From dc923a709b5e39ebfe24d86e0f3392ad99dbb16d Mon Sep 17 00:00:00 2001
From: Niko <nikolaos.papadopoulos@univie.ac.at>
Date: Wed, 27 Nov 2024 20:50:44 +0100
Subject: [PATCH] build mRNA kill list for AGAT
---
08-submission/gff-03-build_kill_list.py | 62 +++++++++++++++++++++++++
1 file changed, 62 insertions(+)
create mode 100644 08-submission/gff-03-build_kill_list.py
diff --git a/08-submission/gff-03-build_kill_list.py b/08-submission/gff-03-build_kill_list.py
new file mode 100644
index 0000000..f0dbced
--- /dev/null
+++ b/08-submission/gff-03-build_kill_list.py
@@ -0,0 +1,62 @@
+#!/usr/bin/env python
+
+# go through a list of short introns produced by agat_sp_list_short_introns.pl
+# and find the corresponding mRNA titles
+
+import argparse
+import re
+
+def build_regex(input_file):
+ regex_list = []
+ # open the input file
+ with open(input_file, 'r') as f:
+ # the first 3 lines are headers
+ f.readline()
+ f.readline()
+ f.readline()
+ # read the file line by line
+ for line in f:
+ # if the line is empty, we have reached the end
+ if line == "\n":
+ break
+ # split the line by tab
+ line = line.strip().split('\t')
+ _locus, locus_id, position, _intron_length = line
+
+ # build the regex
+ regex = re.compile(f"{int(position) - 1}.*{locus_id.upper()}")
+ regex_list.append(regex)
+ return regex_list
+
+
+def grep(regex_list, target):
+ to_fix = set()
+ # grep the target file for the regex
+ with open(target, 'r') as f:
+ for line in f:
+ for regex in regex_list:
+ if re.search(regex, line):
+ attributes = line.strip().split('\t')[-1]
+ attr_dict = {}
+ for attr in attributes.split(';'):
+ key, value = attr.split('=')
+ attr_dict[key] = value
+ to_fix.add(attr_dict['Parent'])
+ return list(to_fix)
+
+def main(input_file, target):
+ short_introns = build_regex(input_file)
+ ids = grep(short_introns, target)
+ for i in ids:
+ print(i)
+
+
+if __name__ == "__main__":
+ # argument parser that will receive the input file
+ parser = argparse.ArgumentParser(description='Get the mRNA titles of the short introns (agat_sp_list_short_introns.pl output file)')
+ parser.add_argument('input_file', type=str, help='The input file containing the short introns')
+ parser.add_argument('target_file', type=str, help='The target GFF file.')
+ args = parser.parse_args()
+ input_file = args.input_file
+ target = args.target_file
+ main(input_file, target)
\ No newline at end of file
--
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