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Cleanup files #126

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merged 6 commits into from
May 21, 2015
Merged

Cleanup files #126

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7014c66
suppress warning output from mcl
andrewjpage May 21, 2015
8cc5b52
delete faa files
andrewjpage May 21, 2015
cf31600
check protein files not cleaned up
andrewjpage May 21, 2015
3e91966
split groups should use temp directory module and close filehandles
andrewjpage May 21, 2015
826730b
update version
andrewjpage May 21, 2015
df023e0
no need to manually delete temp directory
andrewjpage May 21, 2015
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2 changes: 1 addition & 1 deletion dist.ini
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
name = Bio-Roary
version = 2.2.2
version = 2.2.3
author = Andrew J. Page <[email protected]>
license = GPL_3
copyright_holder = Wellcome Trust Sanger Institute
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2 changes: 1 addition & 1 deletion lib/Bio/Roary/External/Mcl.pm
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Expand Up @@ -64,7 +64,7 @@ sub _command_to_run {
" ",
(
$self->mcxdeblast_exec, '-m9', '--score='.$self->_score,
'--line-mode=abc', $self->blast_results,
'--line-mode=abc', $self->blast_results, '2> /dev/null',
'|', $self->mcl_exec, '-', '--abc',
'-I', $self->_inflation_value, '-o', $self->output_file,
$self->_logging
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5 changes: 5 additions & 0 deletions lib/Bio/Roary/PostAnalysis.pm
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Expand Up @@ -218,6 +218,11 @@ sub _delete_intermediate_files
my ($self) = @_;
return if($self->dont_delete_files == 1);

for my $fasta_file (@{$self->fasta_files})
{
unlink($fasta_file) if(-e $fasta_file);
}

unlink($self->_output_mcl_filename) ;
unlink($self->_output_inflate_clusters_filename) ;
unlink($self->_output_group_labels_filename) ;
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29 changes: 8 additions & 21 deletions lib/Bio/Roary/SplitGroups.pm
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Expand Up @@ -24,11 +24,11 @@ has 'outfile' => ( is => 'ro', isa => 'Str', required => 1 );
has 'iterations' => ( is => 'ro', isa => 'Int', default => 5 );
has 'dont_delete' => ( is => 'ro', isa => 'Bool', default => 0 );

has '_outfile_handle' => ( is => 'ro', lazy_build => 1 );
has '_neighbourhood_size' => ( is => 'ro', isa => 'Int', default => 5 );

has '_group_filelist' => ( is => 'rw', isa => 'ArrayRef', lazy_build => 1 );
has '_tmp_dir' => ( is => 'ro', isa => 'Str', default => 'split_groups' );
has '_tmp_dir_object' => ( is => 'ro', isa => 'File::Temp::Dir', default => sub { File::Temp->newdir( DIR => getcwd, CLEANUP => 1 ); } );
has '_tmp_dir' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__tmp_dir' );

has '_analyse_groups_obj' => ( is => 'ro', lazy_build => 1 );
has '_genes_to_files' => ( is => 'ro', lazy_build => 1 );
Expand All @@ -45,11 +45,9 @@ has '_gene_files_temp_dir_obj' =>

has '_do_sorting' => ( is => 'rw', isa => 'Bool', default => 0 ); # set to 1 for testing only

sub _build__outfile_handle {
my ( $self ) = @_;

open( my $fh, '>', $self->outfile );
return $fh;
sub _build__tmp_dir {
my ($self) = @_;
return $self->_tmp_dir_object->dirname();
}

sub _build__analyse_groups_obj {
Expand Down Expand Up @@ -79,14 +77,6 @@ sub _build__group_filelist {
return \@filelist;
}

sub _make_tmp_dir {
my ( $self ) = @_;
my $dir = $self->_tmp_dir;
unless ( -e $dir ) {
make_path($dir) or die "Cannot make dir: $dir\n" ;
}
}

sub _build__genes_to_neighbourhood
{
my ( $self ) = @_;
Expand Down Expand Up @@ -119,8 +109,6 @@ sub _build__genes_to_neighbourhood
sub split_groups {
my ( $self ) = @_;

$self->_make_tmp_dir;

# iteratively
for my $x ( 0..($self->iterations - 1) ){
my ( $in_groups, $out_groups ) = $self->_get_files_for_iteration( $x );
Expand Down Expand Up @@ -168,24 +156,23 @@ sub split_groups {
}
close( $outfile_handle );
}

remove_tree( $self->_tmp_dir ) unless ( $self->dont_delete );
}

sub _set_genes_to_groups {
my ( $self, $groupfile ) = @_;

my %genes2groups;
my $c = 0;
open( GFH, '<', $groupfile );
while( my $line = <GFH> ){
open( my $gfh, '<', $groupfile );
while( my $line = <$gfh> ){
chomp $line;
my @genes = split( /\s+/, $line );
for my $g ( @genes ){
$genes2groups{$g} = $c;
}
$c++;
}
close($gfh);
$self->_genes_to_groups( \%genes2groups );
}

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56 changes: 41 additions & 15 deletions t/Bio/Roary/CommandLine/Roary.t
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Expand Up @@ -53,8 +53,24 @@ cleanup_files();
);

mock_execute_script_and_check_output_sorted_groups( $script_name, \%scripts_and_expected_files, [0,6,7,8,9] );

# Make sure faa files are cleaned up automatically
ok(!(-e 'query_1.gff.proteome.faa'),'Check protein query_1.gff.proteome.faa is cleaned up');
ok(!(-e 'query_2.gff.proteome.faa'),'Check protein query_2.gff.proteome.faa is cleaned up');
ok(!(-e 'query_5.gff.proteome.faa'),'Check protein query_5.gff.proteome.faa is cleaned up');


%scripts_and_expected_files = (
'-j Local --dont_delete_files t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff ' =>
[ 'empty_file', 't/data/empty_file' ],
);
mock_execute_script_and_check_output_sorted_groups( $script_name, \%scripts_and_expected_files, [0,6,7,8,9] );
ok((-e 'query_1.gff.proteome.faa'),'Check protein query_1.gff.proteome.faa is not cleaned up');
ok((-e 'query_2.gff.proteome.faa'),'Check protein query_2.gff.proteome.faa is not cleaned up');
ok((-e 'query_5.gff.proteome.faa'),'Check protein query_5.gff.proteome.faa is not cleaned up');

cleanup_files();

SKIP:
{

Expand Down Expand Up @@ -89,32 +105,42 @@ done_testing();
sub cleanup_files
{
remove_tree('pan_genome_sequences');
unlink('_blast_results');
unlink('_clustered');
unlink('_clustered.bak.clstr');
unlink('_clustered.clstr');
unlink('_combined_files');
unlink('_combined_files.groups');
unlink('_fasta_files');
unlink('_gff_files');
unlink('_inflated_mcl_groups');
unlink('_inflated_unsplit_mcl_groups');
unlink('_labeled_mcl_groups');
unlink('_uninflated_mcl_groups');
unlink('accessory.header.embl');
unlink('accessory.header.tab');
unlink('accessory.tab');
unlink('blast_identity_frequency.Rtab');
unlink('clustered_proteins');
unlink('core_accessory.header.embl');
unlink('core_accessory.header.tab');
unlink('core_accessory.tab');
unlink('core_gene_alignment.aln');
unlink('database_masking.asnb');
unlink('example_1.faa.tmp.filtered.fa');
unlink('example_2.faa.tmp.filtered.fa');
unlink('example_3.faa.tmp.filtered.fa');
unlink('gene_presence_absence.csv');
unlink('query_1.gff.proteome.faa');
unlink('query_2.gff.proteome.faa');
unlink('query_3.gff.proteome.faa');
unlink('_clustered');
unlink('_clustered.bak.clstr');
unlink('pan_genome.fa');
unlink('core_accessory.header.tab');
unlink('accessory.header.tab');
unlink('accessory.tab');
unlink('core_accessory.tab');
unlink('number_of_conserved_genes.Rtab');
unlink('number_of_genes_in_pan_genome.Rtab');
unlink('number_of_new_genes.Rtab');
unlink('number_of_unique_genes.Rtab');
unlink('pan_genome.fa');
unlink('query_1.gff.proteome.faa');
unlink('query_2.gff.proteome.faa');
unlink('query_3.gff.proteome.faa');
unlink('query_5.gff.proteome.faa');
unlink('core_gene_alignment.aln');
unlink('blast_identity_frequency.Rtab');
unlink('real_data_1.gff.proteome.faa');
unlink('real_data_2.gff.proteome.faa');
unlink('accessory.header.embl');
unlink('core_accessory.header.embl');

}
2 changes: 1 addition & 1 deletion t/Bio/Roary/External/Mcl.t
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Expand Up @@ -28,7 +28,7 @@ ok(
is(
$obj->_command_to_run,
$cwd
. '/t/bin/dummy_mcxdeblast -m9 --score=r --line-mode=abc some_blast_results | '
. '/t/bin/dummy_mcxdeblast -m9 --score=r --line-mode=abc some_blast_results 2> /dev/null | '
. $cwd
. '/t/bin/dummy_mcl - --abc -I 1.5 -o output.groups > /dev/null 2>&1',
'Command constructed as expected'
Expand Down