#!/usr/local/bin/perl
use strict;
#
##################################################################################
# update_bacteria_ssa  - create/update all relevant bacterial files for SSA server
#
# Species to be treated are derived from the the directory
# expected in bacteria.dir in the source directory.
# The relevant bacterial files are:
# FPS Files
# FPS File List
# PTR File
# Links to bacterial genome sequences (/db/genome/bacteria/*/*.fna)
# SSA Server Web Pages
#
#
# Giovanna Ambrosini   (Feb 2005)
#
# Giovanna Ambrosini - Upgraded on Jan 2013
#

#
# Update Bacterial PTR File
#
open(BAC_PTR_TMP,">bacteria_crptr.inp");
print BAC_PTR_TMP (" 1. FMT=FASTA\n");
print BAC_PTR_TMP (" 2. DIR=/home/local/db/genome/ptr/bac/\n");
print BAC_PTR_TMP (" 3. SEQ=.fna\n");
print BAC_PTR_TMP (" 4. DOC=.fna\n");
print BAC_PTR_TMP (" 5. KEY=3\n");
print BAC_PTR_TMP (" 6. KLN=  16\n");
print BAC_PTR_TMP (" 7. RCL=  71\n");
print BAC_PTR_TMP (" 8. CAS=U\n");
print BAC_PTR_TMP ("..\n");
my @PTT = `ls -1 /home/local/db/genome/bacteria/*_*/*.ptt`;
foreach my $ptt (@PTT) {
  my ($id) = $ptt =~ /.+\/([^\.]+)\.ptt/;
  print BAC_PTR_TMP ("$id\n");
}
print BAC_PTR_TMP ("\n");
close(BAC_PTR_TMP);
system("/home/local/bin/CRPTR bacteria_crptr.inp 2> /dev/null | sort > tmp_bacteria.ptr");
system("cp -f bacteria.ptr bacteria.ptr.old");
system("cp -f tmp_bacteria.ptr bacteria.ptr");