ADD _fimo.py

cmd/_fimo.py

@@ -0,0 +1,19 @@
+# the fimo command-line tool
+# Author: Jacob Schreiber <jmschreiber91@gmail.com>
+
+import pandas
+
+from tangermeme.tools.fimo import fimo
+
+
+import time
+
+def _run_fimo(args):
+	"""An internal function for running FIMO from the command-line."""
+
+	hits = fimo(args.motif, args.sequence, bin_size=args.bin_size, 
+		eps=args.epsilon, threshold=args.threshold, 
+		reverse_complement=not args.norc)
+
+	hits = pandas.concat(hits).sort_values('p-value')
+	print(hits.to_string(index=False))

requirements.txt

@@ -8,5 +8,4 @@ tqdm >= 4.64.1
 numba >= 0.55.1
 logomaker
 joblib >= 1.3.2
-scikit-learn >= 1.2.2
-llvmlite >= 0.43.0
+scikit-learn >= 1.2.2