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| author | Peter Amstutz | 2020-07-03 20:55:16 +0000 |
|---|---|---|
| committer | Peter Amstutz | 2020-07-03 20:55:16 +0000 |
| commit | c50e611f7be281a3b7955254be097c01e6461c20 (patch) | |
| tree | 6f3165c6dd214c324c358673460a6a535bb71817 /bh20sequploader | |
| parent | 535b8017ddd27a9db683f6d29368258b5c48cf5a (diff) | |
| download | bh20-seq-resource-c50e611f7be281a3b7955254be097c01e6461c20.tar.gz bh20-seq-resource-c50e611f7be281a3b7955254be097c01e6461c20.tar.lz bh20-seq-resource-c50e611f7be281a3b7955254be097c01e6461c20.zip | |
Fix qc_fasta bug closing stream.
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/qc_fasta.py | 4 |
1 files changed, 4 insertions, 0 deletions
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py index e198430..1587def 100644 --- a/bh20sequploader/qc_fasta.py +++ b/bh20sequploader/qc_fasta.py @@ -51,6 +51,8 @@ def qc_fasta(arg_sequence): if seq_type == "text/fasta": # ensure that contains only one entry submitlabel, submitseq = read_fasta(sequence) + sequence.seek(0) + sequence.detach() with tempfile.NamedTemporaryFile() as tmp1: refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta") @@ -92,6 +94,8 @@ def qc_fasta(arg_sequence): return ("sequence.fasta"+gz, seqlabel) elif seq_type == "text/fastq": + sequence.seek(0) + sequence.detach() return ("reads.fastq"+gz, seqlabel) else: raise ValueError("Sequence file does not look like a DNA FASTA or FASTQ") |