added check_format workflow and script

1 files changed, 35 insertions, 0 deletions

diff --git a/workflows/yamlfa2ttl/check_format.py b/workflows/yamlfa2ttl/check_format.py
new file mode 100644
index 0000000..a1b1f14
--- /dev/null
+++ b/workflows/yamlfa2ttl/check_format.py
@@ -0,0 +1,35 @@
+import gzip
+import tempfile
+import pkg_resources
+import magic
+import io
+
+import sys
+
+path_fasta = sys.argv[1]
+format_to_check = sys.argv[2]
+path_valid_formats = sys.argv[3]
+
+
+# ../../bh20sequploader/validation/formats
+
+schema_resource = pkg_resources.resource_stream(__name__, path_valid_formats)
+with tempfile.NamedTemporaryFile() as tmp:
+    tmp.write(schema_resource.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}")