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florealcab committed Feb 21, 2018
1 parent c6d4f0a commit 5255692
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Showing 2 changed files with 3 additions and 1 deletion.
3 changes: 2 additions & 1 deletion src/dgenies/lib/functions.py
Original file line number Diff line number Diff line change
Expand Up @@ -166,8 +166,8 @@ def sort_fasta(job_name, fasta_file, index_file, lock_file, compress=False, mail
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]
Expand All @@ -180,6 +180,7 @@ def sort_fasta(job_name, fasta_file, index_file, lock_file, compress=False, mail
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:
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1 change: 1 addition & 0 deletions src/dgenies/lib/paf.py
Original file line number Diff line number Diff line change
Expand Up @@ -758,6 +758,7 @@ def build_query_chr_as_reference(self):
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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