更新 .gitignore，添加 06.gene_trees 目录；重构 macse.sh 脚本，移除 fs_lr 参数；删除多个不再使用的脚本；添加 check_frameshift.py 和 get_og_seqs.py 脚本以处理阅读框移位和提取单拷贝OG序列；更新 pixi.toml 和 pixi.lock 文件以添加 paml 依赖。

2025-12-20 01:57:25 +08:00
parent e8ba2ed962
commit dba4833905
15 changed files with 433 additions and 117 deletions
@@ -0,0 +1,74 @@
+#! /usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Get primary CDS sequences from a FASTA file containing multiple CDS per gene.
+"""
+
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+import re
+import argparse
+import sys
+
+
+def get_primary_cds(input_fasta, output_fasta):
+    primary_cds_records = []
+    gene = ""
+    length = 0
+    seq = None
+    id = None
+    try:
+        for record in SeqIO.parse(input_fasta, "fasta"):
+            seq_len = len(record.seq)
+            desc = record.description
+            match = re.search(r"\[gene=(\S+)\]", desc)
+            if match:
+                gene_name = match.group(1)
+            else:
+                # Skip if gene name not found
+                continue
+
+            if gene_name != gene:
+                # new gene encountered
+                # print(f"Processing gene: {gene_name}")
+                if length > 0:
+                    # this is not the first record, save the previous longest record
+                    primary_cds_record = SeqRecord(
+                        seq, id=id, description=f"[gene={gene}]"
+                    )
+                    primary_cds_records.append(primary_cds_record)
+                gene = gene_name
+                seq = record.seq
+                id = record.id
+                length = seq_len
+            else:
+                # same gene, check length
+                if seq_len > length:
+                    seq = record.seq
+                    id = record.id
+                    length = seq_len
+        # after loop, save the last gene
+        if gene and length > 0:
+            primary_cds_record = SeqRecord(seq, id=id, description=f"[gene={gene}]")
+            primary_cds_records.append(primary_cds_record)
+        SeqIO.write(primary_cds_records, output_fasta, "fasta")
+        print(f"Primary CDS sequences written to {args.output_fasta}")
+    except Exception as e:
+        print(f"Error processing FASTA file {input_fasta}: {e}")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Extract primary CDS sequences from a FASTA file."
+    )
+    parser.add_argument(
+        "-i", "--input_fasta", help="Input FASTA file containing CDS sequences."
+    )
+    parser.add_argument(
+        "-o", "--output_fasta", help="Output FASTA file to write primary CDS sequences."
+    )
+    args = parser.parse_args()
+
+    get_primary_cds(args.input_fasta, args.output_fasta)