source: branches/properties/lib/macros/keep_listed_SAIs.amc

#!/usr/bin/perl
use strict;
use warnings;

# ------------------------------ configure SAIs to keep

# simply enter names of SAIs to remain in the list below.
my @keep =
  (
   '3_prime',
   '5_prime',
   'gap_align',
   'termini',
   'termini_5_3',
   'ECOLI',
   'HELIX',
   'HELIX_NR',
   'E_coli_I_Accessibility',
   'E_coli_II_Accessibility',
   'E_coli_III_Accessibility',
   'E_coli_IV_Accessibility',
   'E_coli_V_Accessibility',
   'Met_Sedu_I_Accessibility',
   'Met_Sedu_II_Accessibility',
   'Met_Sedu_III_Accessibility',
   'MetSedu_IV_Accessibility', # 'MetSedu' here and 'Met_Sedu' above (bug in silva DB?)
   'MetSedu_V_Accessibility',
   'PirStr1_I_Accessibility',
   'PirStr1_II_Accessibility',
   'SaccCer_I_Accessibility',
   'SaccCer_II_Accessibility',
  );



# ------------------------------ configure SAIs to keep [end]

BEGIN {
  if (not exists $ENV{'ARBHOME'}) { die "Environment variable \$ARBHOME has to be defined"; }
  my $arbhome = $ENV{'ARBHOME'};
  push @INC, "$arbhome/lib";
  push @INC, "$arbhome/PERL_SCRIPTS/lib";
  1;
}

use ARB;
use tools;

my $gb_main = ARB::open(":","r");
if (not $gb_main) {
  my $error = ARB::await_error();
  die "$error";
}

die "This script will delete most SAIs from your database.\nTo use, edit it, uncomment this line and save it locally.\nAlso edit list of kept SAIs to fit your needs.";

# ------------------------------ read existing SAIs

dieOnError(ARB::begin_transaction($gb_main), 'begin_transaction');

my $gb_SAIs = ARB::search($gb_main, '/extended_data', 'NONE');
die 'failed to find SAI-data' if not $gb_SAIs;

my @SAIs = ();

for (my $gb_SAI = ARB::entry($gb_SAIs, 'extended'); $gb_SAI; $gb_SAI = ARB::nextEntry($gb_SAI)) {
  my $gb_name = ARB::entry($gb_SAI, 'name');
  die 'SAI lacks name' if not $gb_name;
  my $name = ARB::read_string($gb_name);
  expectError('read name of SAI') if not $name;
  push @SAIs, $name;
}

dieOnError(ARB::commit_transaction($gb_main), 'commit_transaction');

my $SAIs = scalar(@SAIs);
BIO::message($gb_main, "Found $SAIs SAIs");

# ------------------------------ read existing SAIs [end]
# ------------------------------ decide which SAIs to delete

my %keep = map { $_ => 1; } @keep;
my @delete = grep { not defined $keep{$_}; } @SAIs;

my $keep = scalar(@keep);
my $delete = scalar(@delete);
BIO::message($gb_main, "Deleting $delete SAIs ($keep listed as protected)");

# ------------------------------ decide which SAIs to delete [end]

BIO::remote_action($gb_main,'ARB_NT','sai_admin');

my $count = 0;
foreach my $saidel (@delete) {
  ++$count;
  my $percent = int($count/$delete*100.0);
  print "Deleting field $count/$delete ($percent%, '$saidel')\n";
  BIO::remote_awar($gb_main,'ARB_NT','tmp/focus/sai_name', $saidel);
  BIO::remote_action($gb_main,'ARB_NT','INFO_OF_SAI/DELETE');
}

BIO::message($gb_main, "$delete unlisted SAIs have been deleted.");
BIO::message($gb_main, "Check remaining SAIs before you overwrite your database.");

# recording stopped @ Sun Dec 26 11:19:28 2021
ARB::close($gb_main);