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for-loop - 比较具有重复输入值的两个文件

问题描述

我有以下两个文件

BC.txt

"PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
"PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;

PB.txt

c4  PB  tr  41258945    41270445    .   +   .   g_i "PB.50262"; t_i "PB.50262.10";
c4  PB  Ex  41258945    41259026    .   +   .   g_i "PB.50262"; t_i "PB.50262.10";
c4  PB  Ex  41259626    41259754    .   +   .   g_i "PB.50262"; t_i "PB.50262.10";
c4  PB  Ex  41262664    41262814    .   +   .   g_i "PB.50262"; t_i "PB.50262.10";

我正在尝试将 BC.txt 的 Col1 与 PB.txt 的 Col12 进行比较，并将匹配项彼此相邻打印。对于 BC.txt 的 col1 中的相同值，在 col2 和 Col3 中具有不同的值。因此，在比较时，我只得到 BC.txt 的一个条目的输出。但我想要所有人。 

    awk 'BEGIN {OFS=FS} NR==FNR {a[$1]=($2" "$3);next} $12 in a {print $0,a[$12]}' BC.txt PB.txt

预期产出

c4  PB  tr  41258945    41270445    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
c4  PB  Ex  41258945    41259026    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
c4  PB  Ex  41259626    41259754    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
c4  PB  Ex  41262664    41262814    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
c4  PB  tr  41258945    41270445    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;
c4  PB  Ex  41258945    41259026    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;
c4  PB  Ex  41259626    41259754    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;
c4  PB  Ex  41262664    41262814    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;

我想将 BC.txt 的所有条目与 PB.txt 的条目进行比较；但由于它的值相同，我的代码不起作用。

标签： for-loopif-statementawk

解决方案

如果您不关心与问题中的预期输出相比的输出行顺序，那么将 BC.txt 读入内存，因为它更简洁：

$ cat tst.awk
NR==FNR {
    map[$1,++cnt[$1]] = $2 OFS $3
    next
}
{
    for (c=1; c<=cnt[$12]; c++) {
        print $0, map[$12,c]
    }
}

$ awk -f tst.awk BC.txt PB.txt
c4  PB  tr  41258945    41270445    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
c4  PB  tr  41258945    41270445    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;
c4  PB  Ex  41258945    41259026    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
c4  PB  Ex  41258945    41259026    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;
c4  PB  Ex  41259626    41259754    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
c4  PB  Ex  41259626    41259754    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;
c4  PB  Ex  41262664    41262814    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
c4  PB  Ex  41262664    41262814    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;

但如果你在乎的话：

$ cat tst.awk
NR==FNR {
    map[$12,++cnt[$12]] = $0
    next
}
{
    for (c=1; c<=cnt[$1]; c++) {
        print map[$1,c], $2, $3
    }
}

$ awk -f tst.awk PB.txt BC.txt
c4  PB  tr  41258945    41270445    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
c4  PB  Ex  41258945    41259026    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
c4  PB  Ex  41259626    41259754    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
c4  PB  Ex  41262664    41262814    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AGCGGCCT; BC=TTTCAGCGCCGA;
c4  PB  tr  41258945    41270445    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;
c4  PB  Ex  41258945    41259026    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;
c4  PB  Ex  41259626    41259754    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;
c4  PB  Ex  41262664    41262814    .   +   .   g_i "PB.50262"; t_i "PB.50262.10"; UMI=AAGCGGCC; BC=TTTCAGCGCCGA;

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