Question

我有一个看起来像这样的文件：

LOCUS POS ALIAS VAR TEST P I DESC  
CCL23|disruptive chr17:34340329..34340854        .       2       BURDEN  1       0.43    0/1  
CCL23|disruptive     chr17:34340329..34340854        .       2       BURDEN  1       0.295   0/1  
CCL23|disruptive      chr17:34340329..34340854        .       2       BURDEN  1       0.005   1/1  
CCL23|disruptive     chr17:34340329..34340854        .       2       BURDEN  0.676617        0.005   1/0

我想用“/”分割最后一个字段，然后对这些数字求和，然后用总和推送另一列。例如，我希望输出看起来像：

CCL23|disruptive chr17:34340329..34340854        .       2       BURDEN  1       0.43    0/1 1  
CCL23|disruptive     chr17:34340329..34340854        .       2       BURDEN  1       0.295   0/1 1  
CCL23|disruptive      chr17:34340329..34340854        .       2       BURDEN  1       0.005   1/1 2  
CCL23|disruptive     chr17:34340329..34340854        .       2       BURDEN  0.676617        0.005   1/0 1

我有这段代码，但它不起作用：

#! perl -w

my $file1 = shift@ARGV;

my $NVAR=0;
my @vars;
open (IN, $file1) or die "couldn't read file one";
while(<IN>){
    my@L=split;
    next if ($L[0] =~ m/LOCUS/);
    my@counts=split /\//, $L[7];
    foreach (@counts){
        $NVAR=${$_}[0] + ${$_}[1];
    }

    push @vars,[$L[0],$L[1],$L[2],$L[3],$L[4],$L[5],$L[6],$L[7],$NVAR];
}

close IN;

print "LOCUS POS ALIAS NVAR TEST P I DESC SUM\n";
foreach(@vars){
    print "@{$_}\n";
}

感谢任何帮助。

Answer 1

始终在每个脚本的顶部加入use strict;和use warnings;。

将变量限制在尽可能小的范围内，因为在$NVAR循环之外声明while会引入错误。您的总和可以通过以下方式确定：

my $NVAR = 0;
foreach (@counts){
    #$NVAR=${$_}[0] + ${$_}[1];  <-- this was bad.
    $NVAR += $_;
}

然而，这可以使用perl oneliner来解决

perl -MList::Util=sum -lane 'push @F, sum split "/", $F[-1]; print "@F"' file.txt

或者如果您有标题行：

perl -MList::Util=sum -lane '
        push @F, $. == 1 ? "SUM" : sum split "/", $F[-1];
        print "@F"
    ' file.txt

注意，您也可以在脚本中使用List::Util sum。

拆分列然后求和并将和推送到perl中的数组

1 个答案: