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Update wrappers to isolate outputs #4

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Update wrappers to isolate outputs #4

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20 changes: 9 additions & 11 deletions lib/Bio/RNA/RNAaliSplit/WrapRNAalifold.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ use Moose;
use Path::Class;
use IPC::Cmd qw(can_run run);
use File::Path qw(make_path);
use File::Temp ();
#use diagnostics;

my ($rnaalifold,$oodir);
Expand Down Expand Up @@ -131,6 +132,8 @@ sub run_rnaalifold {
my $this_function = (caller(0))[3];
my ($out_fn,$out,$alnps_fn,$alnps,$alirnaps_fn,$stk_fn);
my ($alirnaps,$alidotps_fn,$alidotps,$alifoldstk);
my $tmpdir_o = File::Temp->newdir( DIR => $oodir );
my $tmpdir = $tmpdir_o->dirname;
my $tag = "";
if ($self->has_ribosum){$tag = ".risobum"}
if ($self->has_basename){
Expand All @@ -153,11 +156,11 @@ sub run_rnaalifold {
$alirnaps_fn = $tag."alirna.ps";
$alidotps_fn = $tag."alidot.ps";
}
$out = file($oodir,$out_fn); # RNAalifold stdout
$alnps = file($oodir,$alnps_fn); # RNAalifold aln.ps
$alirnaps = file($oodir,$alirnaps_fn); # RNAalifold alirna.ps
$alidotps = file($oodir,$alidotps_fn); # RNAalifold alidot.ps
$alifoldstk = file($oodir,$stk_fn); # RNAalifold generated Stockholm file with new CS
$out = file($tmpdir,$out_fn); # RNAalifold stdout
$alnps = file($tmpdir,$alnps_fn); # RNAalifold aln.ps
$alirnaps = file($tmpdir,$alirnaps_fn); # RNAalifold alirna.ps
$alidotps = file($tmpdir,$alidotps_fn); # RNAalifold alidot.ps
$alifoldstk = file($tmpdir,$stk_fn); # RNAalifold generated Stockholm file with new CS

open my $fh, ">", $out;
my $alifold_options = " --aln --color -p --sci --aln-stk ";
Expand All @@ -167,7 +170,7 @@ sub run_rnaalifold {
if ($self->has_sscons){$alifold_options.=" --SS_cons "}
my $cmd = $rnaalifold.$alifold_options.$self->ifile;
my ( $success, $error_message, $full_buf, $stdout_buf, $stderr_buf ) =
run( command => $cmd, verbose => 0 );
run( command => $cmd, verbose => 0, cwd => $tmpdir );
if( !$success ) {
print STDERR "ERROR [$this_function] Call to $rnaalifold unsuccessful\n";
print STDERR "ERROR: $cmd\n";
Expand All @@ -184,11 +187,6 @@ sub run_rnaalifold {

$self->_parse_rnaalifold($stdout_buffer);
$self->alignment_stk($alifoldstk);
rename "aln.ps", $alnps;
rename "alirna.ps", $alirnaps;
rename "alidot.ps", $alidotps;
rename "RNAalifold_results.stk", $alifoldstk;
unlink "alifold.out";
}

# parse RNAalifold output
Expand Down
18 changes: 9 additions & 9 deletions lib/Bio/RNA/RNAaliSplit/WrapRscape.pm
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Expand Up @@ -16,6 +16,7 @@ use Moose;
use Path::Class;
use IPC::Cmd qw(can_run run);
use File::Path qw(make_path);
use File::Temp ();

my ($rscape,$oodir);
my $exe = "R-scape";
Expand Down Expand Up @@ -200,6 +201,8 @@ sub run_rscape {
my $this_function = (caller(0))[3];
my ($out_fn,$sout_fn,$out,$sout,$sum);
my ($rscape_out,$rscape_sout,$rscape_sum);
my $tmpdir_o = File::Temp->newdir( DIR => $oodir );
my $tmpdir = $tmpdir_o->dirname;
my $tag = "";
if ($self->has_statistic){$tag = ".".$self->statistic};

Expand All @@ -215,19 +218,19 @@ sub run_rscape {
$out_fn = $tag."rscape.out";
$sout_fn = $tag."rscape.sorted.out";
}
$out = file($oodir,$out_fn); # R-scape stdout
$sout = file($oodir,$sout_fn); # R-scape sorted stdout
$out = file($tmpdir,$out_fn); # R-scape stdout
$sout = file($tmpdir,$sout_fn); # R-scape sorted stdout

$rscape_out = "rscape.out";
$rscape_out = $out_fn;
$rscape_sout = $rscape_out.".sorted";

my $rscape_options = " -o $rscape_out --rna --outdir $oodir ";
my $rscape_options = " -o $rscape_out --rna --outdir $tmpdir ";
if ($self->has_nofigures && $self->nofigures == 1){$rscape_options.=" --nofigures "};
if ($self->has_statistic){$rscape_options.=" --".$self->statistic." " }
my $cmd = $rscape.$rscape_options.$self->ifile;

my ( $success, $error_message, $full_buf, $stdout_buf, $stderr_buf ) =
run( command => $cmd, verbose => 0 );
run( command => $cmd, verbose => 0, cwd => $tmpdir );
if( !$success ) {
print STDERR "ERROR [$this_function] Call to $rscape unsuccessful\n";
print STDERR "ERROR: $cmd\n";
Expand All @@ -236,10 +239,7 @@ sub run_rscape {
croak $!;
}

$self->_parse_rscape($rscape_out);

rename $rscape_out, $out;
rename $rscape_sout, $sout;
$self->_parse_rscape($out);
}

# parse R-scape output
Expand Down