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Bug 3381, again #8

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merged 5 commits into from
Aug 29, 2012
Merged

Bug 3381, again #8

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a552dc3
Versioning added
daisieh Aug 23, 2012
5123805
Fixes for bug 3381
daisieh Aug 23, 2012
2e63f07
Revert "Fixes for bug 3381"
daisieh Aug 23, 2012
c697dae
Fixes for bug 3381.
daisieh Aug 23, 2012
86f4715
Better, cleaner warnings in tests.
daisieh Aug 23, 2012
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Fixes for bug 3381.
  • Loading branch information
@daisieh
daisieh committed Aug 23, 2012
commit c697dae7134d8520277ab0c451c05200ef74bb09
154 changes: 79 additions & 75 deletions lib/Bio/Tools/Run/Phylo/Hyphy/REL.pm
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Expand Up @@ -2,7 +2,7 @@
#
# BioPerl module for Bio::Tools::Run::Phylo::Hyphy::REL
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Albert Vilella <avilella-at-gmail-dot-com>
#
Expand Down Expand Up @@ -56,15 +56,15 @@ 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
=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
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
Expand Down Expand Up @@ -115,23 +115,24 @@ INCOMPLETE DOCUMENTATION OF ALL METHODS

=cut

BEGIN {
@VALIDVALUES =
BEGIN {
@VALIDVALUES =
(
{'geneticCode' => [ "Universal","VertebratemtDNA","YeastmtDNA","Mold/ProtozoanmtDNA",
"InvertebratemtDNA","CiliateNuclear","EchinodermmtDNA","EuplotidNuclear",
"Alt.YeastNuclear","AscidianmtDNA","FlatwormmtDNA","BlepharismaNuclear"]},
{'tempalnfile' => undef }, # aln file goes here
{'temptreefile' => undef }, # tree file goes here
{'Model' => [ "Null for Test 1", "Null for Test 2", "Alternative"]},
{'temptsvfile' => undef } # site-by-site conditional probabilities go to this file
);
}

=head2 new

Title : new
Usage : my $obj = Bio::Tools::Run::Phylo::Hyphy::REL->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::REL object
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::REL object
Returns : Bio::Tools::Run::Phylo::Hyphy::REL
Args : -alignment => the Bio::Align::AlignI object
-save_tempfiles => boolean to save the generated tempfiles and
Expand All @@ -147,20 +148,22 @@ See also: L<Bio::Tree::TreeI>, L<Bio::Align::AlignI>
sub new {
my($class,@args) = @_;

my $self = $class->SUPER::new(@args);
my ($aln, $tree, $st, $params, $exe,
$ubl) = $self->_rearrange([qw(ALIGNMENT TREE SAVE_TEMPFILES
PARAMS EXECUTABLE)],
@args);
defined $aln && $self->alignment($aln);
defined $tree && $self->tree($tree);
defined $st && $self->save_tempfiles($st);
defined $exe && $self->executable($exe);

$self->set_default_parameters();
if( defined $params ) {
if( ref($params) !~ /HASH/i ) {
$self->warn("Must provide a valid hash ref for parameter -FLAGS");
my $self = $class->SUPER::new(@args);
my ($aln, $tree, $st, $params, $exe,
$ubl) = $self->_rearrange([qw(ALIGNMENT TREE SAVE_TEMPFILES PARAMS EXECUTABLE)], @args);
defined $aln && $self->alignment($aln);
defined $tree && $self->tree($tree);
defined $st && $self->save_tempfiles($st);
defined $exe && $self->executable($exe);

my $tsvfile = $self->tempdir() . "/results.tsv";
$self->{'_params'}{'temptsvfile'} = $tsvfile;


$self->set_default_parameters();
if( defined $params ) {
if( ref($params) !~ /HASH/i ) {
$self->warn("Must provide a valid hash ref for parameter -FLAGS");
} else {
map { $self->set_parameter($_, $$params{$_}) } keys %$params;
}
Expand Down Expand Up @@ -188,33 +191,33 @@ sub run {
$self->prepare($aln,$tree) unless (defined($self->{'_prepared'}));
my ($rc,$results) = (1);
{
my $commandstring;
my $exit_status;
my $tempdir = $self->tempdir;
my $relexe = $self->executable();
$self->throw("unable to find or run executable for 'HYPHY'") unless $relexe && -e $relexe && -x _;
$commandstring = $relexe . " BASEPATH=" . $self->program_dir . " " . $self->{'_wrapper'};
open(RUN, "$commandstring |") or $self->throw("Cannot open exe $relexe");
my @output = <RUN>;
$exit_status = close(RUN);
$self->error_string(join('',@output));
if( (grep { /\berr(or)?: /io } @output) || !$exit_status) {
$self->warn("There was an error - see error_string for the program output");
$rc = 0;
}
my $outfile = $self->outfile_name;
eval {
open(OUTFILE, ">$outfile") or $self->throw("cannot open $outfile for writing");
# FIXME -- needs output parsing -- ask hyphy to clean that up into a tsv?
foreach my $output (@output) {
print OUTFILE $output;
$results .= sprintf($output);
}
close(OUTFILE);
};
if( $@ ) {
$self->warn($self->error_string);
}
my $commandstring;
my $exit_status;
my $tempdir = $self->tempdir;

my $relexe = $self->executable();
$self->throw("unable to find or run executable for 'HYPHY'") unless $relexe && -e $relexe && -x _;
$commandstring = $relexe . " BASEPATH=" . $self->program_dir . " " . $self->{'_wrapper'};
open(RUN, "$commandstring |") or $self->throw("Cannot open exe $relexe");
my @output = <RUN>;
$exit_status = close(RUN);
$self->error_string(join('',@output));
if( (grep { /\berr(or)?: /io } @output) || !$exit_status) {
$self->warn("There was an error - see error_string for the program output");
$rc = 0;
}
my $outfile = $self->outfile_name;
eval {
open(OUTFILE, ">$outfile") or $self->throw("cannot open $outfile for writing");
foreach my $output (@output) {
print OUTFILE $output;
$results .= sprintf($output);
}
close(OUTFILE);
};
if( $@ ) {
$self->warn($self->error_string);
}
}
unless ( $self->save_tempfiles ) {
unlink($self->{'_wrapper'});
Expand All @@ -230,7 +233,7 @@ sub run {
Usage : $self->create_wrapper
Function: It will create the wrapper file that interfaces with the analysis bf file
Example :
Returns :
Returns :
Args :


Expand All @@ -249,7 +252,7 @@ sub create_wrapper {
Title : set_default_parameters
Usage : $rel->set_default_parameters(0);
Function: (Re)set the default parameters from the defaults
(the first value in each array in the
(the first value in each array in the
%VALIDVALUES class variable)
Returns : none
Args : boolean: keep existing parameter values
Expand All @@ -261,28 +264,29 @@ sub set_default_parameters {
my ($self,$keepold) = @_;
$keepold = 0 unless defined $keepold;
foreach my $elem (@VALIDVALUES) {
my ($param,$val) = each %$elem;
# skip if we want to keep old values and it is already set
if (ref($val)=~/ARRAY/i ) {
unless (ref($val->[0])=~/HASH/i) {
push @{ $self->{'_orderedparams'} }, {$param, $val->[0]};
} else {
$val = $val->[0];
}
}
if ( ref($val) =~ /HASH/i ) {
my $prevparam;
while (defined($val)) {
last unless (ref($val) =~ /HASH/i);
last unless (defined($param));
$prevparam = $param;
($param,$val) = each %{$val};
push @{ $self->{'_orderedparams'} }, {$prevparam, $param};
push @{ $self->{'_orderedparams'} }, {$param, $val} if (defined($val));
}
} elsif (ref($val) !~ /HASH/i && ref($val) !~ /ARRAY/i) {
push @{ $self->{'_orderedparams'} }, {$param, $val};
}
keys %$elem; #reset hash iterator
my ($param,$val) = each %$elem;
# skip if we want to keep old values and it is already set
if (ref($val)=~/ARRAY/i ) {
unless (ref($val->[0])=~/HASH/i) {
push @{ $self->{'_orderedparams'} }, {$param, $val->[0]};
} else {
$val = $val->[0];
}
}
if ( ref($val) =~ /HASH/i ) {
my $prevparam;
while (defined($val)) {
last unless (ref($val) =~ /HASH/i);
last unless (defined($param));
$prevparam = $param;
($param,$val) = each %{$val};
push @{ $self->{'_orderedparams'} }, {$prevparam, $param};
push @{ $self->{'_orderedparams'} }, {$param, $val} if (defined($val));
}
} elsif (ref($val) !~ /HASH/i && ref($val) !~ /ARRAY/i) {
push @{ $self->{'_orderedparams'} }, {$param, $val};
}
}
}

Expand All @@ -296,7 +300,7 @@ sub set_default_parameters {
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
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)

Expand All @@ -307,7 +311,7 @@ sub set_default_parameters {

Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)

Expand Down
51 changes: 30 additions & 21 deletions t/Hyphy.t
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Expand Up @@ -7,53 +7,62 @@ use strict;

BEGIN {
use Bio::Root::Test;
test_begin(-tests => 15, -requires_module =>'IO::String');

use_ok('Bio::Root::IO');
test_begin(-tests => 8, -requires_module =>'IO::String');

use_ok('Bio::Tools::Run::Phylo::Hyphy::SLAC');
use_ok('Bio::Tools::Run::Phylo::Hyphy::FEL');
use_ok('Bio::Tools::Run::Phylo::Hyphy::REL');
use_ok('Bio::Tools::Run::Phylo::Hyphy::Modeltest');
use_ok('Bio::AlignIO');
use_ok('Bio::TreeIO');
}

ok my $slac = Bio::Tools::Run::Phylo::Hyphy::SLAC->new();
ok my $rel = Bio::Tools::Run::Phylo::Hyphy::REL->new();
ok my $fel = Bio::Tools::Run::Phylo::Hyphy::FEL->new();
ok my $modeltest = Bio::Tools::Run::Phylo::Hyphy::Modeltest->new();
my $slac = Bio::Tools::Run::Phylo::Hyphy::SLAC->new();

SKIP: {
test_skip(-requires_executable => $slac, -tests => 4);

my $alignio = Bio::AlignIO->new(-format => 'fasta',
-file => 't/data/hyphy1.fasta');

my $treeio = Bio::TreeIO->new(-format => 'newick',
-file => 't/data/hyphy1.tree');

my $aln = $alignio->next_aln;
my $tree = $treeio->next_tree;

$slac->alignment($aln);
$slac->tree($tree);
my ($rc,$results) = $slac->run();
ok defined($results);

if ($rc == 0) {
self->warn("ERROR in SLAC module $rc:" . $slac->error_string() . "\n");
}
ok ($rc != 0, "SLAC module");

my $rel = Bio::Tools::Run::Phylo::Hyphy::REL->new();
$rel->alignment($aln);
$rel->tree($tree);
($rc,$results) = $rel->run();
ok defined($results);

if ($rc == 0) {
self->warn(print "ERROR in REL module $rc:" . $rel->error_string() . "\n");
}
ok ($rc != 0, "REL module");

my $fel = Bio::Tools::Run::Phylo::Hyphy::FEL->new();
$fel->alignment($aln);
$fel->tree($tree);
($rc,$results) = $fel->run();
ok defined($results);

if ($rc == 0) {
self->warn("ERROR in FEL module $rc:" . $fel->error_string() . "\n");
}
ok ($rc != 0, "FEL module");

my $modeltest = Bio::Tools::Run::Phylo::Hyphy::Modeltest->new();
$modeltest->alignment($aln);
$modeltest->tree($tree);
($rc,$results) = $modeltest->run();
ok defined($results);

if ($rc == 0) {
self->warn("ERROR in Modeltest module $rc:" . print $modeltest->error_string() . "\n");
}
ok ($rc != 0, "Modeltest module");

#*** where are the tests?!
}