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-rw-r--r--workflows/yamlfa2ttl/check_format.py31
1 files changed, 31 insertions, 0 deletions
diff --git a/workflows/yamlfa2ttl/check_format.py b/workflows/yamlfa2ttl/check_format.py
new file mode 100644
index 0000000..4472b18
--- /dev/null
+++ b/workflows/yamlfa2ttl/check_format.py
@@ -0,0 +1,31 @@
+import gzip
+import tempfile
+import magic
+import io
+import sys
+
+path_fasta = sys.argv[1]
+format_to_check = sys.argv[2]
+path_valid_formats = sys.argv[3]
+
+with tempfile.NamedTemporaryFile() as tmp:
+ with open(path_valid_formats, 'rb') as f:
+ tmp.write(f.read())
+ tmp.flush()
+
+ check_format = magic.Magic(magic_file=tmp.name, uncompress=False, mime=True)
+
+with open(path_fasta, "rb") as f:
+ gz = ""
+ if path_fasta.endswith(".gz"):
+ gz = ".gz"
+ f = gzip.GzipFile(fileobj=f, mode='rb')
+
+ f = io.TextIOWrapper(f)
+
+ buffer = f.read(4096)
+ seq_type = check_format.from_buffer(buffer).lower()
+ f.detach()
+
+ if seq_type != format_to_check:
+ raise ValueError(f"Input file ({path_fasta}) does not look like a {format_to_check}")