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libsrch.pl
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#!/usr/bin/perl
##$ -clear
#$ -w e
##$ -l arch=glinux -l short=0
#$ -p -50
#$ -S /home/torda/bin/perl
#$ -cwd
#$ -j y
#$ -m e -M torda@zbh.uni-hamburg.de
#$ -q hpc.q
# 18 March 2002
# Most of the other scripts here are for testing with
# deliberately crazy values.
# This one uses the installed, working binary and serious values
# for all parameters.
# rcsid = $Id: libsrch.pl,v 1.18 2005/10/28 11:21:40 torda Exp $
=pod
=head1 NAME
libsrch.pl - Given a structure, align it to a library of templates
=head1 SYNOPSIS
libsrch.pl [options] I<struct_file> I<struct_lib_list> I< S<[ phd_file ]> >
=head1 DESCRIPTION
Given a structure, align it to every member of a library of
templates. The sequence is given by I<struct_file>. The library is
a list of protein names listed in <struct_lib_list>. The last
argument is optional and contains the name of a file with
secondary structure predictions. If it is not present, the script
will look in the directory containing I<struct_file> and strip off
anything that looks like a file extension. Then, it will append
B<.phd> and try to open that (so /boo/bar/1abc.seq gives
/boo/bar/1abc.phd).
If you want to run without secondary structure, it is not enough
to omit the filename. Instead, use the B<-s> option described
below.
=head2 FILE FORMAT
The list of files which make up the template library is in a
simple format. The script will try to read anything that looks
like a four-letter protein name + chain id from the first
column. Leading white space is ignored. A valid form would look
like
1abc_
2qrsB
1xyz This text after first column is ignored
=head2 Changing library and templates.
Typically, a first run will be made with whatever library we are
using. However, one will often want to add extra .bin files
for a particular sequence. To do that,
=over
=item *
Add the new file names to the list of proteins and give it a name
like F<mylist>.
=item *
Make a directory with a name like I<templates> and put the extra
F<.bin> files in there.
=item *
Run the script with the B<-t> option like:
perl libsrch.pl -t templates blahblah.seq mylist
=back
=head2 OPTIONS
=over
=item B<-a> I<N>
Print out details of the best I<N> alignments.
=item B<-d> I<modeldir>
Save final models in I<modeldir> instead of the default
directory, B<modeldir>.
=item B<-h> I<N>
After doing alignments, a default number (maybe 50) will be
printed out. Alternatively, you can ask for the I<N> best scoring
alignments to be printed out.
=item B<-m> I<N>
After alignments, I<N> models will be built, otherwise, a small
default number will appear. Set I<N> to zero if you do not want
any models.
=item B<-s>
Do not use secondary structure predictions. This will cause a
different set of parameters to be used in the calculation.
=item B<-t> I<dir1[,dir2,...]>
Add I<dir1> to the list of places to look for template
files. This is a comma separated list, so you can add more
directories.
=back
=head1 OUTPUT
In all output
=over
=item *
B<SW> refers to the result of the second Smith and Waterman.
=item *
B<NW> refers to the result of the Needleman and Wunsch.
=item *
B<cvr> or B<cover> refers to "coverage". This is the fraction of
sequence residues which are aligned to part of a
structure. Continuing, B<S<sw cvr>> refers to coverage from the
Smith and Waterman calculation.
=item *
The script prints out the coverage in a somewhat pictorial form
which might look like
----XXXXX---XXX
where the X's mean a residue was aligned.
=back
=head1 MODELS
Models will be written in PDB format for the best few
sequences. They will get written to a directory called
F<modeldir>. Maybe this should be made an option.
=head1 OPERATION
Currently the script does
=over
=item Smith and Waterman step 1
This is a locally optimal alignment.
=item Smith and Waterman step 2
This is another locally optimal alignment, but forced to pass
through the same path as the first one. It provides a small
extension to the alignment.
=item Needleman and Wunsch
This is a globally optimal alignment, but forced to pass through
the preceding Smith and Waterman.
=back
=head1 QUESTIONS and CHANGES
=item *
The selection of which scores to print out is a bit arbitrary.
=item *
the coverage picture is very ugly. It could be
beautified.
=item *
The coverage picture corresponds to the Smith and
Waterman. Perhaps it should be the Needleman and
Wunsch. Obviously, both are possible, but just a bit ugly.
=cut
#use lib "$ENV{HOME}/pl/lib/i586-linux-thread-multi"; # Where wurst lives after installation
#use lib "/home/stud2004/tmargraf/pl/lib/i686-linux-thread-multi";
use FindBin;
use lib "$FindBin::Bin/../../wurst/src/Wurst/blib/arch";
use lib "$FindBin::Bin/../../wurst/src/Wurst/blib/lib";
use Wurst;
use vars qw ($MATRIX_DIR $PARAM_DIR
$RS_PARAM_FILE $FX9_PARAM_FILE );
do "$ENV{HOME}/../../torda/c/wurst/scripts/paths.inc" || die $@;
if ($@) {
die "broke reading paths.inc:\n$@"; }
if ( defined ($ENV{SGE_ROOT})) {
$MATRIX_DIR = "$ENV{HOME}/../../torda/c/wurst/matrix";
$PARAM_DIR = "$ENV{HOME}/../../torda/c/wurst/params";
}
use strict;
use POSIX qw(EXIT_SUCCESS EXIT_FAILURE);
# ----------------------- Defaults ---------------------------------
# These are numbers you might reasonably want to change.
# They should (will) be changeable by options.
use vars qw ($N_BRIEF_LIST $N_MODELS $N_ALIGNMENTS);
$N_BRIEF_LIST = 100;
$N_MODELS = 100;
$N_ALIGNMENTS = 100;
use vars qw ($modeldir $DFLT_MODELDIR);
*DFLT_MODELDIR = \ 'modeldir';
$modeldir = $DFLT_MODELDIR;
# ----------------------- Sequence Alignment Constants -----------------------
# These are declared globally, and set by set_params().
use vars qw (
$align_type
$sw1_pgap_open
$sw1_qgap_open
$sw1_pgap_widen
$sw1_qgap_widen
$m_shift
$gauss_err
);
# These parameters will be used for extending alignments via a
# Needleman and Wunsch
use vars qw (
$nw_pgap_open
$nw_qgap_open
$nw_pgap_widen
$nw_qgap_widen
$nw_sec_pnlty
);
use vars qw( @DFLT_STRUCT_DIRS @PROFILE_DIRS
$phd_suffix $bin_suffix $prof_suffix);
*DFLT_STRUCT_DIRS = ['/bm/pdb90_bin'];
*PROFILE_DIRS = ["/bm/pdb90_prof"];
*bin_suffix = \'.bin';
*prof_suffix = \'.prof';
*phd_suffix = \'.phd';
# ----------------------- set_params -----------------------------
# This gets its own function because it can be more complicated
# if, in the future, we have a version depending on various
# options like whether or not we have secondary structure
# information.
# pgap controls penalties in the sequence, qgap in the structure.
sub set_params ()
{
*sw1_pgap_open = \ 3.182;
*sw1_pgap_widen = \ 0.8727;
*sw1_qgap_open = \ $sw1_pgap_open;
*sw1_qgap_widen = \ $sw1_pgap_widen;
*m_shift = \ -0.4954;
*gauss_err = \ 0.4;
*nw_pgap_open = \ $sw1_pgap_open;
*nw_qgap_open = \ $sw1_qgap_open;
*nw_pgap_widen = \ $sw1_pgap_widen;
*nw_qgap_widen = \ $sw1_qgap_widen;
}
# ----------------------- get_prot_list -----------------------------
# Go to the given filename and get a list of proteins from it.
sub get_prot_list ($)
{
my $f = shift;
my @a;
if ( ! open (F, "<$f")) {
print STDERR "Open fail on $f: $!\n";
return undef;
}
while (my $line = <F>) {
chomp ($line);
my @words = split (' ', $line);
if (! defined $words[0]) { next;}
$line = $words[0];
$line =~ s/#.*//; # Toss comments away
$line =~ s/\..*//; # Toss filetypes away
$line =~ s/^ +//; # Leading and
$line =~ s/ +$//; # trailing spaces.
if ($line eq '') {
next; }
substr ($line, 0, 4) = lc (substr ($line, 0, 4)); # 1AGC2 to 1agc2
if (length ($line) == 4) { # Convert 1abc to 1abc_
$line .= '_'; }
push (@a, $line);
}
close (F);
return (@a);
}
# ----------------------- get_path ---------------------------------
# We have a filename and a list of directories where it could
# be. Return the path if we can find it, otherwise return undef.
sub get_path (\@ $)
{
my ($dirs, $fname) = @_;
foreach my $d (@$dirs) {
my $p = "$d/$fname";
if ( -f $p) {
return $p; }
}
return undef;
}
# ----------------------- check_dirs --------------------------------
# Given an array of directory names, check if each one
# exists. Print something if it is missing, but do not give
# up. It could be that there is some crap in the command line
# args, but all the important directories are really there.
# This function is potentially destructive !
# If a directory does not seem to exist, we actually remove it
# from the array we were passed. This saves some futile lookups
# later on.
sub check_dirs (\@)
{
my $a = shift;
my $last = @$a;
for (my $i = 0; $i < $last; $i++) {
if ( ! -d $$a[$i]) {
print STDERR "$$a[$i] is not a valid directory. Removing\n";
splice @$a, $i, 1;
$last--;
$i--;
}
}
}
# ----------------------- check_files -------------------------------
# We are given an array of directories and and array of protein
# names and an extension.
# Check if all the files seem to be there.
sub check_files (\@ \@ $)
{
my ($dirs, $fnames, $ext) = @_;
my $errors = 0;
foreach my $f (@$fnames) {
my $name = "$f$ext";
if (! get_path (@$dirs, $name)) {
$errors++;
print STDERR "Cannot find $name\n";
}
}
return $errors;
}
# ----------------------- usage -----------------------------------
sub usage ()
{
print STDERR "Usage: $0 seq_file struct_file \n";
exit (EXIT_FAILURE);
}
# ----------------------- get_scores --------------------------------
sub get_scores ($ $ $ $)
{
my ($pair_set, $coord1, $coord2, $to_use) = @_;
my ($scr_tot, $coverage, $score1, $geo_gap, $score1_gap);
my ($str1, $crap);
my ($open_cost, $widen_cost, $nseq_gap);
($score1_gap, $score1) = pair_set_score( $pair_set );
($str1, $crap) =
pair_set_coverage ($pair_set, coord_size ($coord1), coord_size ($coord2));
$coverage = ($str1 =~ tr/1//); # This is coverage as an integer
$coverage = $coverage / seq_size (coord_get_seq($coord1)); #and as fraction of query structure
my ($k_scr2, $k_gap_geo, $k_seq_gap, $k_str_gap, $k_str_wdn);
if ($coverage < .05 ) {
$geo_gap = 0;
$nseq_gap = 0;
$open_cost = 0;
$widen_cost = 0;
} else {
($open_cost, $widen_cost) = pair_set_gap($pair_set, 1, 1);
}
$k_str_gap = 2 * $sw1_pgap_open;
$k_str_wdn = 2 * $sw1_pgap_widen;
$scr_tot = $score1 +
$k_str_gap * $open_cost +
$k_str_wdn * $widen_cost;
return ( $scr_tot, $coverage, $score1, $score1_gap,
$nseq_gap, $open_cost);
}
# ----------------------- bad_exit ----------------------------------
# This will run in a server, so if something goes wrong, we
# should at least mail back an indication. The single parameter
# should be the error message returned by the function which was
# unhappy.
# Should we print to stderr or stdout ?
# This should not matter since we have grabbed both file handles.
sub bad_exit ( $ )
{
my $msg = shift;
print STDERR "Error: \"$msg\"\n";
exit (EXIT_FAILURE);
}
# ----------------------- get_alt_scores ---------------------------------
# calculates scores on random paths through the scoring matrix
# parameters: number_of_paths/scores, scoring_matrix, pair_set_of_optimal_path
# return: the scores
sub get_alt_scores($ $ $)
{
my ($num_scrs, $scr_mat, $pair_set) = @_;
my @scr_fin;
for (my $i = 0; $i < $num_scrs; $i++) {
$scr_fin[$i] = find_alt_path_score_simple ($scr_mat, $pair_set); }
return \@scr_fin;
}
# ----------------------- normalize_alt_scores ------------------------------
#
sub normalize_alt_scores($)
{
my ($scrs_ref) = @_;
my $mean = 0.0;
foreach my $scr (@{$scrs_ref}) {
$mean += $scr }
$mean /= @$scrs_ref;
my $deviation = 0.0;
foreach my $scr (@$scrs_ref) {
my $tmp = $scr - $mean;
$deviation += ($tmp * $tmp);
}
$deviation /= (@$scrs_ref - 1);
$deviation = sqrt($deviation);
return ($mean, $deviation);
}
# ----------------------- get_dme_thresh ----------------------------
# Given an alignment and two proteins, return the thresholded DME
sub get_dme_thresh ($ $ $)
{
my ($pair_set, $c1, $c2) = @_;
my $model = make_model ($pair_set, coord_get_seq ($c1), $c2);
if (coord_size($model) < 10) {
return 0.0;}
my $frac;
if ( ! dme_thresh ($frac, $model, $c1, 4.0)){
print STDERR "dme_thresh broke.\n"; }
return ($frac);
}
# ----------------------- do_align ----------------------------------
# This does the alignment. Although it takes secondary structure
# data as an argument, we are not yet using this in our server
# script.
sub do_align ($ $ $)
{
my ($coord1, $coord2, $classfcn)
= @_;
# my($coord1, $coord2, $pvec1, $pvec2) = @_;
my $seq_ptr1 = coord_get_seq($coord1);
my $seq_ptr2 = coord_get_seq($coord2);
# calc prob vectors
my $pvec1 = struct_2_prob_vec($coord1, $classfcn);
my $pvec2 = struct_2_prob_vec($coord2, $classfcn);
# build score matrix
my $matrix = score_mat_new(seq_size($seq_ptr1), seq_size($seq_ptr2));
score_pvec($matrix, $pvec1, $pvec2);
$matrix = score_mat_shift ($matrix, $m_shift);
my ($sw_scr_tot, $sw_coverage, $sw_score1, $sw_score1_gap,
$sw_seq_gap, $sw_strct_gap);
my ($nw_scr_tot, $nw_coverage, $nw_score1, $nw_score1_gap,
$nw_seq_gap, $nw_strct_gap);
my $sw_pair_set =
score_mat_sum_smpl (my $crap_mat, $matrix,
$sw1_pgap_open, $sw1_pgap_widen,
$sw1_qgap_open, $sw1_qgap_widen,
$S_AND_W);
($sw_scr_tot, $sw_coverage, $sw_score1, $sw_score1_gap, $sw_seq_gap, $sw_strct_gap) =
get_scores ($sw_pair_set, $coord1, $coord2, 's_and_w');
my $frac_dme = get_dme_thresh ($sw_pair_set, $coord1, $coord2);
my $num_scrs = 1000;
my $alt_scrs_ref =
get_alt_scores($num_scrs, $matrix, $sw_pair_set);
my ($mean, $deviation) = normalize_alt_scores($alt_scrs_ref);
undef ($alt_scrs_ref);
my $z_scr;
if ($deviation != 0) {
$z_scr = ($sw_scr_tot - $mean) / $deviation; }
else {
$z_scr = 0.0; } # Should not really happen
# If the alignment is tiny, one can get a ridiculous z-score
if ($sw_coverage < 0.03) { # silently wipe these guys out
$z_scr = 0.0; }
my $sec_strct_pnlty = 0.0;
my $nw_pair_set =
score_mat_sum_sec (my $result_mat2, $matrix,
$coord2, $sec_strct_pnlty,
$nw_pgap_open, $nw_pgap_widen,
$nw_qgap_open, $nw_qgap_widen,
$N_AND_W, $sw_pair_set);
($nw_scr_tot, $nw_coverage, $nw_score1, $nw_score1_gap,
$nw_seq_gap, $nw_strct_gap) =
get_scores ($nw_pair_set, $coord1, $coord2, 'n_and_w');
my @r =
($sw_scr_tot, $nw_pair_set, $nw_scr_tot,
$sw_coverage, $nw_coverage, $sw_score1,
$nw_score1, $sw_pair_set, $z_scr, $frac_dme);
return (\@r);
}
# ----------------------- zero_shift_mat ----------------------------
# This shifts a substitution matrix, not an alignment score matrix.
sub zero_shift_mat ($ $)
{
my ($sub_mat, $shift) = @_;
for (my $i = 0; $i < 20; $i++) {
for (my $j = $i; $j < 20 ; $j++) {
my $t = sub_mat_get_by_i ($sub_mat, $i, $j) + $shift;
sub_mat_set_by_i ($sub_mat, $i, $j, $t);
}
}
}
# ----------------------- do_lib -----------------------------------
# Walk over a library, doing alignments and saving interesting
# scores. The definition of interesting is a bit arbitrary.
# There is one very non-obvious coding trick. We need to be able
# to pass the score information into the sorting functions. We
# could put everything into a big, two-dimensional array, but we
# can avoid copying data. Instead, we invent a package and put
# results into @r::r. The downside is that we have to manually
# free it up at the end by calling undef().
# The $formatflag argument is used for cases like the livebench
# server for whom we have to do a bit of file re-writing.
sub do_lib (\@ \@ $ $ $)
{
my ($structlist, $struct_dirs, $query_struct, $title, $formatflag) = @_;
my (@pair_sets);
my $classfile = '/home/torda/protstrct/gundolf/phipsi6c/r6.influ-o-data-1';
my $classfcn = get_clssfcn($classfile, $gauss_err);
my ($coord1, $coord2);
$coord1 = $query_struct;
for (my $i = 0; $i < @$structlist ; $i++) {
$coord2 = coord_read(get_path (@$struct_dirs, $$structlist[$i] . $bin_suffix));
$r::r[$i] = do_align ($coord1, $coord2, $classfcn);
}
my @indices;
for ( my $i = 0; $i < @$structlist; $i++) {
$indices[$i] = $i; }
@indices = sort {
$r::r[$b][9] <=> $r::r[$a][9];
} @indices;
print "\n",
"sw refers to Smith and Waterman alignment, nw refers to Needleman & Wunsch\n",
"z scr : the z-score of the alignment with 1000 alternative alignments\n",
"sw scr: the combined results of score function + gaps for sw alignment\n",
"sw cvr: coverage (fraction of sequence) accounted for by sw alignment\n",
"nw cvr: coverage accounted for by nw alignment\n",
"sw1 : score of sw alignment in first score function\n",
"nw2 : score of nw alignment in second score function\n",
"____________ Summary of best templates _________________________________\n";
my $todo = (@$structlist > $N_BRIEF_LIST ? $N_BRIEF_LIST : @$structlist);
printf "%8s %8s %8s %8s %6s %6s %8s %8s\n",
'struct', 'z scr', 'f_dme', 'sw scr', 'sw cvr', 'nw cvr', 'sw1', 'nw1';
for (my $i = 0; $i < $todo; $i++) {
my $idx = $indices [$i];
my $a = $r::r[$idx];
printf "%8s %8.3g %8.3g %8.1f %6.2f %6.2g %8.2g %8.2g\n",
$$structlist[$idx],
$$a[8], $$a[9], $$a[0], $$a[3], $$a[4],
$$a[5], $$a[6];
}
print "\n";
# If the sequence is not too big, this output is informative.
# If the output is too big, the long lines cause errors !
if ( coord_size ($coord1) > 550) {
print "Sequence length ", coord_size ($coord1), " too big.\n",
"Not going to print out \"Summary of coverage of query structure\"\n";
} else {
print
"____________ Summary of coverage of query structure _______________________\n";
for (my $i = 0; $i < $todo; $i++) {
my $idx = $indices [$i];
my $a = $r::r[$idx];
my $csize =
coord_size ( coord_read (
get_path (@$struct_dirs, $$structlist[$idx] . $bin_suffix)));
my ($str, $crap) =
pair_set_coverage ($$a[7], coord_size ($coord1), $csize);
print "S & W coverage with $$structlist[$idx]\n";
$str =~ s/1/X/g;
$str =~ s/0/\-/g;
print $str, "\n";
}
}
$todo = (@$structlist > $N_ALIGNMENTS ? $N_ALIGNMENTS : @$structlist);
print "\n",
"____________ Best detailed alignments ______________________________\n";
if ( -d $modeldir) {
print "Directory $modeldir exists. Adding new models.\n"; }
else {
if ( ! mkdir("$modeldir",0777)) {
bad_exit( "Fail create modeldir ($modeldir): $!"); } }
my $p1 = coord_name ($coord1);
my $pdb1 = "$modeldir/${p1}.pdb";
#coord_2_pdb ($pdb1, $coord1);
for (my $i = 0; $i < $todo; $i++) {
my $idx = $indices [$i];
my $f = $$structlist[$idx];
my $structfile = get_path (@$struct_dirs, $f . $bin_suffix);
my $pair_set = $r::r[$idx][7];
my $coord2 = coord_read ($structfile) || bad_exit ("from coord_read");
my ($score, $sw_cvr, $nw_cvr);
my $a = $r::r[$idx];
print
"__________________________________________________________________________\n",
"Alignment to $$structlist[$idx]\n";
($score, $sw_cvr, $nw_cvr) = ($$a[8], $$a[3], $$a[4]);
printf "z-score is %.4g sw cover: %.2f nw cover %.2f\n",
$score, $sw_cvr, $nw_cvr;
print pair_set_pretty_string ($pair_set, coord_get_seq ($coord1), coord_get_seq ($coord2));
my $p2 = $f;
my $chim_out="${p1}_${p2}.com";
if ( ! (open (CHIM, ">$chim_out"))) {
warn "Fail opening $chim_out\n";
return EXIT_FAILURE; }
print CHIM "close all\n";
print CHIM "open modeldir/$p1.pdb\n";
print CHIM "open modeldir/$p2.pdb\n";
print CHIM pair_set_chimera ($pair_set, $coord1, $coord2);
close (CHIM);
my $pdb2 = "$modeldir/${p2}.pdb";
#coord_2_pdb ($pdb2, $coord2); # check return value - fix me
my $rmsd = 0.0;
($rmsd, $coord1, $coord2) = coord_rmsd($pair_set, $coord1, $coord2, 0);
if($coord1 != 0){
print "rmsd: $rmsd\n";
coord_2_pdb ($pdb1, $coord1);
coord_2_pdb ($pdb2, $coord2);
}}
undef (@r::r);
return EXIT_SUCCESS;
}
# ----------------------- mymain -----------------------------------
# Arg 1 is a structure file. Arg 2 is a structure list file.
sub mymain ()
{
use Getopt::Std;
my (%opts);
my (@struct_list, @struct_dirs);
my ($structfile, $libfile);
my $fatalflag = undef;
@struct_dirs = @DFLT_STRUCT_DIRS;
if ( !getopts ('a:d:h:m:t:', \%opts)) {
usage(); }
if ( defined ( $opts { a })) {$N_ALIGNMENTS = $opts { a }}
if ( defined ( $opts { d })) {$modeldir = $opts { d }}
if ( defined ( $opts { h })) {$N_BRIEF_LIST = $opts { h }}
if ( defined ( $opts { m })) {$N_MODELS = $opts { m }}
if ( defined ( $opts { t })) {push (@struct_dirs,split( ',', $opts { t }))}
undef %opts;
set_params ();
if ( $#ARGV < 0) {
print STDERR "Must have at least a query structure file\n";
usage(); }
if ( $#ARGV < 1) {
print STDERR "Please give me a structure library / file\n";
usage();
}
my $query_struct = coord_read($ARGV[0]);
$libfile = $ARGV[1];
check_dirs (@struct_dirs);
if (@struct_dirs == 0) {
die "\nNo valid structure directory. Stopping.\n"; }
(@struct_list = get_prot_list($libfile)) || $fatalflag++;
check_files (@struct_dirs, @struct_list, $bin_suffix) && $fatalflag++;
if ($fatalflag) {
print STDERR "struct dirs were @struct_dirs\n"; }
if ( $fatalflag) {
print STDERR "Fatal problems\n";
return EXIT_FAILURE;
}
print
"Library from $libfile with ", $#struct_list + 1,
" template structures\n",
"Brief results printed for $N_BRIEF_LIST templates\n",
"Long alignments printed for $N_ALIGNMENTS templates\n",
"Models made for the best $N_MODELS models and put in $modeldir\n";
print "Sequence read from \'$structfile\' with length ",
seq_size (coord_get_seq ($query_struct)),
" residues\n";
my $title = 'temp title test';
my $formatflag = 'not set';
my $r = do_lib (@struct_list , @struct_dirs, $query_struct,
$title, $formatflag);
if ($r == EXIT_FAILURE) {
bad_exit ('calculation broke') }
print
"__________________________________________________________________________\n",
"Wurst gegessen at ", scalar (localtime()), "\n";
my ($user, $system, $crap, $crap2, $host);
($user, $system, $crap, $crap2) = times();
printf "I took %d:%d min user and %.0f:%.0f min sys time\n",
$user / 60, $user % 60, $system / 60, $system % 60;
use Sys::Hostname;
$host = hostname() || {$host = 'no_host'};
print "Run on $host\n";
return EXIT_SUCCESS;
}
# ----------------------- main -----------------------------------
exit (mymain());