从输入文件中提取匹配的模式并打印到Perl中的输出文件

Question

我有一个来自ncbi blastn的巨大输入文件，格式如下：

<ul id="msgFrm" class=" msg">
Job Title: otu0                  
Database: rRNA_typestrains/prokaryotic_16S_ribosomal_RNA 16S ribosomal RNA (Bacteria and Archaea)
Query #1: otu0 Query ID: lcl|Query_16950 Length: 460

Sequences producing significant alignments:
                                                                  Max    Total Query   E   Per.                  
Description                                                       Score  Score cover Value Ident  Accession        
Bacteroides dorei strain 175 16S ribosomal RNA, partial sequence  839    839   100%  0.0   99.57  NR_041351.1      

Alignments:
>Bacteroides dorei strain 175 16S ribosomal RNA, partial sequence
Sequence ID: NR_041351.1 Length: 1493 
Range 1: 341 to 800

Score:839 bits(454), Expect:0.0, 
Identities:458/460(99%),  Gaps:0/460(0%), Strand: Plus/Plus

Query  1    CCTACGGGGGGCAGCAGTGAGGAATATTGGTCAATGGGCGATGGCCTGAACCAGCCAAGT  60
            |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  341  CCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGATGGCCTGAACCAGCCAAGT  400


Query #2: otu1 Query ID: lcl|Query_16951 Length: 460

Sequences producing significant alignments:
                                                                  Max    Total Query   E   Per.                  
Description                                                       Score  Score cover Value Ident  Accession          
Bacteroides vulgatus ATCC 8482 16S ribosomal RNA, partial...      811    811   100%  0.0   98.48  NR_074515.1      
Bacteroides paurosaccharolyticus strain WK042 16S ribosomal RN... 673    673   100%  0.0   93.06  NR_112668.1      


Alignments:
>Bacteroides dorei strain 175 16S ribosomal RNA, partial sequence
Sequence ID: NR_041351.1 Length: 1493 
Range 1: 341 to 800

Score:833 bits(451), Expect:0.0, 
Identities:457/460(99%),  Gaps:0/460(0%), Strand: Plus/Plus

Query  1    CCTACGGGGGGCAGCAGTGAGGAATATTGGTCAATGGGCGATGGCCTGAACCAGCCAAGT  60
            |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  341  CCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGATGGCCTGAACCAGCCAAGT  400


Query #3: otu2 Query ID: lcl|Query_16952 Length: 460

Sequences producing significant alignments:
                                                                  Max    Total Query   E   Per.                  
Description                                                       Score  Score cover Value Ident  Accession             
Bacteroides sartorii JCM 16497 16S ribosomal RNA, partial...      684    684   100%  0.0   93.48  NR_113064.1      
Bacteroides paurosaccharolyticus strain WK042 16S ribosomal RN... 678    678   100%  0.0   93.28  NR_112668.1      


Alignments:
>Bacteroides dorei strain 175 16S ribosomal RNA, partial sequence
Sequence ID: NR_041351.1 Length: 1493 
Range 1: 341 to 800

Score:839 bits(454), Expect:0.0, 
Identities:458/460(99%),  Gaps:0/460(0%), Strand: Plus/Plus

Query  1    CCTACGGGTGGCAGCAGTGAGGAATATTGGTCAATGGGCGATGGCCTGAACCAGCCAAGT  60
            |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  341  CCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGATGGCCTGAACCAGCCAAGT  400

...and so one

现在，对于文件中的每个"Query #“，我需要提取包含在"Query #”和"Alignments“之间的段落信息，并在另一个输出文件中打印。

我尝试使用以下基本代码，但在Perl编程中遇到了一些困难。有人能帮我解决这个问题吗？非常感谢

#!/usr/bin/perl -w

use warnings;

open(GENBANK, "Bact_ncbi_output.txt") or die;

my $outfile = 'output.txt';
open OUT,'>',$outfile 
  or die "Could not open $outfile : $!";

$content = join("", <GENBANK>);   
close GENBANK;

$content =~ /Query\s+([A-Z0-9_.]+)Alignments$/;         

print OUT "$content\n";

Answer 1

请尝试以下操作：

#!/usr/bin/perl -w

use warnings;

open(GENBANK, "txt.txt") or die "";
local $/; $_= <GENBANK>; my $content = $_;

my $outfile = 'output.txt';
open(OUT,">",$outfile) or die "Could not open $outfile : $!";
my (@fetch) = $content=~m{(Query\s*\#((?:(?!Alignments\:\n).)*)\nAlignments\:\n)}gs;
#print OUT @fetch;
print OUT join "\n", @fetch;

请在您需要的地方更换。

谢谢。