modified: myjupyterlab.sh

[GalaxyCodeBases.git] / perl / popuSNP / pipeline / Std.pm

package Getopt::Std;
require 5.000;
require Exporter;

=head1 NAME

getopt, getopts - Process single-character switches with switch clustering

=head1 SYNOPSIS

    use Getopt::Std;

    getopt('oDI');    # -o, -D & -I take arg.  Sets $opt_* as a side effect.
    getopt('oDI', \%opts);    # -o, -D & -I take arg.  Values in %opts
    getopts('oif:');  # -o & -i are boolean flags, -f takes an argument
                      # Sets $opt_* as a side effect.
    getopts('oif:', \%opts);  # options as above. Values in %opts

=head1 DESCRIPTION

The getopt() function processes single-character switches with switch
clustering.  Pass one argument which is a string containing all switches
that take an argument.  For each switch found, sets $opt_x (where x is the
switch name) to the value of the argument if an argument is expected,
or 1 otherwise.  Switches which take an argument don't care whether
there is a space between the switch and the argument.

The getopts() function is similar, but you should pass to it the list of all
switches to be recognized.  If unspecified switches are found on the
command-line, the user will be warned that an unknown option was given.

Note that, if your code is running under the recommended C<use strict
'vars'> pragma, you will need to declare these package variables
with "our":

    our($opt_x, $opt_y);

For those of you who don't like additional global variables being created, getopt()
and getopts() will also accept a hash reference as an optional second argument. 
Hash keys will be x (where x is the switch name) with key values the value of
the argument or 1 if no argument is specified.

To allow programs to process arguments that look like switches, but aren't,
both functions will stop processing switches when they see the argument
C<-->.  The C<--> will be removed from @ARGV.

=head1 C<--help> and C<--version>

If C<-> is not a recognized switch letter, getopts() supports arguments
C<--help> and C<--version>.  If C<main::HELP_MESSAGE()> and/or
C<main::VERSION_MESSAGE()> are defined, they are called; the arguments are
the output file handle, the name of option-processing package, its version,
and the switches string.  If the subroutines are not defined, an attempt is
made to generate intelligent messages; for best results, define $main::VERSION.

If embedded documentation (in pod format, see L<perlpod>) is detected
in the script, C<--help> will also show how to access the documentation.

Note that due to excessive paranoia, if $Getopt::Std::STANDARD_HELP_VERSION
isn't true (the default is false), then the messages are printed on STDERR,
and the processing continues after the messages are printed.  This being
the opposite of the standard-conforming behaviour, it is strongly recommended
to set $Getopt::Std::STANDARD_HELP_VERSION to true.

One can change the output file handle of the messages by setting
$Getopt::Std::OUTPUT_HELP_VERSION.  One can print the messages of C<--help>
(without the C<Usage:> line) and C<--version> by calling functions help_mess()
and version_mess() with the switches string as an argument.

=cut

@ISA = qw(Exporter);
@EXPORT = qw(getopt getopts);
$VERSION = '1.05';
# uncomment the next line to disable 1.03-backward compatibility paranoia
# $STANDARD_HELP_VERSION = 1;

# Process single-character switches with switch clustering.  Pass one argument
# which is a string containing all switches that take an argument.  For each
# switch found, sets $opt_x (where x is the switch name) to the value of the
# argument, or 1 if no argument.  Switches which take an argument don't care
# whether there is a space between the switch and the argument.

# Usage:
#       getopt('oDI');  # -o, -D & -I take arg.  Sets opt_* as a side effect.

sub getopt (;$$) {
    my ($argumentative, $hash) = @_;
    $argumentative = '' if !defined $argumentative;
    my ($first,$rest);
    local $_;
    local @EXPORT;

    while (@ARGV && ($_ = $ARGV[0]) =~ /^-(.)(.*)/) {
        ($first,$rest) = ($1,$2);
        if (/^--$/) {   # early exit if --
            shift @ARGV;
            last;
        }
        if (index($argumentative,$first) >= 0) {
            if ($rest ne '') {
                shift(@ARGV);
            }
            else {
                shift(@ARGV);
                $rest = shift(@ARGV);
            }
            if (ref $hash) {
                $$hash{$first} = $rest;
            }
            else {
                ${"opt_$first"} = $rest;
                push( @EXPORT, "\$opt_$first" );
            }
        }
        else {
            if (ref $hash) {
                $$hash{$first} = 1;
            }
            else {
                ${"opt_$first"} = 1;
                push( @EXPORT, "\$opt_$first" );
            }
            if ($rest ne '') {
                $ARGV[0] = "-$rest";
            }
            else {
                shift(@ARGV);
            }
        }
    }
    unless (ref $hash) { 
        local $Exporter::ExportLevel = 1;
        import Getopt::Std;
    }
}

sub output_h () {
  return $OUTPUT_HELP_VERSION if defined $OUTPUT_HELP_VERSION;
  return \*STDOUT if $STANDARD_HELP_VERSION;
  return \*STDERR;
}

sub try_exit () {
    exit 0 if $STANDARD_HELP_VERSION;
    my $p = __PACKAGE__;
    print {output_h()} <<EOM;
  [Now continuing due to backward compatibility and excessive paranoia.
   See ``perldoc $p'' about \$$p\::STANDARD_HELP_VERSION.]
EOM
}

sub version_mess ($;$) {
    my $args = shift;
    my $h = output_h;
    if (@_ and defined &main::VERSION_MESSAGE) {
        main::VERSION_MESSAGE($h, __PACKAGE__, $VERSION, $args);
    } else {
        my $v = $main::VERSION;
        $v = '[unknown]' unless defined $v;
        my $myv = $VERSION;
        $myv .= ' [paranoid]' unless $STANDARD_HELP_VERSION;
        my $perlv = $];
        $perlv = sprintf "%vd", $^V if $] >= 5.006;
        print $h <<EOH;
$0 version $v calling Getopt::Std::getopts (version $myv),
running under Perl version $perlv.
EOH
    }
}

sub help_mess ($;$) {
    my $args = shift;
    my $h = output_h;
    if (@_ and defined &main::HELP_MESSAGE) {
        main::HELP_MESSAGE($h, __PACKAGE__, $VERSION, $args);
    } else {
        my (@witharg) = ($args =~ /(\S)\s*:/g);
        my (@rest) = ($args =~ /([^\s:])(?!\s*:)/g);
        my ($help, $arg) = ('', '');
        if (@witharg) {
            $help .= "\n\tWith arguments: -" . join " -", @witharg;
            $arg = "\nSpace is not required between options and their arguments.";
        }
        if (@rest) {
            $help .= "\n\tBoolean (without arguments): -" . join " -", @rest;
        }
        my ($scr) = ($0 =~ m,([^/\\]+)$,);
        print $h <<EOH if @_;                   # Let the script override this

Usage: $scr [-OPTIONS [-MORE_OPTIONS]] [--] [PROGRAM_ARG1 ...]
EOH
        print $h <<EOH;

The following single-character options are accepted:$help

Options may be merged together.  -- stops processing of options.$arg
EOH
        my $has_pod;
        if ( defined $0 and $0 ne '-e' and -f $0 and -r $0
             and open my $script, '<', $0 ) {
            while (<$script>) {
                $has_pod = 1, last if /^=(pod|head1)/;
            }
        }
        print $h <<EOH if $has_pod;

For more details run
        perldoc -F $0
EOH
    }
}

# Usage:
#   getopts('a:bc');    # -a takes arg. -b & -c not. Sets opt_* as a
#                       #  side effect.

sub getopts ($;$) {
    my ($argumentative, $hash) = @_;
    my (@args,$first,$rest,$exit);
    my $errs = 0;
    local $_;
    local @EXPORT;

    @args = split( / */, $argumentative );
    while(@ARGV && ($_ = $ARGV[0]) =~ /^-(.)(.*)/s) {
        ($first,$rest) = ($1,$2);
        if (/^--$/) {   # early exit if --
            shift @ARGV;
            last;
        }
        my $pos = index($argumentative,$first);
        if ($pos >= 0) {
            if (defined($args[$pos+1]) and ($args[$pos+1] eq ':')) {
                shift(@ARGV);
                if ($rest eq '') {
                    ++$errs unless @ARGV;
                    $rest = shift(@ARGV);
                }
                if (ref $hash) {
                    $$hash{$first} = $rest;
                }
                else {
                    ${"opt_$first"} = $rest;
                    push( @EXPORT, "\$opt_$first" );
                }
            }
            else {
                if (ref $hash) {
                    $$hash{$first} = 1;
                }
                else {
                    ${"opt_$first"} = 1;
                    push( @EXPORT, "\$opt_$first" );
                }
                if ($rest eq '') {
                    shift(@ARGV);
                }
                else {
                    $ARGV[0] = "-$rest";
                }
            }
        }
        else {
            if ($first eq '-' and $rest eq 'help') {
                version_mess($argumentative, 'main');
                help_mess($argumentative, 'main');
                try_exit();
                shift(@ARGV);
                next;
            } elsif ($first eq '-' and $rest eq 'version') {
                version_mess($argumentative, 'main');
                try_exit();
                shift(@ARGV);
                next;
            }
            warn "Unknown option: $first\n";
            ++$errs;
            if ($rest ne '') {
                $ARGV[0] = "-$rest";
            }
            else {
                shift(@ARGV);
            }
        }
    }
    unless (ref $hash) { 
        local $Exporter::ExportLevel = 1;
        import Getopt::Std;
    }
    $errs == 0;
}

1;