查找出现两次的模式，每个模式允许 <=2 个不匹配

问题描述

我有一个 400,000 次读取的 fastq 文件（所以速度很重要）。在序列中集成了应该出现两次的条形码。给定一个条形码，我想找到条形码出现两次且

TATCTTGTGGAAAGGACGAAACACCGAACACAAAGCATAGATGCGTTTAAGAGCTATGCTGGAAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCCTTTTTTTATTCGACCGATAGGGGTGGCAGGGGAGGCCGAGGAGTGGCAGGGAGAGGCGAGGAGTGAGCGAAAGAGGGTGACTGAACTGAACTGAACTGAAAGTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCCTTTTTTT TATCTTGTGGAAAGGACGAAACACCGGTCCGAGCAGAAGAAGAAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTTTATTCGACCGATAGGGGTGGCAGGGGAGGCCGAGGAGGAAGGAAGGGAGGAGGAGTGATGGCCGAGGGAGGATGAACTGACCT TATCTTGTGGAAAGGACGAAACACCGAGTCCGAGCAGAAGAAGAAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTATTCGACCGATAGGGGTGGCAGGGGAGGCCGAGGAGGAAGAGAGAGGGAGGAGGAGGAAGCGAGGGAGGATGAACTGAACTGAGTGGATGAACTGAAA TATCTTGTGGAAAGGACGAAACACCGAGTCCGAGCAGAAGAAGAAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTATTCGACGATAGGGGTGGCAGGGGAGGCCGAGGAGGAAGAGAGAGGGAGGAGGAGGAAGAGAGGGAGGATGAACTGAAAGGCAGTGGATGAACTGAAA

请注意，第四个序列中的第一个条形码缺少一个字符。我已经尝试过 biopython 和 regex 但它太慢了，因为我有 5k 条码。我想知道在 python 或 grep、awk 或其他任何东西中是否有可用的快速解决方案。谢谢。

解决方法

使用 GNU awk：

 awk '{ for (i=1;i<=NF;i++) { fnd=0;subs=$i;while (match(subs,"ATTCGACCGATAGG")) { subs=substr(subs,RSTART+RLENGTH);if (RSTART>0) { fnd++;print fnd } } if (fnd <=2) { print $i } } }' file

说明：

 awk '{ for (i=1;i<=NF;i++) {                           # Loop on each space delimited field
         fnd=0;                                         # Initialise fnd variable/counter
         subs=$i;                                       # Initialise substring variable
         while (match(subs,"ATTCGACCGATAGG")) { 
           subs=substr(subs,RSTART+RLENGTH);            # Check for multiple matches of "ATTCGACCGATAGG" in subs.
           if (RSTART>0) { 
              fnd++;                                    # Increment fnd if string found in subs
           } 
         } 
         if (fnd <=2) { 
            print $i                                    # If found twice or less than twice print the field
         }
        } 
       }' file