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| author | AndreaGuarracino | 2021-01-08 23:44:47 +0100 |
|---|---|---|
| committer | AndreaGuarracino | 2021-01-08 23:44:47 +0100 |
| commit | 53a47a18a45270c3f037fabe9cc973c66bfe50bf (patch) | |
| tree | 1fb71fae0d629127a5da6f9ad879fff259016b14 /workflows/yamlfa2ttl/check_sequence.py | |
| parent | 2ddf72a4028475eb65dfeab153f3565e698d5338 (diff) | |
| download | bh20-seq-resource-53a47a18a45270c3f037fabe9cc973c66bfe50bf.tar.gz bh20-seq-resource-53a47a18a45270c3f037fabe9cc973c66bfe50bf.tar.lz bh20-seq-resource-53a47a18a45270c3f037fabe9cc973c66bfe50bf.zip | |
sample_id in the FASTA has to match the sample_id in the YAMLyamlfa2ttl
Diffstat (limited to 'workflows/yamlfa2ttl/check_sequence.py')
| -rw-r--r-- | workflows/yamlfa2ttl/check_sequence.py | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/workflows/yamlfa2ttl/check_sequence.py b/workflows/yamlfa2ttl/check_sequence.py index f92bf6d..58a65b9 100644 --- a/workflows/yamlfa2ttl/check_sequence.py +++ b/workflows/yamlfa2ttl/check_sequence.py @@ -26,7 +26,7 @@ def read_single_fasta(path_fasta): return header, ''.join(sequence) -print("FASTA QC: checking similarity to the reference") +print("FASTA QC: checking similarity to the reference", file=sys.stderr) header, sequence = read_single_fasta(path_fasta) @@ -46,7 +46,7 @@ with tempfile.NamedTemporaryFile() as tmp_fasta: "minimap2", "-c", "-x", "asm20", tmp_sars_cov_2_reference_fasta.name, tmp_fasta.name ] - print(" ".join(cmd)) + print(" ".join(cmd), file=sys.stderr) result = subprocess.run(cmd, stdout=subprocess.PIPE) result.check_returncode() |