在数组散列中向文件名列表中添加前缀

Question

数组@lines包含%hash的键，如下所示

HG00117
HG00119
NA20828

其他许多样品也是如此。我刚刚为下面的例子展示了三个例子。

use strict;
use warnings;

use Data::Dump;

open (FILE, 'input.txt'); 
chomp (my @lines = (<FILE>)); 
close(FILE);

my %hash;

$hash{$_} = [ glob("$_*.bam") ] for @lines;

dd %hash;

这将打印我的数组散列：

(
  "HG00117",
  [
    "HG00117.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam_herc2_data.bam",
    "HG00117.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam_herc2_phase1.bam",
    "HG00117.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam_herc2_data.bam",
    "HG00117.mapped.illumina.mosaik.GBR.exome.20110411.bam_herc2_phase1.bam",
  ],
  "HG00119",
  [
    "HG00119.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam_herc2_data.bam",
    "HG00119.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam_herc2_phase1.bam",
    "HG00119.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam_herc2_data.bam",
    "HG00119.mapped.illumina.mosaik.GBR.exome.20110411.bam_herc2_phase1.bam",
  ],
  "NA20828",
  [
    "NA20828.mapped.ILLUMINA.bwa.TSI.exome.20121211.bam_herc2_data.bam",
    "NA20828.mapped.ILLUMINA.bwa.TSI.low_coverage.20101123.bam_herc2_phase1.bam",
    "NA20828.mapped.ILLUMINA.bwa.TSI.low_coverage.20130415.bam_herc2_data.bam",
    "NA20828.mapped.illumina.mosaik.TSI.exome.20110411.bam_herc2_phase1.bam",
  ],
)

我想在数组的每个元素前加上INPUT=，所以它们如下所示

(
  "HG00117",
  [
    "INPUT=HG00117.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam_herc2_data.bam",
    "INPUT=HG00117.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam_herc2_phase1.bam",
    "INPUT=HG00117.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam_herc2_data.bam",
    "INPUT=HG00117.mapped.illumina.mosaik.GBR.exome.20110411.bam_herc2_phase1.bam",
  ],
  "HG00119",
  [
    "INPUT=HG00119.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam_herc2_data.bam",
    "INPUT=HG00119.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam_herc2_phase1.bam",
    "INPUT=HG00119.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam_herc2_data.bam",
    "INPUT=HG00119.mapped.illumina.mosaik.GBR.exome.20110411.bam_herc2_phase1.bam",
  ],
  "NA20828",
  [
    "INPUT=NA20828.mapped.ILLUMINA.bwa.TSI.exome.20121211.bam_herc2_data.bam",
    "INPUT=NA20828.mapped.ILLUMINA.bwa.TSI.low_coverage.20101123.bam_herc2_phase1.bam",
    "INPUT=NA20828.mapped.ILLUMINA.bwa.TSI.low_coverage.20130415.bam_herc2_data.bam",
    "INPUT=NA20828.mapped.illumina.mosaik.TSI.exome.20110411.bam_herc2_phase1.bam",
  ],
)

我尝试了regex和grep，但是似乎没有什么效果。我想我被foreach的范围搞混了。我也尝试过rename函数，但是它没有工作。

Answer 1

所以，迭代每个元素-你实际上需要两个循环。一个用于“顶级”--哈希值。(它们是数组引用)。

然后，对每个数组引用，在应用转换的数组中迭代。

foreach my $array_ref ( values %hash ) {
   foreach my $oldfilename ( @$array_ref ) {
       $element =~ s/^/INPUT=/;
   }
}

还是真的想要更改磁盘上的文件名？如果是这样的话，你可以使用rename (我不认为这是你想要的)

foreach my $array_ref ( values %hash ) {
   foreach my $oldfilename ( @$array_ref ) {
       rename $oldfilename, 'INPUT='.$oldfilename
   }
}

Answer 2

这可以通过从input.txt内容构建正则表达式并对照它检查所有*.bam文件来实现。

像这样

use strict;
use warnings;

my @patterns = do {
  open my $in_fh, '<', 'input.txt' or die qq{Unable to open "input.txt" for input: $!};
  <$in_fh>;
};
chomp @patterns;
my $re = join '|', map quotemeta, @patterns;

my @files = grep /^(?:$re)/, glob '*.bam';
$_ = "INPUT=$_" for @files;