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check exit code of every subcommand; use xargs #86

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check exit code of every subcommand; use xargs #86

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78 changes: 54 additions & 24 deletions RepeatMasker
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Original file line number Diff line number Diff line change
Expand Up @@ -742,7 +742,7 @@ foreach my $file ( @ARGV ) {
## errors, and create a byte index for all parseable sequences
## in the file. Copy the file so we don't mess with the
## original.
system( " cp $fileori $file " );
systemF( " cp $fileori $file " );
my $db = FastaDB->new(
fileName => $file,
openMode => SeqDBI::ReadWrite,
Expand Down Expand Up @@ -848,11 +848,11 @@ JOBLOOP:
if ( $DEBUG );
## Child completed ok.
## Append log, and stderrs
system( "cat $batchFile.masked.log >> $fullLogFile" )
systemF( "cat $batchFile.masked.log >> $fullLogFile" )
if ( -e "$batchFile.masked.log" );
system( "cat $batchFile.masked.stderr >> $fullErrFile" )
systemF( "cat $batchFile.masked.stderr >> $fullErrFile" )
if ( -e "$batchFile.masked.stderr" );
system( "touch $batchFile.cat" ) if ( !-e "$batchFile.cat" );
systemF( "touch $batchFile.cat" ) if ( !-e "$batchFile.cat" );

# Now remove them
unlink( "$batchFile.masked", "$batchFile.masked.log",
Expand Down Expand Up @@ -948,13 +948,13 @@ JOBLOOP:
&& -e "$file" . "_batch-" . "$nextBatchToConcatenate.cat" )
{
if ( $compressCatFile ) {
system( "gzip -c $file"
systemF( "gzip -c $file"
. "_batch-"
. "$nextBatchToConcatenate.cat "
. ">> $fullcatfile.gz" );
}
else {
system( "cat $file"
systemF( "cat $file"
. "_batch-"
. "$nextBatchToConcatenate.cat "
. ">> $fullcatfile" );
Expand Down Expand Up @@ -1111,14 +1111,14 @@ JOBLOOP:
## The rule of thumb is that if we didn't return
## results we at least have an empty *.cat file.
if ( !-e "$batchSeqFile.cat" ) {
system( "touch $batchSeqFile.cat" );
systemF( "touch $batchSeqFile.cat" );
}
unlink( <$batchSeqFile.tmp.* $batchSeqFile.temp.*> );
}
else {

# Create an emtpy cat file.
system( "touch $batchSeqFile.cat" );
systemF( "touch $batchSeqFile.cat" );
}

if ( $batcher->isBatchFragmented( $batchNums[ $k ] ) ) {
Expand Down Expand Up @@ -1173,22 +1173,27 @@ JOBLOOP:
my $overlapBoundariesHashRef = $batcher->getOverlapBoundaries();
if ( keys( %{$overlapBoundariesHashRef} ) > 0 ) {
if ( $compressCatFile ) {
system(
systemF(
"echo \"## Batch Overlap Boundaries\" | gzip -c >> $fullcatfile.gz" );
}
else {
system( "echo \"## Batch Overlap Boundaries\" >> $fullcatfile" );
systemF( "echo \"## Batch Overlap Boundaries\" >> $fullcatfile" );
}
foreach my $fragSeqName ( keys( %{$overlapBoundariesHashRef} ) ) {
my $overlapList =
join( ", ", @{ $overlapBoundariesHashRef->{$fragSeqName} } );

my $append_fullcatfile=">>$fullcatfile";
if ( $compressCatFile ) {
system( "echo \"## $fragSeqName $overlapList\" | "
. "gzip -c >> $fullcatfile.gz" );
}
else {
system( "echo \"## $fragSeqName $overlapList\" >> $fullcatfile" );
#systemF( "echo \"## $fragSeqName $overlapList\" | "
# . "gzip -c >> $fullcatfile.gz" );
$append_fullcatfile="|gzip -c>>$fullcatfile.gz";
}
# else { systemF( "echo \"## $fragSeqName $overlapList\" >> $fullcatfile" ); }
open(FULLCATFILE, $append_fullcatfile) or die "Error - cannot write to $append_fullcatfile";
print FULLCATFILE "## $fragSeqName $overlapList\n";
close(FULLCATFILE);($? >> 8) and die
"Error -- command returned nonzero status code:\n$append_fullcatfile\nDied ";
}
}

Expand Down Expand Up @@ -1246,10 +1251,10 @@ JOBLOOP:

if ( -s "$fileori.alert" && !$options{'is_clip'} ) {
if ( $compressCatFile ) {
&systemint( "gzip -c $fileori.alert >> $file.cat.gz" );
&systemint( "gzip -c $fileori.alert >> $file.cat.gz" ) and die;
}
else {
&systemint( "cat $fileori.alert >> $file.cat" );
&systemint( "cat $fileori.alert >> $file.cat" ) and die;
}
}

Expand Down Expand Up @@ -1821,7 +1826,7 @@ sub locateISElements {
}
print "$ISreport\n";
if ( $options{'is_only'} || $options{'is_clip'} ) {
system( "cat $file >> $outFilesPrefix.withoutIS" );
systemF( "cat $file >> $outFilesPrefix.withoutIS" );
if ( $qualname ) {
my $qualout = "$outFilesPrefix.qual.withoutIS";
$qualout =~ s/.seq.qual.withoutIS/.qual.withoutIS/;
Expand Down Expand Up @@ -2870,7 +2875,7 @@ sub runStage {

if ( $DEBUG ) {
print "Saving pre-stage maskfile to: $maskfile-$stage\n";
system( "cp $maskfile $maskfile-$stage" );
systemF( "cp $maskfile $maskfile-$stage" );
}

my ( $minmatch, $bandwidth, $resultsCollection ) = &search(
Expand Down Expand Up @@ -3405,7 +3410,12 @@ sub runLowComplexTests {
}

if ( <$file.tmp.t*> ) {
systemint( "cat $file.tmp.t* > $file.cat" );
#systemint( "cat $file.tmp.t* > $file.cat" ) and die;
unlink "$file.cat";
my $i = rindex($file,"/");
my $d = substr($file,0,$i);
my $f = substr($file,$i+1);
systemint( "find $d -name '$f.tmp.t*' -type f -print0| xargs -0 cat >> $file.cat" ) and die;
}

return;
Expand Down Expand Up @@ -3942,7 +3952,12 @@ sub runHMMERSearchStages {
}

if ( <$file.tmp.*> ) {
systemint( "cat $file.tmp.* > $file.cat" );
#systemint( "cat $file.tmp.* > $file.cat" ) and die;
unlink "$file.cat";
my $i = rindex($file,"/");
my $d = substr($file,0,$i);
my $f = substr($file,$i+1);
systemint( "find $d -name '$f.tmp.t*' -type f -print0| xargs -0 cat >> $file.cat" ) and die;
}

if ( -s "$file.cat" ) {
Expand Down Expand Up @@ -4698,7 +4713,12 @@ sub runSearchStages {
}

if ( <$file.tmp.*> ) {
systemint( "cat $file.tmp.* > $file.cat" );
#systemint( "cat $file.tmp.* > $file.cat" ) and die;
unlink "$file.cat";
my $i = rindex($file,"/");
my $d = substr($file,0,$i);
my $f = substr($file,$i+1);
systemint( "find $d -name '$f.tmp.*' -type f -print0| xargs -0 cat >> $file.cat" ) and die;
}

# Once and for all let's create a sorted cat file...what do you say?
Expand Down Expand Up @@ -6874,9 +6894,15 @@ FORK:
else {
die "Can't fork! Errorcode: $!\n";
}
return 0; # success
}
}

sub systemF {
my ( $cmd ) = @_;
system( @_ ) and die "Exec $cmd failed\n";
}

##-------------------------------------------------------------------------##
## Use: my &cleanUp( \%options, $runnumber, $tempdir, $fileori,
## $fileend, $file, $originaldir, $compressed );
Expand Down Expand Up @@ -6933,8 +6959,12 @@ sub cleanUp {
}

if ( $compressed ) {
&systemint( "gzip $fileori" ) if $compressed eq 'zipped';
&systemint( "compress $fileori" ) if $compressed eq 'Zed';
if( $compressed eq 'zipped') {
&systemint( "gzip $fileori" ) and die;
}
elsif( $compressed eq 'Zed' ) {
&systemint( "compress $fileori" ) and die;
}
}
}

Expand Down