插入标题行后文本文件中出现空白行

Question

我想在每个 .tsv 文件中插入自定义标头，解析每个文件的内容并附加到最​​终的变体文件。我试图在一个循环中完成此操作，但它不起作用，所以我尝试了两个单独的循环。第一个循环将标题插入到每个 .tsv 文件中，但是，第二个循环将插入的标题替换为空白行。有人可以解释为什么会发生这种情况以及如何解决这个问题吗？谢谢

#!perl
use strict;
use warnings;

my $home="/data/";                                                     
my $tsv_directory = $home."test_all_runs/".$ARGV[0];
my $tsvfiles = $home."test_all_runs/".$ARGV[0]."/tsv_files.txt";

my @run_directory = (); @run_directory = split /\//, $tsv_directory; print "The run directory is #############".$run_directory[3]."\n";

my $cmd = `ls $tsv_directory/FOCUS*\.tsv > $tsvfiles`; #print "$cmd";
my $cmda = "ls $tsv_directory/FOCUS*\.tsv > $tsvfiles"; #print "$cmda";

my @tsvfiles =();
#this code opens the vcf_files.txt file and passes each line into an array for indidivudal manipulation
open(TXT2, "$tsvfiles");
        while (<TXT2>){  
                push (@tsvfiles, $_);   
                }
close(TXT2);

foreach (@tsvfiles){
        chop($_);
}
#this loop works fine
for my $tsv_file (@tsvfiles){

    $tsv_file =~ m|([^/]+)-oncomine.tsv$| or die "Can't extract Sample ID";
    my $sample_id = $1;
    print "The sample ID is ############## $sample_id\n";
    my $headerline = $run_directory[3]."/".$sample_id;
   my $cmd9 = `sed -i '1i$headerline' $tsv_file`; print $cmd9;#local @ARGV = ($tsv_file);  
}

my $final_variants = $home."test_all_runs/".$ARGV[0]."/final_variant_file.txt";
open my $out_fh, '>', $final_variants or die qq{Unable to open "$final_variants" for output: $!};

my @tsv_files_new = glob $tsv_directory."/FOCUS*.tsv";

##this loop unintentionally replaces the newly inserted header with a blank line.
for my $tsv_file_new ( @tsv_files_new ) {

    print "The current VCF is ############# $tsv_file_new\n";

    $tsv_file_new =~ m|([^/]+)-oncomine.tsv$| or die "Can't extract Sample ID";
    my $sample_id = $1;
    print "The sample ID is ############## $sample_id\n";

    open my $in_fh, '<', $tsv_file_new
            or die qq{Unable to open "$tsv_file_new" for input: $!};

    while ( <$in_fh> ) {

        next if /^#/;
        next if /\b(?:CNV|intronic|synonymous|utr_3|utr_5)\b/;
        next if /\b(?:FORMAT.1.FSRF)\b/;# remove the original headers from Ion Reporter.

        my @fields = split;
        next if ($fields[70] =~ m|([0.])/\1|);
        my $chr = $fields[9]."check";

        my @wanted = ( 10, 21, 67, 68, 70, 77, 78, 81, 83, 84, 88, 92, 98, 100 );
        my $current_line = join "\t", @fields[@wanted];
        my $current_final_line = $sample_id."\t".$chr."\t".$current_line;
        print $out_fh $current_final_line, "\n";
    }
}
exit;

Answer 1

试试这个：

use strict;
use warnings;
use Tie::File;

my $tsv_file = 'test.txt';

tie my @textFile, 'Tie::File', $tsv_file, recsep => "\n"  or die $!;
for my $line (@textFile) {
    $line = "New Sample\n" if($line =~ /FORMAT\.1\.FSRF/);
}
untie @textFile;

Answer 2

在 Perl 中，您可以将 AAA 替换为 BBB

$string =~ s/AAA/BBB/;

所以如果你想：

#replace lines containing "FORMAT.1.FSRF" with "New Sample"

然后尝试：

$string =~ s/FORMAT\.1\.FSRF/New Sample/g;

如果您只想对每一行进行一次替换，请删除最后一个 g。