/usr/share/perl5/Bio/Tools/Run/WrapperBase.pm is in libbio-perl-run-perl 1.7.1-3.
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# BioPerl module for Bio::Tools::Run::WrapperBase
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables
=head1 SYNOPSIS
# do not use this object directly, it provides the following methods
# for its subclasses
my $errstr = $obj->error_string();
my $exe = $obj->executable();
$obj->save_tempfiles($booleanflag)
my $outfile= $obj->outfile_name();
my $tempdir= $obj->tempdir(); # get a temporary dir for executing
my $io = $obj->io; # Bio::Root::IO object
my $cleanup= $obj->cleanup(); # remove tempfiles
$obj->run({-arg1 => $value});
=head1 DESCRIPTION
This is a basic module from which to build executable wrapper modules.
It has some basic methods to help when implementing new modules.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of
the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 CONTRIBUTORS
Sendu Bala, bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Run::WrapperBase;
use strict;
# Object preamble - inherits from Bio::Root::Root
use base qw(Bio::Root::Root);
use File::Spec;
use File::Path qw(); # don't import anything
=head2 run
Title : run
Usage : $wrapper->run({ARGS HERE});
Function: Support generic running with args passed in
as a hashref
Returns : Depends on the implementation, status OR data
Args : hashref of named arguments
=cut
sub run {
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 error_string
Title : error_string
Usage : $obj->error_string($newval)
Function: Where the output from the last analysis run is stored.
Returns : value of error_string
Args : newvalue (optional)
=cut
sub error_string{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_error_string'} = $value;
}
return $self->{'_error_string'} || '';
}
=head2 arguments
Title : arguments
Usage : $obj->arguments($newval)
Function: Commandline parameters
Returns : value of arguments
Args : newvalue (optional)
=cut
sub arguments {
my ($self,$value) = @_;
if(defined $value) {
$self->{'_arguments'} = $value;
}
return $self->{'_arguments'} || '';
}
=head2 no_param_checks
Title : no_param_checks
Usage : $obj->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
=cut
sub no_param_checks{
my ($self,$value) = @_;
if( defined $value || ! defined $self->{'no_param_checks'} ) {
$value = 0 unless defined $value;
$self->{'no_param_checks'} = $value;
}
return $self->{'no_param_checks'};
}
=head2 save_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function: Get/set the choice of if tempfiles in the temp dir (see tempdir())
are kept or cleaned up. Default is '0', ie. delete temp files.
NB: This must be set to the desired value PRIOR to first creating
a temp dir with tempdir(). Any attempt to set this after tempdir creation will get a warning.
Returns : boolean
Args : none to get, boolean to set
=cut
sub save_tempfiles{
my $self = shift;
my @args = @_;
if (($args[0]) && (exists ($self->{'_tmpdir'}))) {
$self->warn ("Tempdir already created; setting save_tempfiles will not affect cleanup behavior.");
}
return $self->io->save_tempfiles(@_);
}
=head2 outfile_name
Title : outfile_name
Usage : my $outfile = $wrapper->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
=cut
sub outfile_name{
my ($self,$nm) = @_;
if( defined $nm || ! defined $self->{'_outfilename'} ) {
$nm = 'mlc' unless defined $nm;
$self->{'_outfilename'} = $nm;
}
return $self->{'_outfilename'};
}
=head2 tempdir
Title : tempdir
Usage : my $tmpdir = $self->tempdir();
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args : none
=cut
sub tempdir{
my ($self) = shift;
$self->{'_tmpdir'} = shift if @_;
unless( $self->{'_tmpdir'} ) {
$self->{'_tmpdir'} = $self->io->tempdir(CLEANUP => ! $self->save_tempfiles );
}
unless( -d $self->{'_tmpdir'} ) {
mkdir($self->{'_tmpdir'},0777);
}
return $self->{'_tmpdir'};
}
=head2 cleanup
Title : cleanup
Usage : $wrapper->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none
=cut
sub cleanup{
my ($self) = @_;
$self->io->_io_cleanup();
if( defined $self->{'_tmpdir'} && -d $self->{'_tmpdir'} ) {
my $verbose = ($self->verbose >= 1) ? 1 : 0;
File::Path::rmtree( $self->{'_tmpdir'}, $verbose);
}
}
=head2 io
Title : io
Usage : $obj->io($newval)
Function: Gets a Bio::Root::IO object
Returns : Bio::Root::IO object
Args : none
=cut
sub io{
my ($self) = @_;
unless( defined $self->{'io'} ) {
$self->{'io'} = Bio::Root::IO->new(-verbose => $self->verbose);
}
return $self->{'io'};
}
=head2 version
Title : version
Usage : $version = $wrapper->version()
Function: Returns the program version (if available)
Returns : string representing version of the program
Args : [Optional] value to (re)set version string
=cut
sub version{
my ($self,@args) = @_;
return;
}
=head2 executable
Title : executable
Usage : my $exe = $factory->executable();
Function: Finds the full path to the executable
Returns : string representing the full path to the exe
Args : [optional] name of executable to set path to
[optional] boolean flag whether or not warn when exe is not found
=cut
sub executable {
my ($self, $exe, $warn) = @_;
if (defined $exe) {
$self->{'_pathtoexe'} = $exe;
}
unless( defined $self->{'_pathtoexe'} ) {
my $prog_path = $self->program_path;
if ($prog_path) {
if (-f $prog_path && -x $prog_path) {
$self->{'_pathtoexe'} = $prog_path;
}
elsif ($self->program_dir) {
$self->warn("executable not found in $prog_path, trying system path...") if $warn;
}
}
unless ($self->{'_pathtoexe'}) {
my $exe;
if ( $exe = $self->io->exists_exe($self->program_name) ) {
$self->{'_pathtoexe'} = $exe;
}
else {
$self->warn("Cannot find executable for ".$self->program_name) if $warn;
$self->{'_pathtoexe'} = undef;
}
}
}
# bail if we never found the executable
unless ( defined $self->{'_pathtoexe'}) {
$self->throw("Cannot find executable for ".$self->program_name .
". path=\"".$self->program_path."\"");
}
return $self->{'_pathtoexe'};
}
=head2 program_path
Title : program_path
Usage : my $path = $factory->program_path();
Function: Builds path for executable
Returns : string representing the full path to the exe
Args : none
=cut
sub program_path {
my ($self) = @_;
my @path;
push @path, $self->program_dir if $self->program_dir;
push @path, $self->program_name.($^O =~ /mswin/i ? '.exe' : '') if $self->program_name;
return File::Spec->catfile(@path);
}
=head2 program_dir
Title : program_dir
Usage : my $dir = $factory->program_dir();
Function: Abstract get method for dir of program. To be implemented
by wrapper.
Returns : string representing program directory
Args : none
=cut
sub program_dir {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 program_name
Title : program_name
Usage : my $name = $factory->program_name();
Function: Abstract get method for name of program. To be implemented
by wrapper.
Returns : string representing program name
Args : none
=cut
sub program_name {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 quiet
Title : quiet
Usage : $factory->quiet(1);
if ($factory->quiet()) { ... }
Function: Get/set the quiet state. Can be used by wrappers to control if
program output is printed to the console or not.
Returns : boolean
Args : none to get, boolean to set
=cut
sub quiet {
my $self = shift;
if (@_) { $self->{quiet} = shift }
return $self->{quiet} || 0;
}
=head2 _setparams()
Title : _setparams
Usage : $params = $self->_setparams(-params => [qw(window evalue_cutoff)])
Function: For internal use by wrapper modules to build parameter strings
suitable for sending to the program being wrapped. For each method
name supplied, calls the method and adds the method name (as modified
by optional things) along with its value (unless a switch) to the
parameter string
Example : $params = $self->_setparams(-params => [qw(window evalue_cutoff)],
-switches => [qw(simple large all)],
-double_dash => 1,
-underscore_to_dash => 1);
If window() and simple() had not been previously called, but
evalue_cutoff(0.5), large(1) and all(0) had been called, $params
would be ' --evalue-cutoff 0.5 --large'
Returns : parameter string
Args : -params => [] or {} # array ref of method names to call,
or hash ref where keys are method names and
values are how those names should be output
in the params string
-switches => [] or {}# as for -params, but no value is printed for
these methods
-join => string # define how parameters and their values are
joined, default ' '. (eg. could be '=' for
param=value)
-lc => boolean # lc() method names prior to output in string
-dash => boolean # prefix all method names with a single dash
-double_dash => bool # prefix all method names with a double dash
-mixed_dash => bool # prefix single-character method names with a
# single dash, and multi-character method names
# with a double-dash
-underscore_to_dash => boolean # convert all underscores in method
names to dashes
=cut
sub _setparams {
my ($self, @args) = @_;
my ($params, $switches, $join, $lc, $d, $dd, $md, $utd) =
$self->_rearrange([qw(PARAMS
SWITCHES
JOIN
LC
DASH
DOUBLE_DASH
MIXED_DASH
UNDERSCORE_TO_DASH)], @args);
$self->throw('at least one of -params or -switches is required') unless ($params || $switches);
$self->throw("-dash, -double_dash and -mixed_dash are mutually exclusive") if (defined($d) + defined($dd) + defined($md) > 1);
$join ||= ' ';
my %params = ref($params) eq 'HASH' ? %{$params} : map { $_ => $_ } @{$params};
my %switches = ref($switches) eq 'HASH' ? %{$switches} : map { $_ => $_ } @{$switches};
my $param_string = '';
for my $hash_ref (\%params, \%switches) {
while (my ($method, $method_out) = each %{$hash_ref}) {
my $value = $self->$method();
next unless (defined $value);
next if (exists $switches{$method} && ! $value);
$method_out = lc($method_out) if $lc;
my $method_length = length($method_out) if $md;
$method_out = '-'.$method_out if ($d || ($md && ($method_length == 1)));
$method_out = '--'.$method_out if ($dd || ($md && ($method_length > 1)));
$method_out =~ s/_/-/g if $utd;
if ( exists $params{$method} ) {
# if value are quoted with " or ', re-quote it
if ( $value =~ m{^[\'\"]+(.+)[\'\"]+$} ) {
$value = '"'. $1 . '"';
}
# quote values that contain spaces
elsif ( $value =~ m{\s+} ) {
$value = '"'. $value . '"';
}
}
$param_string .= ' '.$method_out.(exists $switches{$method} ? '' : $join.$value);
}
}
return $param_string;
}
sub DESTROY {
my $self= shift;
unless ( $self->save_tempfiles ) {
$self->cleanup();
}
$self->SUPER::DESTROY();
}
1;
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