a/src/dgenies/lib/functions.py
+++ b/src/dgenies/lib/functions.py
@@ -166,8 +166,8 @@ class Functions:
is_compressed = fasta_file.endswith(".gz")
if is_compressed:
fasta_file = Functions.uncompress(fasta_file)
- seq = SeqIO.index(fasta_file, "fasta")
fasta_file_o = fasta_file + ".sorted"
+ seq = SeqIO.index(fasta_file, "fasta")
with open(fasta_file_o, "w") as fasta_out:
for name, props in index.items():
sequence = seq[name]
@@ -180,6 +180,7 @@ class Functions:
sequence.name = s_name
sequence.description = s_description
SeqIO.write(sequence, fasta_out, "fasta")
+ seq.close()
if is_compressed:
os.remove(fasta_file)
if compress:
diff --git a/src/dgenies/lib/paf.py b/src/dgenies/lib/paf.py
index c8ca29b..9a8c6fa 100644
--- a/src/dgenies/lib/paf.py
+++ b/src/dgenies/lib/paf.py
@@ -758,6 +758,7 @@ class Paf:
seq = query_f[contig]
seq.id += "_unaligned"
SeqIO.write(seq, out, "fasta")
+ query_f.close()
if uncompressed:
os.remove(query_fasta)
status = "success"
--
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