feat: add sequence placement functionality with command line interface

Author: rvosa

tests/data/seqplacer.py

@@ -0,0 +1,26 @@
+from polytomy.sequence_placer import SequencePlacer
+from polytomy.tree_parser import TreeParser
+import argparse
+
+# parse command line arguments: --tree, --alignment, --output, --threads, --model, --prefix, --keep-files, --output-dir
+parser = argparse.ArgumentParser()
+parser.add_argument("--intree", "-i", required=True)
+parser.add_argument("--alignment", "-a", required=True)
+parser.add_argument("--output", "-o", required=True)
+parser.add_argument("--threads", "-t", type=int, default=6)
+parser.add_argument("--model", "-m", default="GTRGAMMA")
+parser.add_argument("--prefix", "-p", default="seq_placement")
+parser.add_argument("--keep-files", "-k", action="store_true")
+parser.add_argument("--dir", "-d", default=".")
+args = parser.parse_args()
+
+parser = TreeParser()
+backbone_tree = parser.parse_from_file(args.intree)
+placer = SequencePlacer(backbone_tree, config={
+    'threads': args.threads,
+    'model': args.model,
+    'prefix': args.prefix,
+    'keep_files': args.keep_files,
+    'output_dir': args.dir
+})
+result_tree = placer.place_sequences(args.alignment, prefilter=True)