getgenbankannot

#!/usr/bin/perl

use strict;
use Getopt::Long;

my %opt;
$opt{tmp} = "/mnt/scratch/tmp/genbank";
GetOptions(\%opt, "field=s@", "xml", "tmp", "gene");

die "usage: getgenbankannot <genbankid>\n" unless @ARGV;

my $id = shift @ARGV;

mkdir($opt{tmp}); chmod(0777, $opt{tmp});

my $p;
if ($id =~ /^\d+$/) {
    $p="$opt{tmp}/$id.gene";
    if ( ! -s $p ) {
        system("wget -q -O - 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=$id&rettype=gb' > $p");
    }
} else {
	$p="$opt{tmp}/$id.gb";
	if ( ! -s $p ) {
		system("wget -q -O - 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$id&rettype=gb' > $p");
	}
}

if ($id =~ /^\d+$/) {
	my @d=slurp($p)=~m/<p class="([^"]+)"[^<>]*>(.*?)<\/p>/g;
	for (my $i=0;$i<@d;$i+=2) {
		$d[$i+1] =~ s/<[^<>]*?>//g;
		$d[$i+1] =~ s/\s+$//;
		next unless $d[$i];
		next unless $d[$i+1];
		print "$d[$i]\t$d[$i+1]\n";
	}
	for (xmltag(slurp($p),'dl')) {
		my $n=xmltag($_, "dt");
		$n =~ s/\s*:\s*//;
		$n = lc($n);
		my $v=xmltag($_, "dd");
		print "$n\t$v\n";
	}
} else {
	for (xmltag(slurp($p),'GBQualifier')) {
		my $n=xmltag($_, "GBQualifier_name");
		my $v=xmltag($_, "GBQualifier_value");
		print "$n\t$v\n";
	}
}


sub slurp {
	local $/=undef;
	open SL, $p;
	return <SL>;
}

sub xmltag {
	my ($x, $t) = @_;
	my @x = $x =~ m{<$t[^<>]*>(.+?)</$t>}gs;
	map s/^\s+//s, @x;
	map s/\s+$//s, @x;
	return wantarray ? @x : $x[0];
}