查找两次出现的模式，并允许每个模式上出现<=2个不匹配

Question

我有一个40万次读取的fastq文件（因此速度很重要）。序列中集成了条形码，应显示两次。给定一个条形码，我想查找条形码出现两次的序列<；=2个不匹配。因此，使用条形码“ATTCGACCGATAGG”，我想检索以下所有序列-

TATCTTGTGGAAAGGACGAAACACCGAACACAAAGCATAGATGCGTTTAAGAGCTATGCTGGAAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTTATTCGACCGATAGGGGTGGCAGGGGAGGCCGAGGAGGAAGAAGGGGAGGTGGCAGATTCGACCGATAGGTGGCGTAACTAGATCTTGAGACAAA TATCTTGTGGAAAGGACGAAACACCGGTCCGAGCAGAAGAAGAAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTTATTCGACCGATAGGGGTGGCAGGGGAGGCCGAGGAGGAAGAAGGGGAGGTGGCAGATTCGACCGATAGGTGGCGTAACTAGATCTTGAGACAAA TATCTTGTGGAAAGGACGAAACACCGAGTCCGAGCAGAAGAAGAAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTTATTCGACCGATAGGGGTGGCAGGGGAGGCCGAGGAGGAAGAAGGGGAGGTGGCAGATTCGACCGATAGGTGGCGTAACTAGATCTTGAGACAAA TATCTTGTGGAAAGGACGAAACACCGAGTCCGAGCAGAAGAAGAAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTTATTCGACGATAGGGGTGGCAGGGGAGGCCGAGGAGGAAGAAGGGGAGGTGGCAGATTCGACCGATAGGTGGCGTAACTAGATCTTGAGACAAA

请注意，第四个序列中的第一个条形码缺少一个字符。我试过使用biopython和regex，但考虑到我有5公里的条形码，速度太慢了。我想知道是否有一个快速的解决方案在python或类似于grep、awk或其他任何东西中可用。谢谢

Answer 1

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