Adding the find_path.py file

gaftools/cli/find_path.py

@@ -0,0 +1,42 @@
+"""
+Statistics of a GAF File
+"""
+
+import sys
+import logging
+import itertools
+from gaftools.gaf import GAF, Read
+from gaftools.cli import log_memory_usage
+from gaftools.timer import StageTimer
+from gaftools.gfa import GFA
+
+logger = logging.getLogger(__name__)
+
+
+def run_find_path(gfa_path, input_path, output=None):
+	timers = StageTimer()
+
+	graph = GFA(gfa_path)
+
+	path_seq = graph.extract_path(input_path)
+	print(path_seq)	
+
+	logger.info("\n== SUMMARY ==")
+	total_time = timers.total()
+	log_memory_usage()
+	logger.info("Total time:                                  %9.2f s", total_time)
+
+
+def add_arguments(parser):
+    arg = parser.add_argument
+    # Positional arguments
+    arg("gfa_path", metavar="GFA", help="Input GFA file (can be bgzip-compressed)")
+    arg("input_path", metavar="path", help="GFA path to retrieve the sequence (e.g., \">s82312<s82313\").")
+    arg("-o", "--output", default=None, help="Output file. If omitted, use standard output.")
+
+def validate(args, parser):
+    return True
+
+
+def main(args):
+    run_find_path(**vars(args))