Question

我想基于两个文件之间的匹配字符串组合两个文件。在File1中，字符串位于第4列，在File2中，字符串位于符号＆＃34;：＆＃34;和＆＃34; - ＆＃34;

File1中：

chr1    Rfam    ncRNA   157784  157887  66.91   -       .       ID=RF00026.1;Name=RF00026;Alias=U6;Note=AL627309.15/147374-147271
chr1    Rfam    ncRNA   564813  564881  36.11   +       .       ID=RF00005.1;Name=RF00005;Alias=tRNA;Note=AC114498.2/43445-43513
chr1    Rfam    ncRNA   564879  564950  32.30   -       .       ID=RF00005.2;Name=RF00005;Alias=tRNA;Note=AC114498.2/43582-43511
chr1    Rfam    ncRNA   564952  565019  28.17   +       .       ID=RF00005.3;Name=RF00005;Alias=tRNA;Note=AC114498.2/43584-43651
chr1    Rfam    ncRNA   566062  566129  31.36   +       .       ID=RF00005.4;Name=RF00005;Alias=tRNA;Note=AC114498.2/44694-44761
chr1    Rfam    ncRNA   566137  566205  30.82   -       .       ID=RF00005.5;Name=RF00005;Alias=tRNA;Note=AC114498.2/44837-44769
chr1    Rfam    ncRNA   566207  566279  35.81   -       .       ID=RF00005.6;Name=RF00005;Alias=tRNA;Note=AC114498.2/44911-44839
chr1    Rfam    ncRNA   566311  566376  26.05   -       .       ID=RF00005.7;Name=RF00005;Alias=tRNA;Note=AC114498.2/45008-44943

文件2：

chr1:157783-157887      aaaaatatggaatgcttcacaaatttgcatgtcattctttcacagaggccgtgccaatctctctattgttccaacttaagtatgtgtgctactgaggcaagcaT
chr1:564812-564881      AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTcta
chr1:564878-564950      ctaggactatgagaatcgaacccatccctgagaatccaaaattctccgtgccacctatcacaccccatccta
chr1:564951-565019      AGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATATCCTTCCCGTACTA
chr1:566061-566129      AGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTG
chr1:566136-566205      TAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTT
chr1:566206-566279      CTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTA
chr1:566310-566376      AAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCTCAGAGCT
chr1:566376-566441      GGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACC
chr1:568068-568136      AAGATATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCTAAATCCTATATATCTTA
chr1:568843-568913      CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA

输出：

输出应包含两个文件中的所有列。

chr1    Rfam    ncRNA   157784  157887  66.91   -       .       ID=RF00026.1;Name=RF00026;Alias=U6;Note=AL627309.15/147374-147271 chr1:157783-157887      aaaaatatggaatgcttcacaaatttgcatgtcattctttcacagaggccgtgccaatctctctattgttccaacttaagtatgtgtgctactgaggcaagcaT
....
....

我之前将此代码编写为类似但不完全相同的问题：

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

my @files = qw| input.log input1.log |; #you can give here path of files, or use @ARGV if you wish to pass files from command line 
my %data;

foreach my $filename (@files)
{
    open my $fh, '<', $filename or die "Cannot open $filename for reading: $!";
    while (my $line = <$fh>)
    {
        chomp $line;
        my ($col1, $col2) = split /\s+/, $line;
        push @{ $data{$col1} }, $col2; #create an hash of array
    }
}
foreach my $col1 (sort keys %data)
{
    print join("\t", $col1, @{ $data{$col1} }), "\n";    
}

Answer 1

这将连接请求的列/数据上的两个文件。如果匹配，它只会打印行。

编辑：显示包含新样本数据的结果：

$ cat f1
chr1    Rfam    ncRNA   157783  157887  66.91   -   0   ID=RF00026.1;Name=RF00026;Alias=U6;Note=AL627309.15/147374-147271
chr1    Rfam    ncRNA   564812  564881  36.11   +   0   ID=RF00005.1;Name=RF00005;Alias=tRNA;Note=AC114498.2/43445-43513
chr1    Rfam    ncRNA   564878  564950  32.3    -   0   ID=RF00005.2;Name=RF00005;Alias=tRNA;Note=AC114498.2/43582-43511
chr1    Rfam    ncRNA   564951  565019  28.17   +   0   ID=RF00005.3;Name=RF00005;Alias=tRNA;Note=AC114498.2/43584-43651
chr1    Rfam    ncRNA   566061  566129  31.36   +   0   ID=RF00005.4;Name=RF00005;Alias=tRNA;Note=AC114498.2/44694-44761
chr1    Rfam    ncRNA   566136  566205  30.82   -   0   ID=RF00005.5;Name=RF00005;Alias=tRNA;Note=AC114498.2/44837-44769
chr1    Rfam    ncRNA   566206  566279  35.81   -   0   ID=RF00005.6;Name=RF00005;Alias=tRNA;Note=AC114498.2/44911-44839
chr1    Rfam    ncRNA   566310  566376  26.05   -   0   ID=RF00005.7;Name=RF00005;Alias=tRNA;Note=AC114498.2/45008-44943
chr1    Rfam    ncRNA   566376  566441  37.46   -   0   ID=RF00005.8;Name=RF00005;Alias=tRNA;Note=AC114498.2/45073-45009
chr1    Rfam    ncRNA   568068  568136  31.45   +   0   ID=RF00005.9;Name=RF00005;Alias=tRNA;Note=AC114498.2/46701-46768

$ cat f2
chr1:157783-157887  aaaaatatggaatgcttcacaaatttgcatgtcattctttcacagaggccgtgccaatctctctattgttccaacttaagtatgtgtgctactgaggcaagcaT
chr1:564812-564881  AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTcta
chr1:564878-564950  ctaggactatgagaatcgaacccatccctgagaatccaaaattctccgtgccacctatcacaccccatccta
chr1:564951-565019  AGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATATCCTTCCCGTACTA
chr1:566061-566129  AGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTG
chr1:566136-566205  TAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTT
chr1:566206-566279  CTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTA
chr1:566310-566376  AAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCTCAGAGCT
chr1:566376-566441  GGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACC
chr1:568068-568136  AAGATATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCTAAATCCTATATATCTTA


$ awk 'BEGIN {FS="[\t :-]+"} NR==FNR {a[$4]=$0; next} $2 in a {print a[$2], $0}' f1 f2
chr1    Rfam    ncRNA   157783  157887  66.91   -   0   ID=RF00026.1;Name=RF00026;Alias=U6;Note=AL627309.15/147374-147271 chr1:157783-157887  aaaaatatggaatgcttcacaaatttgcatgtcattctttcacagaggccgtgccaatctctctattgttccaacttaagtatgtgtgctactgaggcaagcaT
chr1    Rfam    ncRNA   564812  564881  36.11   +   0   ID=RF00005.1;Name=RF00005;Alias=tRNA;Note=AC114498.2/43445-43513 chr1:564812-564881  AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTcta
chr1    Rfam    ncRNA   564878  564950  32.3    -   0   ID=RF00005.2;Name=RF00005;Alias=tRNA;Note=AC114498.2/43582-43511 chr1:564878-564950  ctaggactatgagaatcgaacccatccctgagaatccaaaattctccgtgccacctatcacaccccatccta
chr1    Rfam    ncRNA   564951  565019  28.17   +   0   ID=RF00005.3;Name=RF00005;Alias=tRNA;Note=AC114498.2/43584-43651 chr1:564951-565019  AGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATATCCTTCCCGTACTA
chr1    Rfam    ncRNA   566061  566129  31.36   +   0   ID=RF00005.4;Name=RF00005;Alias=tRNA;Note=AC114498.2/44694-44761 chr1:566061-566129  AGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTG
chr1    Rfam    ncRNA   566136  566205  30.82   -   0   ID=RF00005.5;Name=RF00005;Alias=tRNA;Note=AC114498.2/44837-44769 chr1:566136-566205  TAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTT
chr1    Rfam    ncRNA   566206  566279  35.81   -   0   ID=RF00005.6;Name=RF00005;Alias=tRNA;Note=AC114498.2/44911-44839 chr1:566206-566279  CTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTA
chr1    Rfam    ncRNA   566310  566376  26.05   -   0   ID=RF00005.7;Name=RF00005;Alias=tRNA;Note=AC114498.2/45008-44943 chr1:566310-566376  AAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCTCAGAGCT
chr1    Rfam    ncRNA   566376  566441  37.46   -   0   ID=RF00005.8;Name=RF00005;Alias=tRNA;Note=AC114498.2/45073-45009 chr1:566376-566441  GGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACC
chr1    Rfam    ncRNA   568068  568136  31.45   +   0   ID=RF00005.9;Name=RF00005;Alias=tRNA;Note=AC114498.2/46701-46768 chr1:568068-568136  AAGATATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCTAAATCCTATATATCTTA

将两个文件组合在一个公共字符串中

1 个答案: