--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/bin/fetchReads.py	Mon Dec 02 10:40:55 2024 -0500
@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+
+import os
+import sys
+from glob import glob
+import argparse
+
+# Parse args
+parser = argparse.ArgumentParser(description='Fetch Reads')
+parser.add_argument('--read_dir', type=str, help='path to directory containing read files')
+parser.add_argument('--read_filetype', type=str, help='read filetype information')
+parser.add_argument('--forward_suffix', type=str, help='forward suffix')
+parser.add_argument('--reverse_suffix', type=str, help='reverse suffix')
+parser.add_argument('--trim_name', type=str, help='trim name')
+args = parser.parse_args()
+
+# Get path to directory containing read files
+read_dir = os.path.abspath(args.read_dir)
+if not os.path.isdir(read_dir):
+    sys.exit("--read_dir is not a valid path: " + str(read_dir))
+
+# Get read filetype information
+read_filetype = args.read_filetype
+if not read_filetype.startswith("."):
+    read_filetype = "." + read_filetype
+forward_suffix = args.forward_suffix
+reverse_suffix = args.reverse_suffix
+trim_name = args.trim_name
+
+# Check if sequence files exist in directory, ignoring undetermined reads
+read_files = sorted(glob(read_dir+"/*"+read_filetype))
+read_files = [r for r in read_files if not os.path.basename(r).startswith("Undetermined_")]
+
+if len(read_files) == 0:
+    sys.exit("No "+read_filetype +" files detected in "+read_dir)
+
+# Get data for paired-end and single-end reads
+left_files = [s for s in read_files if s.endswith(forward_suffix)]
+right_files = [s for s in read_files if s.endswith(reverse_suffix)]
+
+# Identify pairs based on file name
+left_pairs = list()
+right_pairs = list()
+paired_files = list(set([x.replace(forward_suffix, '') for x in left_files]).intersection([y.replace(reverse_suffix, '') for y in right_files]))
+
+for pair in paired_files:
+    left_pairs.append(pair+forward_suffix)
+    right_pairs.append(pair+reverse_suffix)
+single_end = [x for x in read_files if x not in left_pairs + right_pairs]
+
+for left in left_pairs:
+    base = str(os.path.basename(left).replace(forward_suffix,"").replace(trim_name,""))
+    print(",".join([base,"Paired",";".join([left,left.replace(forward_suffix,reverse_suffix)])]))
+
+for single in single_end:
+    if single.endswith(forward_suffix):
+        base = str(os.path.basename(single).replace(forward_suffix,"").replace(trim_name,""))
+    else:
+        base = str(os.path.basename(single).replace(read_filetype,"").replace(trim_name,""))
+    print(",".join([base,"Single",single]))