Question

我有2个文件，如下所示：

FILE1.TXT：

0  117nt, >gene_73|GeneMark.hm... *
0   237nt, >gene_3097|GeneMark.... *
0   237nt, >gene_579|GeneMark.h... *
0   237nt, >gene_988|GeneMark.h... *
0   189nt, >gene_97|GeneMark.hm... *
0   183nt, >gene_97|GeneMark.hm... *

file2.fasta：

＆GT; gene_735 | GeneMark.hmm | 237_nt | + | 798985 | 799221   TTGTGGTTCGTGCCGCGCGACGCGTTGCGTCTGCAAACGCCCGACGAAGACATCGCGACCTATCTGTTCAACAAGCATGTGATTCGGCATCGGTTCTGTCCGACCTGCGGGATTCATCCGTTCGCGGAAGGCACGGACCCGAAGGGCAACGCGATGGCGGCCGTCAATCTTCGCTGCGTCGACGGCGTCGATCTCGACGCGTTGAGCGTCCGCCATTTCGACGGGCGCGCGCTCTGA   ＆GT; gene_579 | GeneMark.hmm | 237_nt | + | 667187 | 667423   ATGTACCACGGCGCCGAATTTGCCGCTGCCAAGGGCATGCGCTGGCTGCGAGATGCCGCCAACGGCTCTGCCTTCATCGCACCGGGCAGTCCGTGGCAAAACGGTTTCGTCGAGCGTTTCAACGGCAAGCTGCATGACGAATTGCTGAACCGGGAATGGTTCCGCGGCCGTGCCGAGACCAAGATGCTCATCGAACGCTCCGGCTACGGTCCGTCGAGTCTGACCGGATTCCGATGA   ＆GT; gene_1876 | GeneMark.hmm | 234_nt | - | 2168498 | 2168731   ATGCTGTTCTTTTCGCGCGCGGGCGTGTCGCGTGCGGCCGGCGGCCAATCATGCGGCGAGTCGTTTTGTCGCGGCTCGCGGCGCTTGCCGACGTTGGAATCGCGCGCGCCGATGCGCGGATCGGGGCGGCAACGTTTGCGTATGAGGAATGATGCGTTTGCGCATCGGGAATGGGCGCCTCGCCCCGGTTTCGCCGCGATTCCGCCCGACTCGAGGCAGTCGTTTTTCCGCTAA   ＆GT; gene_3097 | GeneMark.hmm | 237_nt | - | 3467022 | 3467258   GTGTCGAACGAACGTCGCGGCGAACGGCCGCTGCGGGCATCGCCGCAGGACGTCACACGGCGAACGTCGCGCGCGATCCTCGGCGGCCGCGAACGTGGGCCGTCCCGTGGCACGTTCGGCTCGCTCGGCATGGCGAACGACCGCCGCATCGCGCATCGCCGTCGCGCGGCCTCCAAAAAAACGGCGGTCAGCGACCGCCGGCTTTGGCCGAAACCGATGCGTCGTACGAATCAGTGA   ＆GT; gene_988 | GeneMark.hmm | 237_nt | + | 1121027 | 1121263
  ATGACCTTGTCAGGCAACATCAAGGACGGCGACTGGACGGTCGAGGTGACGACATCGCCGGTGCAGGGCGGTTACGTGTGCGACATCGAGGTGATGCACGGCGCGCCGGGCGGCGCGTTCCGGCACGCGTTCCGGCACGGCGGCACTTATCCGGCCGAGCGCGACGCGATGATCGAGGGGCTGCGCGCGGGCATGACCTGGATCGAGCTGAAGATGTCGAAAGCATTCAATCTGTAA   ＆GT; gene_97 | GeneMark.hmm | 105_nt | + | 90122 | 90226   GTGACGCGTTTCGCGACGCGCGTCGATGGGGCGGGCGCGAAACCCGTTCGCCGCGATGCGGCGGACGGGGTATGGCCGAGCGCCGTCCGTCGCGGCGAGAGTTGA   ＆GT; gene_97 | GeneMark.hmm | 183_nt | - | 107002 | 107184   ATGGAGGCAATCGTGATCGAGCAAGTGATACTGGGCGTCTTTCTCGTACTGCCGCTTCTCATCGTCGCGGTGCTGTACTCCGACGAACTCTGGCAAGAACACCGCCTGCAGCATCCGCGCGACGAGCACACGCCACATATCGACTGGCGTCATCCGTGGCGGATCCTGCGGCGAGGGCACTAA   ＆GT; gene_97 | GeneMark.hmm | 189_nt | - | 98624 | 98812   GTGAAATACACGAGCGACCATTACGCGGGCGTCAAATTTGGCGCGCTGTACGGGTTCTCGAACGCGGCGAACTTCGCCGACAACCGCGCTCGCCGGCGCATGCGCGGCGTTCGCATACGCGATCGGCAAAAGCGGCGTGATGTGCGGTTGCCTGCCGCGCTCGCGCTATGCGCGGCACGCCATCGATGA   ＆GT; gene_97 | GeneMark.hmm | 234_nt | + | 105494 | 105727   ATGAAGATTCAAATCGCCATTGTTTATTTTGTCGCCCGTCACGCAAACGAGCAGGCGCGAAGCGGATCGGCGCGCATTGGCGAAGAGCCGGCGCGCATCGGCATCGCGCTCGCGCGACACATGCGCGCCGCGCGCGGCCGGTCGACGCCGGATTCGCCTGTCGATCGATCCGGTGCGCCCCGAGCCGATGAGCGGTACGCTTCGGCGCGCGCGCGACACGCGCGACACGCGTGA   ＆GT; gene_979 | GeneMark.hmm | 225_nt | - | 1115442 | 1115666   TTGATCGACGCGCGGGGCCGGCCGGGCCGCGGGGTATCGAAGGCGATCGACGCGCAACACGAATCGCCGCCGCGCGCCGAAACCTCGCTATGCGCGTCGCGCGCACGCGCGGCCGGCGGCGCACGCGCGGGTGTGCGCGGGCCGGCGGCGCGGCCGCTCGCACTGCGCGACCGCTCGCGCGCACGCCTTCCTCGGCACGCGCCGGGAATCCCGGCCCTTCAATGA

我期望的输出是：

＆GT; gene_579 | GeneMark.hmm | 237_nt | + | 667187 | 667423   ATGTACCACGGCGCCGAATTTGCCGCTGCCAAGGGCATGCGCTGGCTGCGAGATGCCGCCAACGGCTCTGCCTTCATCGCACCGGGCAGTCCGTGGCAAAACGGTTTCGTCGAGCGTTTCAACGGCAAGCTGCATGACGAATTGCTGAACCGGGAATGGTTCCGCGGCCGTGCCGAGACCAAGATGCTCATCGAACGCTCCGGCTACGGTCCGTCGAGTCTGACCGGATTCCGATGA   ＆GT; gene_3097 | GeneMark.hmm | 237_nt | - | 3467022 | 3467258   GTGTCGAACGAACGTCGCGGCGAACGGCCGCTGCGGGCATCGCCGCAGGACGTCACACGGCGAACGTCGCGCGCGATCCTCGGCGGCCGCGAACGTGGGCCGTCCCGTGGCACGTTCGGCTCGCTCGGCATGGCGAACGACCGCCGCATCGCGCATCGCCGTCGCGCGGCCTCCAAAAAAACGGCGGTCAGCGACCGCCGGCTTTGGCCGAAACCGATGCGTCGTACGAATCAGTGA   ＆GT; gene_988 | GeneMark.hmm | 237_nt | + | 1121027 | 1121263
  ATGACCTTGTCAGGCAACATCAAGGACGGCGACTGGACGGTCGAGGTGACGACATCGCCGGTGCAGGGCGGTTACGTGTGCGACATCGAGGTGATGCACGGCGCGCCGGGCGGCGCGTTCCGGCACGCGTTCCGGCACGGCGGCACTTATCCGGCCGAGCGCGACGCGATGATCGAGGGGCTGCGCGCGGGCATGACCTGGATCGAGCTGAAGATGTCGAAAGCATTCAATCTGTAA   ＆GT; gene_97 | GeneMark.hmm | 183_nt | - | 107002 | 107184   ATGGAGGCAATCGTGATCGAGCAAGTGATACTGGGCGTCTTTCTCGTACTGCCGCTTCTCATCGTCGCGGTGCTGTACTCCGACGAACTCTGGCAAGAACACCGCCTGCAGCATCCGCGCGACGAGCACACGCCACATATCGACTGGCGTCATCCGTGGCGGATCCTGCGGCGAGGGCACTAA   ＆GT; gene_97 | GeneMark.hmm | 189_nt | - | 98624 | 98812   GTGAAATACACGAGCGACCATTACGCGGGCGTCAAATTTGGCGCGCTGTACGGGTTCTCGAACGCGGCGAACTTCGCCGACAACCGCGCTCGCCGGCGCATGCGCGGCGTTCGCATACGCGATCGGCAAAAGCGGCGTGATGTGCGGTTGCCTGCCGCGCTCGCGCTATGCGCGGCACGCCATCGATGA

有4个基因编号为97的序列，但全长不同。我希望只有在file1.txt中列出的正确基因长度的序列才能在output.fasta文件中输出。到目前为止我所做的如下（但失败并有一些错误）：

#!/usr/bin/perl

use strict;
use warnings;

my @genes;

open my $list, '<file1.txt';

while (my $line = <$list>) {
    push (@genes, $1) if $line =~/\>(.*?)\|/gs;
}

my $tag1 = "0\t"; 
my $tag2  = "nt"; 

while (my $line = <$list>) { 
    if ($line =~ /$tag1(.*?)$tag2/) {
        my $match1 = $1;
    } 
} 
my $input;

{
    local $/ = undef;
    open my $fasta, '<file2.fasta';
    my $tag3 = "GeneMark.hmm"; 
    my $tag4  = "_nt"; 
    while (my $input = <$fasta>) { 
        if ($input =~ /$tag3(.*?)$tag4/) { 
            my $match2 = $1; }} 
    close $fasta; 
}

my @lines = split(/>/,$input);
foreach my $l (@lines) {
    if ($l =~ /(.+?)\|/) {
        my $real_name = $1;
         if ($real_name ~~ @genes) {
            if ($match2 = $match1) {
            open (OUTFILE, '>>output.fasta');
            print OUTFILE ">$l"; }
         }
    }
}

有人能给我一些指导来纠正代码吗？或者有更好的方法吗？任何帮助将非常感谢！谢谢！：）

Answer 1

以下是使用Bio::SeqIO的选项：

use strict;
use warnings;
use Bio::SeqIO;

my %hash;
open my $fh, '<', $ARGV[0] or die $!;

while (<$fh>) {
    push @{ $hash{$2} }, $1 if /\s+(\d+)nt,.+?>(gene_\d+)\|/;
}

close $fh;

my $in  = Bio::SeqIO->new( -file => $ARGV[1], -format => 'Fasta' );
my $out = Bio::SeqIO->new( -fh   => \*STDOUT, -format => 'Fasta' );

while ( my $seq = $in->next_seq() ) {
    $out->write_seq($seq)
      if $seq->id =~ /(gene_\d+)\|.+?\|(\d+)_nt\|/ and grep /$2/, @{ $hash{$1} };
}

用法：perl script.pl file1.txt file2.fasta [>outFile.fasta]

第二个可选参数将输出定向到文件。

您的数据输出：

>gene_579|GeneMark.hmm|237_nt|+|667187|667423
ATGTACCACGGCGCCGAATTTGCCGCTGCCAAGGGCATGCGCTGGCTGCGAGATGCCGCC
AACGGCTCTGCCTTCATCGCACCGGGCAGTCCGTGGCAAAACGGTTTCGTCGAGCGTTTC
AACGGCAAGCTGCATGACGAATTGCTGAACCGGGAATGGTTCCGCGGCCGTGCCGAGACC
AAGATGCTCATCGAACGCTCCGGCTACGGTCCGTCGAGTCTGACCGGATTCCGATGA
>gene_3097|GeneMark.hmm|237_nt|-|3467022|3467258
GTGTCGAACGAACGTCGCGGCGAACGGCCGCTGCGGGCATCGCCGCAGGACGTCACACGG
CGAACGTCGCGCGCGATCCTCGGCGGCCGCGAACGTGGGCCGTCCCGTGGCACGTTCGGC
TCGCTCGGCATGGCGAACGACCGCCGCATCGCGCATCGCCGTCGCGCGGCCTCCAAAAAA
ACGGCGGTCAGCGACCGCCGGCTTTGGCCGAAACCGATGCGTCGTACGAATCAGTGA
>gene_988|GeneMark.hmm|237_nt|+|1121027|1121263
ATGACCTTGTCAGGCAACATCAAGGACGGCGACTGGACGGTCGAGGTGACGACATCGCCG
GTGCAGGGCGGTTACGTGTGCGACATCGAGGTGATGCACGGCGCGCCGGGCGGCGCGTTC
CGGCACGCGTTCCGGCACGGCGGCACTTATCCGGCCGAGCGCGACGCGATGATCGAGGGG
CTGCGCGCGGGCATGACCTGGATCGAGCTGAAGATGTCGAAAGCATTCAATCTGTAA
>gene_97|GeneMark.hmm|183_nt|-|107002|107184
ATGGAGGCAATCGTGATCGAGCAAGTGATACTGGGCGTCTTTCTCGTACTGCCGCTTCTC
ATCGTCGCGGTGCTGTACTCCGACGAACTCTGGCAAGAACACCGCCTGCAGCATCCGCGC
GACGAGCACACGCCACATATCGACTGGCGTCATCCGTGGCGGATCCTGCGGCGAGGGCAC
TAA
>gene_97|GeneMark.hmm|189_nt|-|98624|98812
GTGAAATACACGAGCGACCATTACGCGGGCGTCAAATTTGGCGCGCTGTACGGGTTCTCG
AACGCGGCGAACTTCGCCGACAACCGCGCTCGCCGGCGCATGCGCGGCGTTCGCATACGC
GATCGGCAAAAGCGGCGTGATGTGCGGTTGCCTGCCGCGCTCGCGCTATGCGCGGCACGC
CATCGATGA

Bio :: SeqIO用于解析fasta（和其他此类）文件，因此上述功能可以利用这一功能。从file1.txt创建数组散列（HoA）后，将处理fasta文件，并且仅打印匹配的fasta记录。

希望这有帮助！

Perl：如何根据基因数和核苷酸长度提取序列？

1 个答案: