#!/usr/bin/perl

#############################################################################
#retrieve_sequences_from_ncbi.pl
#version 0.1
#Retrieving sequences from NCBI
#Only one request every three seconds!!!
#Copyright (c) 2005 Diego Mauricio Riaño Pachón
#http://www.geocities.com/dmrp.geo
#
#This program is free software; you can redistribute it and/or
#modify it under the terms of the GNU General Public License
#as published by the Free Software Foundation; either version 2
#of the License, or (at your option) any later version.
#
#This program is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License
#along with this program; if not, write to the Free Software
#Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
#############################################################################

use strict;
use warnings;
use diagnostics;
use Getopt::Long;
use LWP::Simple;

my $ids_file='';
my $output='';
my $license='';
my $format='';
my $help='';

GetOptions(
    'ids|i=s' => \$ids_file,
    'output|o=s' => \$output,
    'format|f=s' => \$format,  
    'license|l' => \$license,
    'help|h|?' => \$help
);

if ($ids_file && $output){
    open IN, $ids_file;
    open OUT, ">$output";
    while(my $line=<IN>){
	chomp $line;
	my ($id,$coords)=split(/\t/,$line);
	my $fetch="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$id&retmode=text";
	if(defined($format) && $format ne ""){
	    $fetch.="&rettype=$format";
	}
	else{
	    $fetch.="&rettype=fasta";
	}
	if (defined($coords)){
	    my ($start,$end)=split(/-/,$coords);
	    $fetch.="&seq_start=$start&seq_stop=$end";
	}
	my $result=get($fetch);
	print OUT "$result\n" || die "Cannot write to file $output\n";
	print STDERR "Retrieving sequence id: $id\t". localtime(time)."\n";
	sleep 3;
    }
}
elsif($license){
    &license;
}
else{
    &usage;
}

sub usage{
    print STDERR "$0 version 0.1, Copyright (C) 2005 Diego Mauricio Riaño Pachón\n";
    print STDERR "$0 comes with ABSOLUTELY NO WARRANTY; for details type `$0 -l'.\n";
    print STDERR "This is free software, and you are welcome to redistribute it under certain conditions;\n";
    print STDERR "type `$0 -l' for details.\n";
    print STDERR <<EOF;
NAME
    retrieve_sequences_from_ncbi   Retrieve sequences from NCBI.

USAGE
    retrieve_sequences_from_ncbi -f list_file -o output_file -f format

OPTIONS
    --ids,     -i    File with list of Accession numbers to retrieve.
                     Start and stop position are optional.
                     If they exist they should be just after ID separated by a TAB (e.g. AL161505.2    234-456).
    --output,  -o    Output file
    --format,  -f    Format: fasta, gb, gbwithparts or any other acepted by NCBI\'s efetch 
    --help,    -h    This help
    --license, -l    License.

EOF
    exit;
}

sub license{
    print STDERR <<EOF;

Copyright (C) 2005 Diego Mauricio Riaño Pachón
http://www.geocities.com/dmrp.geo
e-mail: diriano\@gmail.com

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
EOF
exit;
}