#!/usr/bin/env perl

# PURPOSE: wrapper to eutils that allows sequential search and fetch

# EXAMPLES:

# ncbi_eutil -search db=nucleotide term=AC207960 -fetch rettype=qual > AC207960.qual

# ncbi_eutil -search db=protein term='chicken[orgn]+AND+hox' -fetch rettype=fasta retmode=text outfile=Gallus-gallus_NCBI_2006-08-30_HOX.pfa3

# ncbi_eutil -search db=protein term='chicken[orgn]+AND+hox' -fetch rettype=fasta > Gallus-gallus_NCBI_2006-08-30_HOX.pfa3

# ncbi_eutil -search db=protein term='chicken[orgn]+AND+hox' -fetch 1            > Gallus-gallus_NCBI_2006-08-30_HOX.pfa3

use lib qw(/home/mec/local/src/NCBI_PowerScripting);
use strict;
use NCBI_PowerScripting;

use Getopt::Long;

my (%search, %fetch, %post, %fetch, %summary, %uids);
my %params;
my $result=GetOptions(
		      "post=s{,}" => \%post, # typically db, id (could be a filename)
		      "search=s{,}" => \%search, # db, term
		      "fetch:s{,}" => \%fetch, #rettype retmode outfile
		      "summary=s{,}" => \%summary, # outfile
		     );

################################################################################
# SET DEFAULTS
################################################################################

if (%summary) {
  $summary{outfile} ||= '-';
}

if (%fetch) {
  $fetch{outfile} ||= '-';	# instead of 'fetch.out'
  $fetch{rettype} ||= 'fasta';
  $fetch{retmode} ||= 'text';
}

################################################################################
# PROCESS
################################################################################

%params = epost_file(%params, %post) if %post;

%params = esearch(%params, %search) if %search;

if (%uids) {
  my @uids = get_uids(%params);
  foreach (@uids) { print "$_ "; }
  print "\n";
}

%params = efetch_batch(%fetch, %params) if %fetch;

%params = esummary_batch(%summary, %params) if %summary;

exit 0;