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我正在尝试将一个列表（screens.txt ）中第1列的每个元素与另一个列表（ new_list.txt ）中第1列的任何元素进行比较，如果匹配，则打印列表的整行（screens.txt）一个单独的文本文件（matched.txt）。我设法选择了正确的列，但我得到的输出是列表中的行（new_list.txt）而不是列表（screens.txt），并且只找到一个命中，所以看起来循环也有问题.

new_list.txt格式 => first_column->double_tab->the_rest

我是 perl 编程的新手。任何帮助将不胜感激！

这是我到目前为止所做的：

#!usr/bin/perl

use warnings;

$list = "new_list.txt";
$screens = "screens.txt";
$result = "matched.txt";

open (FA, "<$list") or die "Can't read source file $list: $!\n";
open (RES, ">$result") or die "Can't write on file $result: $!\n";

$n = 0;
$column = 10;
while ($line = <FA>) {
    @description = split (' ', $line);
    @ID = split ('\\t', $description[0]);   
       #print just first column from the list
      #  print "$ID[0]\n";
}

close (FA);

open (FA, "$screens") or die "Can't read source file $screens: $!\n";

while ($file = <FA>) {
    @table = split (' ', $file);
    @accession_no = split ('\ ', $table[0]);
      # print the first column from the list    
      #  print "$accession_no[0]\n";
}

open (FA, "<$list") or die "Can't read source file $list: $!\n";

while ($line = <FA>) {
    print "$line\n";
    @description = split (' ', $line);
    @ID = split ('\\t', $description[0]);
    if ($accession_no eq $ID[0]) {
        $n = $n+1;
        for ($i = 0; $i < $column; $i++) {
            print RES "$file";
        }

        print "\n";
    }   
}

close (FA);
close (RES);

print "Hits found: $n\n";

这是 next_list.txt 的示例：Q9UKA8 RCAN3_HUMAN 0

Q9UKA8-2 RCAN3_HUMAN 0

Q9UKA8-3 RCAN3_HUMAN 0

Q9UKA8-4 RCAN3_HUMAN 0

Q9UKA8-5 RCAN3_HUMAN 0

Q9GZP0 PDGFD_HUMAN 0

这是screens.txt的输入文件：

Q9GZP0 GDLDLASEST 支架连接因子 B2 (SAF-B2) SAFB2

Q9UKA8-5 QKAFNSSSFN Ran GTPase 激活蛋白 1 (RanGAP1) RANGAP1

我有兴趣检查Q9GZP0和Q9UKA8-5（第一列）

来自screens.txt是在new_list.txt的第一列，如果他们

然后从screen.txt打印整行/行。

先感谢您！

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2 回答 2

1

用块的力量过滤屏幕的最小代码map

#!/usr/bin/perl

use strict;
use warnings;

my $input1 = 'new_list.txt';
my $input2 = 'screens.txt';

my %seen;

open my $fh1, "< $input1"
    or die "Couldn't open $input1";

map{ $seen{$1} = $2 if /(\S+)\s(.*)/ } <$fh1>;

close $fh1;

open my $fh2, "< $input2"
    or die "Couldn't open $input2";

map{ print if /(\S+)\s+(.*)/ and $seen{$1} } <$fh2>;

close $fh2;

输入：new_list.txt

Q9UKA8 RCAN3_HUMAN 0
Q9UKA8-2 RCAN3_HUMAN 0
Q9UKA8-3 RCAN3_HUMAN 0
Q9UKA8-4 RCAN3_HUMAN 0
Q9UKA8-5 RCAN3_HUMAN 0
Q9GZP0 PDGFD_HUMAN 0

输入：screens.txt

Q9GZP0 GDLDLASEST Scaffold attachment factor B2 (SAF-B2) SAFB2
Q9UKA8-5 QKAFNSSSFN Ran GTPase-activating protein 1 (RanGAP1) RANGAP1

输出：

Q9GZP0 GDLDLASEST Scaffold attachment factor B2 (SAF-B2) SAFB2
Q9UKA8-5 QKAFNSSSFN Ran GTPase-activating protein 1 (RanGAP1) RANGAP1

笔记：

Linux——使用命令使程序可执行chmod og+x program.pl

Windows——运行程序为perl program.pl

使用命令将输出重定向到文件中：

Linux -program.pl > matched.txt

窗户 -perl program.pl > matched.txt

于 2020-01-16T22:31:23.113 回答
0

看看这是否对您有帮助：

#!/usr/bin/perl

use strict;
use warnings;

my $file1 = "file_pr1.txt";
my $file2 = "file_pr2.txt";
my $resulted_list = "result_list.txt";

my (@description, @ID, @data);

open (my $FA, "<$file1") or die "Can't read source file $file1: $!\n";

while (my $line = <$FA>) {
    chomp($line);
    @description = split (/\s+/, $line);
    push (@ID, $description[0]);   
}
close($FA);

my %params = map { $_ => 1 } @ID; #add each elements into hash

open (my $RES, ">$resulted_list") or die "Open as write error : $!\n";

open (my $FB, "<$file2") or die "Can't read source file $file2: $!\n";

while (my $line = <$FB>) {
    chomp($line);
    @data = split (/\s+/, $line);
    print $RES $line."\n" if(exists($params{$data[0]})); #Write to result file
}
close($RES);
于 2020-01-16T15:01:38.380 回答