合并前

因為100kb以下的雙交換片段存在概率較低

采用的策略：

起始位置減去終止位置為標記長度均唉，如果距離大于100kb，保留這一行肚菠，如果標記是1或2舔箭，下一個標記(0，來自親本1)的長度小于100kb蚊逢，則合并起始位置

（這里主要保留導入片段）

import sys

def process_file(filename):
    # 存儲處理后的行
    processed_lines = []

    # 用于臨時存儲上一行的信息
    last_line = None

    with open(filename, 'r') as file:
        for line_number, line in enumerate(file, 1):
            try:
                # 分割每行數(shù)據(jù)
                parts = line.strip().split('\t')
                if len(parts) < 4:
                    continue

                chrom, start, end, tag = parts[0], int(parts[1]), int(parts[2]), int(parts[3])

                # 計算長度
                length = end - start

                # 如果是第一個標記层扶，直接保存
                if last_line is None:
                    last_line = (chrom, start, end, tag, length)
                    continue

                # 檢查是否需要合并
#                if last_line[3] in [1, 2] and length < 100 * 1024:  # 100kb

                if last_line[0] == chrom and last_line[3] in [1, 2] and length < 100 * 1024:  # 100kb

                        # 合并
                    last_line = (last_line[0], last_line[1], end, last_line[3], end - last_line[1])
                else:
                    # 添加上一行到結果列表
                    processed_lines.append(f"{last_line[0]}\t{last_line[1]}\t{last_line[2]}\t{last_line[3]}")
                    last_line = (chrom, start, end, tag, length)

            except ValueError as e:
                print(f"Error processing line {line_number}: {e}")
            except Exception as e:
                print(f"Unexpected error on line {line_number}: {e}")

        # 添加最后一行
        if last_line is not None:
            processed_lines.append(f"{last_line[0]}\t{last_line[1]}\t{last_line[2]}\t{last_line[3]}")

    return processed_lines

if __name__ == "__main__":
    if len(sys.argv) != 2:
        print("Usage: python script.py filename")
        sys.exit(1)

    filename = sys.argv[1]
    result = process_file(filename)

    # 輸出結果
    for line in result:
        print(line)

注意這里有相同的連續(xù)標記了

合并相同標記

import sys

prev_chr = None
prev_mark = None
min_start = None
max_end = None

with open(sys.argv[1], 'r') as file:
#    next(file)  # 跳過表頭行
    for line in file:
        columns = line.strip().split()
        if len(columns) < 4:
            continue
        
        current_chr = columns[0]
        current_start = int(columns[1])
        current_end = int(columns[2])
        current_mark = columns[3]

        if current_chr == prev_chr and current_mark == prev_mark:
            max_end = current_end
        else:
            if prev_chr is not None:
                print(f"{prev_chr}\t{min_start}\t{max_end}\t{prev_mark}")
            prev_chr = current_chr
            prev_mark = current_mark
            min_start = current_start
            max_end = current_end

    if prev_chr is not None:
        print(f"{prev_chr}\t{min_start}\t{max_end}\t{prev_mark}")

合并后的結果