提交饱和编辑的相关设计，及检验代码

select_primedesign.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+import csv
+import gzip
+import random
+import pandas as pd
+
+from tqdm import tqdm
+
+seed = 42
+
+
+total_codons = {
+  "丙氨酸": ["GCT", "GCC", "GCA", "GCG"],
+  "精氨酸": ["CGT", "CGC", "CGA", "CGG", "AGA", "AGG"],
+  "天冬酰胺": ["AAT", "AAC"],
+  "天冬氨酸": ["GAT", "GAC"],
+  "半胱氨酸": ["TGT", "TGC"],
+  "谷氨酰胺": ["CAA", "CAG"],
+  "谷氨酸": ["GAA", "GAG"],
+  "甘氨酸": ["GGT", "GGC", "GGA", "GGG"],
+  "组氨酸": ["CAT", "CAC"],
+  "异亮氨酸": ["ATT", "ATC", "ATA"],
+  "亮氨酸": ["TTA", "TTG", "CTT", "CTC", "CTA", "CTG"],
+  "赖氨酸": ["AAA", "AAG"],
+  "甲硫氨酸": ["ATG"],
+  "苯丙氨酸": ["TTT", "TTC"],
+  "脯氨酸": ["CCT", "CCC", "CCA", "CCG"],
+  "丝氨酸": ["TCT", "TCC", "TCA", "TCG", "AGT", "AGC"],
+  "苏氨酸": ["ACT", "ACC", "ACA", "ACG"],
+  "色氨酸": ["TGG"],
+  "酪氨酸": ["TAT", "TAC"],
+  "缬氨酸": ["GTT", "GTC", "GTA", "GTG"],
+  "终止密码子": ["TAA", "TAG", "TGA"]
+}
+
+
+def load_finished(ref):
+    df = pd.read_excel(ref)
+    
+    genes = {}
+    for _, row in df.iterrows():
+        gene = row["gene"]
+        pos = row["aa_pos"]
+        
+        if gene not in genes:
+            genes[gene] = set()
+        genes[gene].add(str(pos))
+    return genes
+
+
+def reader(path):
+    with gzip.open(path, "rt") as r:
+        dict_reader = csv.DictReader(r)
+
+        for row in tqdm(dict_reader):
+            yield row
+
+
+def filter_(args):
+    finished, path, output = args
+
+    data = {}
+
+    for row in reader(path):
+
+        # 提取各种id
+        key = row['Target_name'].split("_")
+        gene = key[0]
+        pos = key[1].replace("AA", "")
+        dst = key[-1]
+
+        #
+        uid = f"{key}_{pos}_{dst}"
+        for k, codons in total_codons.items():
+            if dst in codons:
+                if gene in finished and pos not in finished[gene]:
+                    row["dst"] = k
+                    row["aa_pos"] = pos
+                    row["gene"] = gene
+
+                    if uid not in data:
+                        data[uid] = []
+                    data[uid].append(row)
+
+    dict_writer = None
+    with gzip.open(output, "wt+") as w:
+        for _, lines in tqdm(data.items()):
+            if len(lines) > 2:
+                random.seed(seed)
+                lines = random.sample(lines, 2)
+
+            if dict_writer is None:
+                for row in lines:
+                    dict_writer = csv.DictWriter(w, fieldnames=row.keys())
+                    dict_writer.writeheader()
+                    break
+
+            # 写入数据行
+            dict_writer.writerows(lines)
+
+
+def main(ref, indir, outdir):
+    
+    finished = load_finished(ref)
+    filter_([finished, indir, outdir])
+
+
+if __name__ == '__main__':
+    from fire import Fire
+    Fire(main)
+
+