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#!/usr/bin/perl
use strict 'vars';
use lib '..','../blib/lib','.','./blib/lib';
use Boulder::Stream;
use Boulder::Genbank;
use Getopt::Long;
use Text::Abbrev;
my ($ACCESSOR,$DELAY,$FIRST,$BOULDER,$DB);
GetOptions('accessor=s' => \$ACCESSOR,
'boulder' =>\$BOULDER,
'db=s' => \$DB,
'delay=i' => \$DELAY) || die <<USAGE;
Usage: $0 [options] [accession] [accession] ...
Retrieves Genbank entries from a list of accession
numbers. If no accession numbers are present on the
command line, or if the magic "-" argument is given,
will read accession numbers from standard in.
Outputs a series of Genbank records for each accession
number.
Options:
-accessor <Entrez|Yank> Use the Entrez|Yank methods
for retrieving records.
-boulder Return boulder format file
-db Database
-delay <seconds> Seconds to sleep between retrievals (10)
Options may be abbreviated, i.e. -acc E
Database specifiers:
m MEDLINE
p Protein
n Nucleotide
t 3-D structure
c Genome
USAGE
;
$ACCESSOR ||= 'Entrez';
unless (defined $DELAY) {
warn "Warning: No -delay parameter. Introducing a 1 second delay between fetches\n";
$DELAY = 1;
}
my @accession_numbers;
my $from_stdin = !@ARGV;
my $abbrev = abbrev qw(Entrez Yank entrez yank);
my $accessor = $abbrev->{$ACCESSOR} || die "Unknown access method $ACCESSOR";
substr($accessor,0,1)=~tr/a-z/A-Z/; #canonicalize
while (defined (my $a = shift)) {
$from_stdin++,last if $a eq '-';
push(@accession_numbers,$a);
}
if ($from_stdin) {
while (<>) {
chomp;
next if /^\#/;
my ($a) = /^(\w+)/;
next unless $a;
push(@accession_numbers,$a);
}
}
$DB ||= 'n';
my $stream = new Boulder::Stream;
my $gb = new Boulder::Genbank(-accessor=>$accessor,-fetch=>\@accession_numbers,-db=>$DB)
|| die "Couldn't open new Boulder::Genbank object";
my $count;
while (1) {
last if $count++ > @accession_numbers;
next unless my $s = $gb->get;
sleep $DELAY if $FIRST++ && $DELAY > 0;
unless ($BOULDER) {
print $s->Blob,"//\n";
} else {
$stream->put($s);
}
}
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