Question

我正在尝试将FASTA文件放入哈希值，以便稍后可以操作它，ID为键，序列为值。但我的输出只打印最后一个ID并将所有序列连接在一起。

输入

r = 0;
t1 = clock ();
for (v = 0; v < 2000000 - 1; v++) r += isprime2 (v);
t2 = clock ();
printf (" isprime2 (%lf sec) - %u primes\n", (t2-t1)/CLOCKS_PER_SEC, r);

r = 0;
t1 = clock ();
for (v = 0; v < 2000000 - 1; v++) r += isprime3 (v);
t2 = clock ();
printf (" isprime3 (%lf sec) - %u primes\n", (t2-t1)/CLOCKS_PER_SEC, r);

我的输出是

>cel-mir-35 MI0000006 Caenorhabditis elegans miR-35 stem-loop
UCUCGGAUCAGAUCGAGCCAUUGCUGGUUUCUUCCACAGUGGUACUUUCCAUUAGAACUA
UCACCGGGUGGAAACUAGCAGUGGCUCGAUCUUUUCC

>cel-mir-36 MI0000007 Caenorhabditis elegans miR-36 stem-loop
CACCGCUGUCGGGGAACCGCGCCAAUUUUCGCUUCAGUGCUAGACCAUCCAAAGUGUCUA
UCACCGGGUGAAAAUUCGCAUGGGUCCCCGACGCGGA

>cel-mir-37 MI0000008 Caenorhabditis elegans miR-37 stem-loop
UUCUAGAAACCCUUGGACCAGUGUGGGUGUCCGUUGCGGUGCUACAUUCUCUAAUCUGUA
UCACCGGGUGAACACUUGCAGUGGUCCUCGUGGUUUCU

>cel-mir-38 MI0000009 Caenorhabditis elegans miR-38 stem-loop
GUGAGCCAGGUCCUGUUCCGGUUUUUUCCGUGGUGAUAACGCAUCCAAAAGUCUCUAUCA
CCGGGAGAAAAACUGGAGUAGGACCUGUGACUCAU

我想将每个ID和相应的序列作为输出

码

cel-mir-38 MI0000009 Caenorhabditis elegans miR-38 stem-loop     UCUCGGAUCAGAUCGAGCCAUUGCUGGUUUCUUCCACAGUGGUACUUUCCAUUAGAACUAUCACCGGGUGGAAACUAGGGCUCGAUCUUUUCCCACCGCUGUCGGGGAACCGCGCCAAUUUUCGCUUCAGUGCUAGACCAUCCAAAGUGUCUAUCACCGGGUGAAAAUUCGCAUGGGUCCCCGACGCGGAUUCUAGAAACCCUUGGACCAGUGUGGGUGUCCGUUGCGGUGCUACAUUCUCUAAUCUGUAUCACCGGGUGAACACUUGCAGUGGUCCUCGUGGUUUCUGUGAGCCAGGUCCUGUUCCGGUUUUUUCCGUGGUGAUAACGCAUCCAAAAGUCUCUAUCACCGGGAGAAAAACUGGAGUAGGACCUGUGACUCAU
cel-mir-38 MI0000009 Caenorhabditis elegans miR-38 stem-loop     UCUCGGAUCAGAUCGAGCCAUUGCUGGUUUCUUCCACAGUGGUACUUUCCAUUAGAACUAUCACCGGGUGGAAACUAGGGCUCGAUCUUUUCCCACCGCUGUCGGGGAACCGCGCCAAUUUUCGCUUCAGUGCUAGACCAUCCAAAGUGUCUAUCACCGGGUGAAAAUUCGCAUGGGUCCCCGACGCGGAUUCUAGAAACCCUUGGACCAGUGUGGGUGUCCGUUGCGGUGCUACAUUCUCUAAUCUGUAUCACCGGGUGAACACUUGCAGUGGUCCUCGUGGUUUCUGUGAGCCAGGUCCUGUUCCGGUUUUUUCCGUGGUGAUAACGCAUCCAAAAGUCUCUAUCACCGGGAGAAAAACUGGAGUAGGACCUGUGACUCAU
cel-mir-38 MI0000009 Caenorhabditis elegans miR-38 stem-loop     UCUCGGAUCAGAUCGAGCCAUUGCUGGUUUCUUCCACAGUGGUACUUUCCAUUAGAACUAUCACCGGGUGGAAACUAGGGCUCGAUCUUUUCCCACCGCUGUCGGGGAACCGCGCCAAUUUUCGCUUCAGUGCUAGACCAUCCAAAGUGUCUAUCACCGGGUGAAAAUUCGCAUGGGUCCCCGACGCGGAUUCUAGAAACCCUUGGACCAGUGUGGGUGUCCGUUGCGGUGCUACAUUCUCUAAUCUGUAUCACCGGGUGAACACUUGCAGUGGUCCUCGUGGUUUCUGUGAGCCAGGUCCUGUUCCGGUUUUUUCCGUGGUGAUAACGCAUCCAAAAGUCUCUAUCACCGGGAGAAAAACUGGAGUAGGACCUGUGACUCAU
cel-mir-38 MI0000009 Caenorhabditis elegans miR-38 stem-loop     UCUCGGAUCAGAUCGAGCCAUUGCUGGUUUCUUCCACAGUGGUACUUUCCAUUAGAACUAUCACCGGGUGGAAACUAGGGCUCGAUCUUUUCCCACCGCUGUCGGGGAACCGCGCCAAUUUUCGCUUCAGUGCUAGACCAUCCAAAGUGUCUAUCACCGGGUGAAAAUUCGCAUGGGUCCCCGACGCGGAUUCUAGAAACCCUUGGACCAGUGUGGGUGUCCGUUGCGGUGCUACAUUCUCUAAUCUGUAUCACCGGGUGAACACUUGCAGUGGUCCUCGUGGUUUCUGUGAGCCAGGUCCUGUUCCGGUUUUUUCCGUGGUGAUAACGCAUCCAAAAGUCUCUAUCACCGGGAGAAAAACUGGAGUAGGACCUGUGACUCAU

我应该改变哪一部分？

另外，如何将序列作为键和id作为值？

Answer 1

您没有正确地累积哈希值，并且您也没有打印它。

    while (<FILE>) {
        chomp;

        if($_ =~ /^>(.+)/){
            $id = $1;

        } elsif (/^[A-Z]+$/) {
            $seq .= $_;

        } else {
            $fastahash{$id} = $seq;   # Populate the hash.
        }
    }

   for my $id (keys %fastahash) {
      print "$id $fastahash{$id}\n";  # Print it.

   }

Answer 2

我认为，当您应该分配$_时，您需要将$seq分配给fastahash。此外，你永远不会重置id或seq，所以有一个潜在的错误。尝试这样的事情：

while (<FILE>) {
    chomp;

    if (/^>(.+)/) {
        $id = $1;
    } elsif (/^[A-Z]+$/) {
        $seq .= $_;
    } else {
        $fastahash{$id} = $seq if $id;
        $id = undef;
        $seq = '';
    }
}

$fastahash{$id} = $seq if $id;

Answer 3

我意识到这不是代码审核，但我认为对您的代码做一些评论会很有用

在声明变量时，通常不需要定义变量。实际上，如果将标量变量设置为空字符串
最佳做法是使用词法文件句柄和open的三参数形式。所以
```
open FILE, "file.fasta", or die $!;
```
最好写成
```
open my $fh, '<', 'file.fasta' or die $!;
```
（请注意，您的原始代码中也有一个多余的逗号。）

词法文件句柄通常会删除它们close的必要性，因为它们在超出范围时会被销毁时隐式关闭
您可能不熟悉Perl的默认变量$_，但如果使用它，代码可以更清晰，更简洁

您已将其与chomp一起使用，相当于chomp $_，而$_ =~ /^>(.+)/只需/^>(.+)/
请注意，foreach完全等同于for，大多数熟悉Perl的程序员都会更喜欢前者

我会写你的程序

use strict;
use warnings;

open my $fh, '<', 'file.fasta' or die $!;

my %fasta_hash;
my ($id, $seq);

while ( <$fh> ) {

    chomp;

    if ( /^>(.+)/ ) {
        $id = $1;
    }
    elsif ( /\S/ and not /[^ACGTU]/ ) {
        $seq .= $_;
    }
    else {
        $fasta_hash{$id} = $seq;
    }
}

for my $id ( keys %fasta_hash ) {
    print "$id -- $fasta_hash{$id}\n";
}

输出

cel-mir-35 MI0000006 Caenorhabditis elegans miR-35 stem-loop -- UCUCGGAUCAGAUCGAGCCAUUGCUGGUUUCUUCCACAGUGGUACUUUCCAUUAGAACUAUCACCGGGUGGAAACUAGCAGUGGCUCGAUCUUUUCC
cel-mir-37 MI0000008 Caenorhabditis elegans miR-37 stem-loop -- UCUCGGAUCAGAUCGAGCCAUUGCUGGUUUCUUCCACAGUGGUACUUUCCAUUAGAACUAUCACCGGGUGGAAACUAGCAGUGGCUCGAUCUUUUCCCACCGCUGUCGGGGAACCGCGCCAAUUUUCGCUUCAGUGCUAGACCAUCCAAAGUGUCUAUCACCGGGUGAAAAUUCGCAUGGGUCCCCGACGCGGAUUCUAGAAACCCUUGGACCAGUGUGGGUGUCCGUUGCGGUGCUACAUUCUCUAAUCUGUAUCACCGGGUGAACACUUGCAGUGGUCCUCGUGGUUUCU
cel-mir-36 MI0000007 Caenorhabditis elegans miR-36 stem-loop -- UCUCGGAUCAGAUCGAGCCAUUGCUGGUUUCUUCCACAGUGGUACUUUCCAUUAGAACUAUCACCGGGUGGAAACUAGCAGUGGCUCGAUCUUUUCCCACCGCUGUCGGGGAACCGCGCCAAUUUUCGCUUCAGUGCUAGACCAUCCAAAGUGUCUAUCACCGGGUGAAAAUUCGCAUGGGUCCCCGACGCGGA

至于如何反转哈希以便将序列用作键，在我上面的版本中，您只需将行$fasta_hash{$id} = $seq;更改为$fasta_hash{$seq} = $id;

从哈希中获取fasta文件序列

输入

我的输出是

码

3 个答案:

输出