From d415c46d193ecad834ffbf956364a56391c8d0a4 Mon Sep 17 00:00:00 2001
From: Sam Fletcher <147140110+sof202@users.noreply.github.com>
Date: Thu, 12 Dec 2024 15:08:28 +0000
Subject: [PATCH] feat: add parse option (#10)

* refactor: remove unneeded logic

This isn't required as the value is already true or false

* feat: add parsable option
---
 Python_Scripts/peak_compare.py | 29 ++++++++++++++++-------------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/Python_Scripts/peak_compare.py b/Python_Scripts/peak_compare.py
index 8295028..5b471a3 100644
--- a/Python_Scripts/peak_compare.py
+++ b/Python_Scripts/peak_compare.py
@@ -80,20 +80,16 @@ def main(args: argparse.Namespace) -> None:
         reference_labelled_peaks,
         args.cutoff
     )
-    if args.unmerged:
-        metric = calculate_metric(
-            reference_labelled_peaks,
-            pseudopeaks,
-            include_merged_peaks=False
-        )
+    metric = calculate_metric(
+        reference_labelled_peaks,
+        pseudopeaks,
+        include_merged_peaks=(not args.unmerged)
+    )
+    if args.parsable:
+        print(metric)
     else:
-        metric = calculate_metric(
-            reference_labelled_peaks,
-            pseudopeaks,
-            include_merged_peaks=True
-        )
-    print(f"The metric for these datasets over the range {start} to {end} ",
-          f"for chromosome {chromosome} is: {metric}.")
+        print("The metric for these datasets over the range ",
+              f"{start} to {end} for chromosome {chromosome} is: {metric}.")
 
 
 if __name__ == "__main__":
@@ -101,6 +97,13 @@ def main(args: argparse.Namespace) -> None:
         prog="PeakCompare",
         description="Determine how likely a peak is to be in two datasets."
     )
+    parser.add_argument(
+        "-p",
+        "--parsable",
+        action="store_true",
+        help=("Set this if you want the output of the script to be computer ",
+              "parsable (and not human readable).")
+    )
     parser.add_argument(
         "--unmerged",
         action="store_true",