build mRNA kill list for AGAT

08-submission/gff-03-build_kill_list.py

+#!/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)
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