Início / coding / Perguntas / 77698932
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pedro
Asked: 2023-12-21 23:23:11 +0800 CST

Valor da coluna Grep na mesma linha e linha de impressão

  • 772

Eu tenho este arquivo de 5 colunas:

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

Para cada linha, preciso usar o grep do valor da última coluna $5 no segundo campo $2. Então, preciso imprimir a mesma linha com uma coluna $6 adicional com o resultado do grep com uma condição:, if ($3 == rev)o $6 é o resultado do grep + 12 caracteres após o grep ou if ($3 == fwd)o resultado do grep + 12 caracteres antes do grep.

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

Os valores de $ 5 são necessários 16 caracteres e o padrão que procuro é sempre de 12 caracteres. Então, minha saída de $ 6 tem 28 caracteres.

Resultado esperado:

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

Mas não consigo o que quero.

bash

2 respostas

  1. Best Answer

    Você pode usar o script abaixo para alcançar seu resultado:

    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

    Basicamente, o roteiro:

    1. primeiro encontra o índice do $5valor no segundo campo. Se o valor for encontrado (idx != 0).

      a. ele verifica o valor do terceiro campo.
      b. Se for "rev", extrai a 28-charactersubstring começando 12 caracteres antes do índice.
      c. caso contrário, extrai a substring começando no índice.

    CÓDIGO DE DEMONSTRAÇÃO

    • 2

  2. Algo assim fará isso, usando qualquer awk:

    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

    Para sua informação, para perguntas futuras, aqui está como seria um exemplo reproduzível mínimo2 , usando em vez de 12o número de caracteres adicionais a serem impressos:

    Exemplo de entrada:

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

    Resultado esperado:

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

    com o qual poderíamos testar para ver facilmente se a solução potencial funciona ou não:

    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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