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根据Accession id下载NCBI基因组

发布时间 2023-11-01 15:08:02作者: 天使不设防

usage：
image
脚本就不注释了，会perl的都看得懂；测试了下，速度感人OTZ，淦！

#!/usr/bin/env perl
use strict;
use warnings;
use Cwd qw/getcwd/;
use Getopt::Long;
use Net::FTP;
use feature 'say';

my @argv = @ARGV;
my $version = "0.1.0";
my $outdir ||= getcwd();
my ($input,$list,$all,$help,$ver);

my $HOST = "ftp.ncbi.nlm.nih.gov";
&usage() unless  GetOptions(
	"i|input=s" =>\$input,
	"l|list=s" => \$list,
	"a|all" => \$all,
	"o|outdir=s" =>\$outdir,
	"h|help" => \$help,
	"v|version" => \$ver,
);


sub usage{
	say <<USAGE;

USAGE: $0 [OPTIONS]

OPTIONS:
    -i, --input   <String>    Set accession id, can't use with option --list
    -l, --list    <String>    Accession id list file, one id per line and no blankline, can't use with option --input
    -a, --all     <Flag>      If specified, download all files
    -o, --outdir  <String>    Set output dir, default: [$outdir]
    -h, --help    <Flag>      Show this help
    -v, --version <Flag>      Show version
USAGE
	exit -1;
}


&usage() if $help || @argv == 0;
say "Version: $version"  if defined $ver;
die "Error: option --input can't use with option --list\n" if $input && $list;
say "Info: the output directory:[$outdir] does not exist, building...\n" unless -e $outdir;

unless(-e $outdir){
	mkdir $outdir;
}


my $ftp = Net::FTP->new($HOST);
$ftp->login() or die "Cannot login \n", $ftp->message;

if($input){
	chdir $outdir;
	&download($input, $all);
}

if($list){
	open F,"$list" || die "can't open file $list";
	chdir $outdir;
	while(<F>){
		chomp;
		next if /^\s*$/;
		&download($_, $all);
	}
	close F;
}


sub download {
	my $input = shift;
	my $all = shift;
	my $url = &get_url($input);

	my @acc_dirs = $ftp->ls($url);
	my $last_version = $acc_dirs[-1];
	my $pre = (split /_/,$last_version)[-1];
	say $pre;
	my $fna = $pre."_genomic.fna.gz";
	my $gff = $pre."_genomic.gff.gz";

	my @all = $ftp->ls($last_version);
	my @select = $all ? @all : grep {$_ =~/($fna|$gff)$/ } @all;
	foreach my $k(@select){
		say "downloading ... $k";
		$ftp->get($k) or die "get failed", $ftp->message;
	}
	
	$ftp->quit;
}


sub get_url {
	my $name = shift;
	my ($gcty, $gcid) = (split /_/,$name)[0,1];
	my ($id, $subid) = (split /\./,$gcid)[0,1];
	my @part_num = $id =~/\d{3}/g;
	my $url = "/genomes/all/$gcty/". join("/",@part_num);

	return $url
}