Question

我试图仅打印具有chrX或chrY的行，并且在由\ t分隔的文件中的第4列中为正。

输入

1373    NM_016303       chrX    +       103356451       10335846
1059    NM_015666       chr20   +       62183024        62202754
116     NM_015340       chr3    +       45388582        45548836 
10      NM_001206850    chrY    -       14522607        14843968

输出

1373    NM_016303       chrX    +       103356451       10335846

我的代码

#!/usr/bin/perl

use strict;
use warnings;

print "type in the path of the file\n";
my $file_name = <>;
chomp($file_name); 

open (FILE, $file_name) or die "#!"; 

my @line;
my @array1;

while(<FILE>){
    @line = split(/\t/);
    $array1[2]=$line[2];
    $array1[3]=$line[3];
}
my $positive;
my $chr;

#select only positives
if ($line[3] =~ m/\+/i ) {
    $positive = $array1[3];
} 
#only chrX or chrY
elsif ($line[2] =~ m/chrX/i or $line[2] =~ m/chrY/i ) {
    $chr = $array1[2];
}
else {
    print "no chrY or chrX\n";
}
print "$chr $positive\n";

close(FILE);
exit;

但是我收到了错误

Use of uninitialized value $chr in concatenation (.) or string at file.pl line 34, <FILE> line 61287.

我尝试了一些修改，但它只是打印

chrX  +

而不是整条线。我应该改变什么？感谢。

Answer 1

所有测试都应该在while循环中，而不是在外部。你使用了太多看起来毫无用处的变量。使用$_将使您的代码更短，更易读：

#!/usr/bin/perl
use strict;
use warnings;

print "Type in the path of the file:\n";
my $filename = <>;
chomp($filename); 

open my $fh, '<', $filename
    or die "$!"; 

while(<$fh>) {
    # split $_ (the current line) on whitespaces
    my @fields = split;
    # print $_ if the condition is true  
    print if ($fields[2] =~ /^chr[XY]$/ and $fields[3] eq "+");
}

close($fh);

选项卡分隔文件上的选择行

1 个答案: