Maintenance - Mise à jour mensuelle Lundi 7 Décembre 2021 entre 7h00 et 9h00

Commit 5255692b authored by Floreal Cabanettes's avatar Floreal Cabanettes
Browse files

Close SeqIO

parent c6d4f0ac
...@@ -166,8 +166,8 @@ class Functions: ...@@ -166,8 +166,8 @@ class Functions:
is_compressed = fasta_file.endswith(".gz") is_compressed = fasta_file.endswith(".gz")
if is_compressed: if is_compressed:
fasta_file = Functions.uncompress(fasta_file) fasta_file = Functions.uncompress(fasta_file)
seq = SeqIO.index(fasta_file, "fasta")
fasta_file_o = fasta_file + ".sorted" fasta_file_o = fasta_file + ".sorted"
seq = SeqIO.index(fasta_file, "fasta")
with open(fasta_file_o, "w") as fasta_out: with open(fasta_file_o, "w") as fasta_out:
for name, props in index.items(): for name, props in index.items():
sequence = seq[name] sequence = seq[name]
...@@ -180,6 +180,7 @@ class Functions: ...@@ -180,6 +180,7 @@ class Functions:
sequence.name = s_name sequence.name = s_name
sequence.description = s_description sequence.description = s_description
SeqIO.write(sequence, fasta_out, "fasta") SeqIO.write(sequence, fasta_out, "fasta")
seq.close()
if is_compressed: if is_compressed:
os.remove(fasta_file) os.remove(fasta_file)
if compress: if compress:
......
...@@ -758,6 +758,7 @@ class Paf: ...@@ -758,6 +758,7 @@ class Paf:
seq = query_f[contig] seq = query_f[contig]
seq.id += "_unaligned" seq.id += "_unaligned"
SeqIO.write(seq, out, "fasta") SeqIO.write(seq, out, "fasta")
query_f.close()
if uncompressed: if uncompressed:
os.remove(query_fasta) os.remove(query_fasta)
status = "success" status = "success"
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment