perl - Perl 中未定义的子例程和主要错误

Question

我正在尝试从该 FASTA 文件中提取 DNA 序列，使其达到每行指定的碱基长度，例如 40。

> sample dna  (This is a typical fasta header.)
agatggcggcgctgaggggtcttgggggctctaggccggccacctactgg
tttgcagcggagacgacgcatggggcctgcgcaataggagtacgctgcct
gggaggcgtgactagaagcggaagtagttgtgggcgcctttgcaaccgcc
tgggacgccgccgagtggtctgtgcaggttcgcgggtcgctggcgggggt

使用此 Perl 模块 (fasta.pm):

package fasta;
use strict;

sub read_fasta ($filename) {
    my $filename = @_;
    open (my $FH_IN, "<", $filename) or die "Can't open file: $filename $!";
    my @lines = <$FH_IN>;
    chomp @lines;
    return @lines;
}

sub read_seq (\@lines) {
    my $linesRef = @_;
    my @lines = @{$linesRef};
    my @seq;
    foreach my $line (@lines) {
        if ($line!~ /^>/) {
            print "$line\n";
            push (@seq, $line);
        }
    }
    return @seq;
}

sub print_seq_40 (\@seq) {
    my $linesRef = @_;
    my @lines = @{$linesRef};
    my $seq;
    foreach my $line (@lines) {
        $seq = $seq.$line;
    }

    my $i= 0;
    my $seq_line;
    while (($i+1)*40 < length ($seq)) {
        my $seq_line = substr ($seq, $i*40, 40);
        print "$seq_line\n";
        $i++;
    }
    $seq_line = substr ($seq, $i*40);
    print "$seq_line\n";
}
1;

主要脚本是

use strict;
use warnings;
use fasta;

print "What is your filename: ";
my $filename = <STDIN>;
chomp $filename;

my @lines = read_fasta ($filename);
my @seq = read_seq (\@lines);
print_seq_40 (\@seq);
exit;

这是我得到的错误

Undefined subroutine &main::read_fasta called at q2.pl line 13, <STDIN> line 1.

谁能告诉我我哪里做错了？

Answer 1

看起来你在这方面毫无进展。

我认为您选择使用模块和子例程有点奇怪，因为您只调用每个子例程一次并且确实对应很少的代码。

你的程序和模块都需要以use strict和use warnings开始，并且你不能使用像Perl子例程中那样的原型(prototype)。包括许多其他错误，这更接近您需要的代码。

package Fasta;

use strict;
use warnings;
use 5.010;
use autodie;

use base 'Exporter';

our @EXPORT = qw/ read_fasta read_seq print_seq_40 /;

sub read_fasta {
  my ($filename) = @_;

  open my $fh_in, '<', $filename;
  chomp(my @lines = <$fh_in>);

  @lines;
}

sub read_seq {
  my ($lines_ref) = $_[0];

  grep { not /^>/ } @$lines_ref;
}

sub print_seq_40 {
  my ($lines_ref) = @_;

  print "$_\n" for unpack '(A40)*', join '', @$lines_ref;
}

1;

q2.pl

use strict;
use warnings;

use Fasta qw/ read_fasta read_seq print_seq_40 /;

print "What is your filename: ";
my $filename = <STDIN>;
chomp $filename;

my @lines = read_fasta($filename);
my @seq = read_seq(\@lines);
print_seq_40(\@seq);