Rename seqs by gc3 width

Utilities/for_fastas/OG6_A_G.py

@@ -0,0 +1,87 @@
+#Author, date: Godwin Ani, 24th- Nov - 2023.
+#Dependencies: Python3, Biopython
+#Inputs: A folder of containing ReadyToGo files, PerSequenceStatSummaries, rules file and the script.
+#The csv file should contain 10 digit codes and the limits(column headers are name, lower, and upper).
+#Outputs: a folder of curated ready to go files.
+#Example: python OG6_A_G.py -i (input folder of r2gs), -r (rules csv file), -s (folder of per seq stats) '''
+#
+
+
+
+import os
+import argparse
+from Bio import SeqIO
+os.makedirs('output', exist_ok= True)
+
+def process_OG6_A_G(input_dir, rules_csv_path, stats_csv_dir):
+    # Read rules from CSV into a dictionary
+    rules = {}
+    with open(rules_csv_path, encoding='utf-8') as rules_file:
+        next(rules_file)  # Skip the header
+        for line in rules_file:
+            name, lower, upper = line.strip().split(',')
+            rules[name] = {'lower': float(lower), 'upper': float(upper)}
+
+    # Initialize dictionaries for storing sequences
+    tot_neutral = {}
+    tot_A = {}
+    tot_G = {}
+
+    # Process CSV files in 'PerSequenceStatSummaries' directory
+    for file in os.listdir(stats_csv_dir):
+        if file.endswith('.csv'):
+            rule = rules.get(file[:10], {'lower': 0.0, 'upper': 1.0})
+            lower, upper = rule['lower'], rule['upper']
+
+            neutral_sequences, A_sequences, G_sequences = [], [], []
+            with open(os.path.join(stats_csv_dir, file), encoding='utf-8') as csv_file:
+                header = next(csv_file).strip().split(',')
+                sequence_index, gc3_degen_index = header.index('Sequence'), header.index('GC3-Degen')
+                for line in csv_file:
+                    parts = line.strip().split(',')
+                    sequence, gc3_degen = parts[sequence_index], float(parts[gc3_degen_index])
+                    if lower <= gc3_degen <= upper:
+                        neutral_sequences.append(sequence)
+                    elif gc3_degen < lower:
+                        A_sequences.append(sequence)
+                    elif gc3_degen > upper:
+                        G_sequences.append(sequence)
+            tot_neutral[file[:10]] = neutral_sequences
+            tot_A[file[:10]] = A_sequences
+            tot_G[file[:10]] = G_sequences
+
+    # Process sequence files in 'Input' directory
+    for file in os.listdir(input_dir):
+        sequences = []
+        with open(os.path.join(input_dir, file), encoding='latin-1') as fasta_file:
+            for record in SeqIO.parse(fasta_file, 'fasta'):
+                file_key = file[:10]
+                if record.id in tot_neutral[file_key]:
+                    record.description = record.id
+                    sequences.append(record)
+                elif record.id in tot_A[file_key]:
+                    # Create a new record for 'OGA' version
+                    record_oga = record[:]
+                    record_oga.id = f"{record.id.split('_OG6')[0]}_OGA{record.id.split('_OG6')[1]}"
+                    record_oga.description = record_oga.id
+                    sequences.append(record_oga)
+                elif record.id in tot_G[file_key]:
+                    # Create a new record for 'OGG' version
+                    record_ogg = record[:]
+                    record_ogg.id = f"{record.id.split('_OG6')[0]}_OGG{record.id.split('_OG6')[1]}"
+                    record_ogg.description = record_ogg.id
+                    sequences.append(record_ogg)
+        SeqIO.write(sequences, 'output/' + file, 'fasta')
+
+def main():
+    parser = argparse.ArgumentParser(description='Process files based on rules.')
+    parser.add_argument('-i', '--input_dir', required=True, help='Path to the input directory containing sequence files.')
+    parser.add_argument('-r','--rules_csv_path', required=True, help='Path to the rules CSV file.')
+    parser.add_argument('-s','--stats_csv_dir', required=True, help='Path to the directory containing statistics CSV files.')
+
+    args = parser.parse_args()
+
+    process_OG6_A_G(args.input_dir, args.rules_csv_path, args.stats_csv_dir)
+
+if __name__ == "__main__":
+    main()