主页 / coding / 问题 / 77698932
Accepted
pedro
Asked: 2023-12-21 23:23:11 +0800 CST

在同一行和打印行中查找列值

  • 772

我有这个 5 列文件：

m64071_220512_054244/46858502/ccs TCTACACGACGCTCTTCCGATCTTATTGGGCACGGTGTCGCCATCTGATCGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGAGGTTTGCAGCTATTTTATTTACAAGTATACATTTAACACAATGAAATAAACACTGATATACTGAAGCCTAGTTAATAGTAGTGTAACAATATGCATCATTTTGATGATTACATTATTTTAAACAACAAACTACACTGAAAAATTAATGCCGATAAAATTCTTGGTCATAATATTAAGAAATACAATATATAAATTGAAAATATGATTGCTTAAAATTTGAAAATGGAAGTGAACTCATTTGGACAGACTCAGAGTTAACATAATCTGAAGGGAGGGGAGCTCTGACCCAAATGATATCTTTCAGGTTAACAGAAGAAAAAAGAAGCATAGTTTATCTTCAAGGAGAACGGGCAGTTTGCTTCTTCAGGTA fwd pet047-9952 TATTGGGCACGGTGTC
m64071_220512_054244/52233509/ccs AGCTTTTTTGGAATCTTCTGCTAAAGAAAATCAGACTGCTGTGGATGTTTTTCGAAGGATAATTTTGGAGGCAGAAAAAATGGACGGGGCAGCTTCACAAGGCAAGTCTTCATGCTCGGTGATGTGATTCTGCTGCAAAGCCTGAGGACACTGGGAATATATTCTACCTGAAGAAGCAAACTGCCCGTTCTCCTTGAAGATAAACTATGCTTCTTTTTTCTTCTGTTAACCTGAAAGATATCATTTGGGTCAGAGCTCCCCTCCCTTCAGATTATGTTAACTCTGAGTCTGTCCAAATGAGTTCACTTCCATTTTCAAATTTTAAGCAATCATATTTTCAATTTATATATTGTATTTCTTAATATTATGACCAAGAATTTTATCGGCATTAATTTTTCAGTGTAGTTTGTTGTTTAAAATAATGTAATCATCAAAATGATGCATATTGTTACACTACTATTAACTAGGCTTCAGTATATCAGTGTTTATTTCATTGTGTTAAATGTATACTTGTAAATAAAATAGCTGCAAACCTCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACGATCAGATGGCGACACCGTGCCCAATAAGATCGGAAGAGCGTCGTGTAGA rev pet047-9952 GACACCGTGCCCAATA
m64071_220512_054244/91226755/ccs TCTACACGACGCTCTTCCGATCTTATTGGGCACGGTGTCGCCATCTGATCGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGAGGTTTGCAGCTATTTTATTTACAAGTATACATTTAACACAATGAAATAAACACTGATATACTGAAGCCTAGTTAATAGTAGTGTAACAATATGCATCATTTTGATGATTACATTATTTTAAACAACAAACTACACTGAAAAATTAATGCCGATAAAATTCTTGGTCATAATATTAAGAAATACAATATATAAATTGAAAATATGATTGCTTAAAATTTGAAAATGGAAGTGAACTCATTTGGACAGACTCAGAGTTAACATAATCTGAAGGGAGGGGAGCTCTGACCCAAATGATATCTTTCAGGTTAACAGAAGAAAAAAGAAGCATAGTTTATCTTCAAGGAGAACGGGCAGTTTGCTTCTTCAGGTAGAATATATTCCCAGTGTCCTCAGGCTTTGCAGCAGAATCACATCACCGAGCATGAAGACTTGCCTTGTGAAGCTGCCCCGTCCATTTTTTCTGCCTCCAA fwd pet047-9952 TATTGGGCACGGTGTC

对于每一行，我需要 grep 第二个字段 $2 中的最后一列值 $5。然后，我需要在同一行上打印一个额外的 $6 列，其中包含带有条件的 grep 结果：if ($3 == rev)，$6 是 grep 结果 + grep 之后的 12 个字符或if ($3 == fwd)grep 结果 + grep 之前的 12 个字符。

awk '$2~/$5/ {match($0, /$5/); if ($4=="rev") print substr($0, RSTART +12, RLENGTH + 12); else print substr($0, RSTART + 0, RLENGTH + 12) ;}' file

$5 值需要 16 个字符，而我寻找的模式始终是 12 个字符。然后，我的 $6 输出是 28 个字符。

预期输出：

m64071_220512_054244/46858502/ccs TCTACACGACGCTCTTCCGATCTTATTGGGCACGGTGTCGCCATCTGATCGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGAGGTTTGCAGCTATTTTATTTACAAGTATACATTTAACACAATGAAATAAACACTGATATACTGAAGCCTAGTTAATAGTAGTGTAACAATATGCATCATTTTGATGATTACATTATTTTAAACAACAAACTACACTGAAAAATTAATGCCGATAAAATTCTTGGTCATAATATTAAGAAATACAATATATAAATTGAAAATATGATTGCTTAAAATTTGAAAATGGAAGTGAACTCATTTGGACAGACTCAGAGTTAACATAATCTGAAGGGAGGGGAGCTCTGACCCAAATGATATCTTTCAGGTTAACAGAAGAAAAAAGAAGCATAGTTTATCTTCAAGGAGAACGGGCAGTTTGCTTCTTCAGGTA fwd pet047-9952 TATTGGGCACGGTGTC TATTGGGCACGGTGTCGCCATCTGATCG
m64071_220512_054244/52233509/ccs AGCTTTTTTGGAATCTTCTGCTAAAGAAAATCAGACTGCTGTGGATGTTTTTCGAAGGATAATTTTGGAGGCAGAAAAAATGGACGGGGCAGCTTCACAAGGCAAGTCTTCATGCTCGGTGATGTGATTCTGCTGCAAAGCCTGAGGACACTGGGAATATATTCTACCTGAAGAAGCAAACTGCCCGTTCTCCTTGAAGATAAACTATGCTTCTTTTTTCTTCTGTTAACCTGAAAGATATCATTTGGGTCAGAGCTCCCCTCCCTTCAGATTATGTTAACTCTGAGTCTGTCCAAATGAGTTCACTTCCATTTTCAAATTTTAAGCAATCATATTTTCAATTTATATATTGTATTTCTTAATATTATGACCAAGAATTTTATCGGCATTAATTTTTCAGTGTAGTTTGTTGTTTAAAATAATGTAATCATCAAAATGATGCATATTGTTACACTACTATTAACTAGGCTTCAGTATATCAGTGTTTATTTCATTGTGTTAAATGTATACTTGTAAATAAAATAGCTGCAAACCTCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACGATCAGATGGCGACACCGTGCCCAATAAGATCGGAAGAGCGTCGTGTAGA rev pet047-9952 GACACCGTGCCCAATA CGATCAGATGGCGACACCGTGCCCAATA
m64071_220512_054244/91226755/ccs TCTACACGACGCTCTTCCGATCTTATTGGGCACGGTGTCGCCATCTGATCGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGAGGTTTGCAGCTATTTTATTTACAAGTATACATTTAACACAATGAAATAAACACTGATATACTGAAGCCTAGTTAATAGTAGTGTAACAATATGCATCATTTTGATGATTACATTATTTTAAACAACAAACTACACTGAAAAATTAATGCCGATAAAATTCTTGGTCATAATATTAAGAAATACAATATATAAATTGAAAATATGATTGCTTAAAATTTGAAAATGGAAGTGAACTCATTTGGACAGACTCAGAGTTAACATAATCTGAAGGGAGGGGAGCTCTGACCCAAATGATATCTTTCAGGTTAACAGAAGAAAAAAGAAGCATAGTTTATCTTCAAGGAGAACGGGCAGTTTGCTTCTTCAGGTAGAATATATTCCCAGTGTCCTCAGGCTTTGCAGCAGAATCACATCACCGAGCATGAAGACTTGCCTTGTGAAGCTGCCCCGTCCATTTTTTCTGCCTCCAA fwd pet047-9952 TATTGGGCACGGTGTC TATTGGGCACGGTGTCGCCATCTGATCG

但我没有得到我想要的。

bash

2 个回答

  1. Best Answer

    您可以使用以下脚本来实现您的结果：

    awk '{
    idx = index($2, $5);
    if (idx != 0) {
        if ($3 == "rev") {
            substr_28 = substr($2, idx - 12, 28);
        } else {
            substr_28 = substr($2, idx, 28);
        }
        print $0, substr_28;
    }
}' your_file_containing_inp

    基本上，脚本：

    1. $5首先查找第二个字段中值的索引。如果找到该值(idx != 0)。

      A。它检查第三个字段的值。
      b. 如果是"rev"，则提取28-character从索引之前 12 个字符开始的子字符串。
      C。否则，它提取从索引开始的子字符串。

    代码演示

    • 2

  2. 使用任何 awk 就可以做到这一点：

    awk 'match($2,$5) {
        print $0, ( $3 == "fwd" \
                    ? substr($2,RSTART,RLENGTH+12) \
                    : substr($2,RSTART-12,RLENGTH+12) \
                  )
    }' file
m64071_220512_054244/46858502/ccs TCTACACGACGCTCTTCCGATCTTATTGGGCACGGTGTCGCCATCTGATCGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGAGGTTTGCAGCTATTTTATTTACAAGTATACATTTAACACAATGAAATAAACACTGATATACTGAAGCCTAGTTAATAGTAGTGTAACAATATGCATCATTTTGATGATTACATTATTTTAAACAACAAACTACACTGAAAAATTAATGCCGATAAAATTCTTGGTCATAATATTAAGAAATACAATATATAAATTGAAAATATGATTGCTTAAAATTTGAAAATGGAAGTGAACTCATTTGGACAGACTCAGAGTTAACATAATCTGAAGGGAGGGGAGCTCTGACCCAAATGATATCTTTCAGGTTAACAGAAGAAAAAAGAAGCATAGTTTATCTTCAAGGAGAACGGGCAGTTTGCTTCTTCAGGTA fwd pet047-9952 TATTGGGCACGGTGTC TATTGGGCACGGTGTCGCCATCTGATCG
m64071_220512_054244/52233509/ccs AGCTTTTTTGGAATCTTCTGCTAAAGAAAATCAGACTGCTGTGGATGTTTTTCGAAGGATAATTTTGGAGGCAGAAAAAATGGACGGGGCAGCTTCACAAGGCAAGTCTTCATGCTCGGTGATGTGATTCTGCTGCAAAGCCTGAGGACACTGGGAATATATTCTACCTGAAGAAGCAAACTGCCCGTTCTCCTTGAAGATAAACTATGCTTCTTTTTTCTTCTGTTAACCTGAAAGATATCATTTGGGTCAGAGCTCCCCTCCCTTCAGATTATGTTAACTCTGAGTCTGTCCAAATGAGTTCACTTCCATTTTCAAATTTTAAGCAATCATATTTTCAATTTATATATTGTATTTCTTAATATTATGACCAAGAATTTTATCGGCATTAATTTTTCAGTGTAGTTTGTTGTTTAAAATAATGTAATCATCAAAATGATGCATATTGTTACACTACTATTAACTAGGCTTCAGTATATCAGTGTTTATTTCATTGTGTTAAATGTATACTTGTAAATAAAATAGCTGCAAACCTCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACGATCAGATGGCGACACCGTGCCCAATAAGATCGGAAGAGCGTCGTGTAGA rev pet047-9952 GACACCGTGCCCAATA CGATCAGATGGCGACACCGTGCCCAATA
m64071_220512_054244/91226755/ccs TCTACACGACGCTCTTCCGATCTTATTGGGCACGGTGTCGCCATCTGATCGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGAGGTTTGCAGCTATTTTATTTACAAGTATACATTTAACACAATGAAATAAACACTGATATACTGAAGCCTAGTTAATAGTAGTGTAACAATATGCATCATTTTGATGATTACATTATTTTAAACAACAAACTACACTGAAAAATTAATGCCGATAAAATTCTTGGTCATAATATTAAGAAATACAATATATAAATTGAAAATATGATTGCTTAAAATTTGAAAATGGAAGTGAACTCATTTGGACAGACTCAGAGTTAACATAATCTGAAGGGAGGGGAGCTCTGACCCAAATGATATCTTTCAGGTTAACAGAAGAAAAAAGAAGCATAGTTTATCTTCAAGGAGAACGGGCAGTTTGCTTCTTCAGGTAGAATATATTCCCAGTGTCCTCAGGCTTTGCAGCAGAATCACATCACCGAGCATGAAGACTTGCCTTGTGAAGCTGCCCCGTCCATTTTTTCTGCCTCCAA fwd pet047-9952 TATTGGGCACGGTGTC TATTGGGCACGGTGTCGCCATCTGATCG

    供以后的问题参考，这里是一个最小的可重现示例，使用2而不是12作为要打印的附加字符数：

    输入示例：

    $ cat file
this abcdefghi fwd foobar cd
that abcdefghi rev bar de
other abcdefghi fwd foo ef

    预期输出：

    this abcdefghi fwd foobar cd cdef
that abcdefghi rev bar de bcde
other abcdefghi fwd foo ef efgh

    然后我们可以对其进行测试，以轻松查看潜在的解决方案是否有效：

    awk 'match($2,$5) {
        print $0, ( $3 == "fwd" \
                    ? substr($2,RSTART,RLENGTH+2) \
                    : substr($2,RSTART-2,RLENGTH+2) \
                  )
    }' file
this abcdefghi fwd foobar cd cdef
that abcdefghi rev bar de bcde
other abcdefghi fwd foo ef efgh
    • 2

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