view release on metacpan or  search on metacpan

lib/Bio/DB/Sam.pm  view on Meta::CPAN

    $result;
}

sub mtime {
    my $path = shift;
    (stat($path))[9];
}


1;
__END__

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scripts/plot_timings.R  view on Meta::CPAN

## three dimensional plots as contourplots

ggplot(datOpenMP, aes(x = Workers, y = Num_threads, z = fitTime)) +
  geom_contour(aes(colour = after_stat(level))) +theme_bw() + theme(
    panel.grid.minor = element_blank(),
    panel.grid.major = element_blank(),
    axis.text.x = element_text(size = 8),
    legend.position="bottom"
  ) + 

scripts/plot_timings.R  view on Meta::CPAN

  units = "in",
  dpi = 1200
)

ggplot(datOpenMP, aes(x = Workers, y = Num_threads, z = fitSpaceTime)) +
  geom_contour(aes(colour = after_stat(level))) +theme_bw() + theme(
    panel.grid.minor = element_blank(),
    panel.grid.major = element_blank(),
    axis.text.x = element_text(size = 8),
    legend.position="bottom"
  ) + 

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lib/Bio/ToolBox/db_helper/bam.pm  view on Meta::CPAN

	my $bamfile = shift;
	return if ( $bamfile =~ /^(?:http | ftp)/xi );    # I can't do much with remote files

	# we will check the modification time to make sure index is newer
	my $bam_mtime = ( stat($bamfile) )[9];

	# optional index names
	my $bam_index = "$bamfile.bai";                   # .bam.bai
	my $alt_index = $bamfile;
	$alt_index =~ s/bam$/bai/i;    # picard uses .bai instead of .bam.bai as samtools does

	# check for existing index
	if ( -e $bam_index ) {
		if ( ( stat($bam_index) )[9] < $bam_mtime ) {

			# index is older than bam file
			print " index $bam_index is old. Attempting to update time stamp.\n";
			my $now = time;
			utime( $now, $now, $bam_index ) || Bio::DB::Bam->reindex($bamfile);
		}
	}
	elsif ( -e $alt_index ) {
		if ( ( stat($alt_index) )[9] < $bam_mtime ) {

			# index is older than bam file
			print " index $alt_index is old.\n";
		}

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lib/Bio/Tools/Phylo/PAML/Result.pm  view on Meta::CPAN

      }
  }
  if( $stats ) {
      if( ref($stats) =~ /HASH/i ) {
      while( my ($stat,$val) = each %$stats) {
          $self->add_stat($stat,$val);
      }
      } else {
      $self->warn("Must provide a valid hash reference initialize stats");
      }
  }

lib/Bio/Tools/Phylo/PAML/Result.pm  view on Meta::CPAN

 Args    : (optional) sequence name to retrieve nt freqs for

=head2 add_stat

 Title   : add_stat
 Usage   : $result->add_stat($stat,$value);
 Function: Add some misc stat valuess (key/value pairs)
 Returns : none
 Args    : $stat  stat name
           $value stat value

=head2 get_stat

 Title   : get_stat
 Usage   : my $value = $result->get_stat($name);
 Function: Get the value for a stat of a given name
 Returns : scalar value
 Args    : name of the stat

=head2 get_stat_names

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inc/Module/Install.pm  view on Meta::CPAN

	# then make will detect this and cause it to re-run over and over
	# again. This is bad. Rather than taking action to touch it (which
	# is unreliable on some platforms and requires write permissions)
	# for now we should catch this and refuse to run.
	if ( -f $0 ) {
		my $s = (stat($0))[9];

		# If the modification time is only slightly in the future,
		# sleep briefly to remove the problem.
		my $a = $s - time;
		if ( $a > 0 and $a < 5 ) { sleep 5 }

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lib/Bio/Tools/Run/Infernal.pm  view on Meta::CPAN

                           # set one if no file specified. output to
                           # outfile_name, returns Bio::SeqIO or (if -a is set)
                           # Bio::AlignIO
  $factory->cmcalibrate($file); # calibrates specified cov. model; output to
                                # STDOUT
  $factory->cmstat($file); # summary stats for cov. model; set one if no file
                           # specified; output to STDOUT

  # run based on the setting of the program parameter

  my $factory = Bio::Tools::Run::Infernal->new(-program => 'cmsearch',

lib/Bio/Tools/Run/Infernal.pm  view on Meta::CPAN

}

=head2 cmstat

 Title   :   cmstat
 Usage   :   $obj->cmstat($seq)
 Function:   Runs Infernal cmstat and saves output
 Returns :   None
 Args    :   None; set model_file() to use a specific model

=cut

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Bio/DB/GFF/Adaptor/berkeleydb.pm  view on Meta::CPAN

  return $loaded;
}

sub _mtime {
  my $file = shift;
  my @stat = stat($file);
  return $stat[9];
}

sub _index_file {
  my $self = shift;

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lib/BioX/Seq/Fetch.pm  view on Meta::CPAN

    my $fn_idx  = $self->{fn} . '.fai';
    $self->write_index if (! -e $fn_idx);

    # make sure FASTA file is not newer than its index; otherwise index file
    # may be out of date and cause silent corruption downstream
    my $mtime_fas = stat($self->{fn})->mtime;
    my $mtime_idx = stat($fn_idx)->mtime;
    if ($mtime_fas > $mtime_idx) {
        die "Index file exists but is older than FASTA file and probably out"
            . " of date. Refresh or remove the existing index before"
            . " proceeding.\n"
    }

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script/filedetails.pl  view on Meta::CPAN

    my $basename = basename($file);
    my $details = File::Details->new($file);

    my ( $hash, $size, $ctime, $actime, $mtime ) = (
        $details->hash, $details->size,
        ctime( stat($file)->ctime ),
        ctime( stat($file)->atime ),
        ctime( stat($file)->mtime )
    );

    my $hsize = $human->format($size);

    my $info = <<EOF;

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Bioinf.pl  view on Meta::CPAN

				#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
				# Getting statistics
				#_________________________________________
				$evalue=$s;
				$E_mult_factor1=1;
				@output=@{&get_isearch_result_stat(\%stat2, \@pdbg_seqs, \$evalue,
									\$base, \$E_mult_factor1,  $leng_thresh, \%msp_00)};
				%correct=%{$output[3]};
				%final_stat_big_hash=(%final_stat_big_hash, %correct);
				if($verbose){
						@keys=sort keys %correct;

Bioinf.pl  view on Meta::CPAN

     return(\%correcting_pairs);
}

#__________________________________________________________________
# Title     : get_isearch_result_stat
# Usage     : &get_self_isearch_stat(\%stat2, \@pdbg_seqs, \$evalue);
# Function  :
# Example   : Following input (hash eg: %stat2, input with the first word as key)
#              will become columnar output.
#
#    d1ash__ d1bam__ d1mba__ d2lhb__

Bioinf.pl  view on Meta::CPAN

          elsif(-s $out_gz_name){ $existing_msp=$out_file_gz_name }

          #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
          # If the dates of files created are long ago, overwrite to refresh
          #____________________________________________________________________
          if(  (localtime(time- (stat($existing_sso))[9]))[3] > $age_in_days_of_out_file ){
               $over_write_sso_by_age='o';
          }
          if(  (localtime(time- (stat($existing_msp))[9]))[3] > $age_in_days_of_out_file ){
               $over_write_msp_by_age='o';
          }

          #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
          #  To check if the target seq DB is in ../

Bioinf.pl  view on Meta::CPAN

       if(-s $out_sso_file){ $existing_sso=$out_sso_file }
       elsif(-s $out_sso_gz_name){ $existing_sso=$out_sso_gz_name }
       if(-s $out_msp_file){ $existing_msp=$out_msp_file }
       elsif(-s $out_gz_name){ $existing_msp=$out_gz_name }
       if(  (localtime(time- (stat($existing_sso))[9]))[3] > $age_in_days_of_out_file ){
            $over_write_sso_by_age='o';
       }
       if(  (localtime(time- (stat($existing_msp))[9]))[3] > $age_in_days_of_out_file ){
            $over_write_msp_by_age='o';
       }

       #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       #  To check if the target seq DB is in ../

Bioinf.pl  view on Meta::CPAN

    if(@_ < 2){ print "\n# if_file_older_than_x_days needs 2 args\n"; exit; }
    my $file=${$_[0]} || $_[0];
    $days=${$_[1]} || $_[1];
    unless(-s $file){  print "\n# if_file_older_than_x_days: $file does NOT exist\n"; exit; }

    if(lstat($file)){ # to handle Symbolyc link
       print "\n# (i) if_file_older_than_x_days: running lstat\n";
       $how_old_days=(localtime(time- (lstat($file))[9]))[3]; ## should be lstat not stat
    }else{
       print "\n# (i) if_file_older_than_x_days: running stat\n";
       $how_old_days=(localtime(time- (stat($file))[9]))[3]; ## should be lstat not stat
    }
    if($how_old_days > $days and $how_old_days < 10000){
       print "\n# if_file_older_than_x_days: $file is older than $days\n";
       return(\$days);
    }else{

Bioinf.pl  view on Meta::CPAN

                                              $seq_file_msp_gz_name="$seq_name\.msp\.gz";
                                              $first_char= substr("\U$seq_name", 0, 1);
                                              if(-s "$first_char\/$seq_file_msp_name"){  $existing_msp_file="$first_char\/$seq_file_msp_name"; }
                                              elsif(-s "$first_char\/$seq_file_msp_gz_name"){  $existing_msp_file="$first_char\/$seq_file_msp_gz_name"; }

                                              if(  (localtime(time- (stat($existing_msp_file))[9]))[3] > $age_in_days_of_out_file ) {
                                                                     $overwrite_by_age='o';
                                                                     print "\n# interm_lib_search: $seq_file_msp_name is older than $age_in_days_of_out_file days, ovrwrting\n";
                                              }

                                              if( !$over_write  and (-s "$first_char\/$seq_file_msp_name" or -s "$first_char\/$seq_file_msp_gz_name")

Bioinf.pl  view on Meta::CPAN

										 $seq_file_msp_gz_name="$seq_name\.msp\.gz";
										 $first_char= substr("\U$seq_name", 0, 1);
										 if(-s "$first_char\/$seq_file_msp_name"){  $existing_msp_file="$first_char\/$seq_file_msp_name"; }
										 elsif(-s "$first_char\/$seq_file_msp_gz_name"){  $existing_msp_file="$first_char\/$seq_file_msp_gz_name"; }

										 if(  (localtime(time- (stat($existing_msp_file))[9]))[3] > $age_in_days_of_out_file ) {
													$overwrite_by_age='o';
													print "\n# interm_lib_search : $seq_file_msp_name is older than $age_in_days_of_out_file days, ovrwrting\n";
										 }

					 if( !$over_write  and (-s "$first_char\/$seq_file_msp_name" or -s "$first_char\/$seq_file_msp_gz_name")

Bioinf.pl  view on Meta::CPAN

                             return(\$final_dir);
			 }#~~~~~~~ End of sub ~~~~~~~~~~~

		 @read_files = @{&read_file_names_only(\$in_dir, \@target_file_names)};
		 for($i=0; $i < @read_files; $i ++){
					@stat=stat($read_files[$i]);
					$size_sum+=$stat[7];
					if($stat[7] > 1000000){ $big_files{$stat[7]} = $read_files[$i]; }
					if( ($read_files[$i]=~/^[\W]+$/)||($read_files[$i] =~ / +/)){
							splice( @read_files, $i, 1 ); $i--  }
					if( ($read_files[$i]=~/\.\.+/)||($read_files[$i] =~ /\#+/)||($read_files[$i]=~/\,+/)){

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inc/Module/Install.pm  view on Meta::CPAN

	# then make will detect this and cause it to re-run over and over
	# again. This is bad. Rather than taking action to touch it (which
	# is unreliable on some platforms and requires write permissions)
	# for now we should catch this and refuse to run.
	if ( -f $0 ) {
		my $s = (stat($0))[9];

		# If the modification time is only slightly in the future,
		# sleep briefly to remove the problem.
		my $a = $s - time;
		if ( $a > 0 and $a < 5 ) { sleep 5 }

 view release on metacpan or  search on metacpan

inc/Module/Install.pm  view on Meta::CPAN

	# then make will detect this and cause it to re-run over and over
	# again. This is bad. Rather than taking action to touch it (which
	# is unreliable on some platforms and requires write permissions)
	# for now we should catch this and refuse to run.
	if ( -f $0 ) {
		my $s = (stat($0))[9];

		# If the modification time is only slightly in the future,
		# sleep briefly to remove the problem.
		my $a = $s - time;
		if ( $a > 0 and $a < 5 ) { sleep 5 }

 view release on metacpan or  search on metacpan

inc/Module/Install.pm  view on Meta::CPAN

# If the script that is loading Module::Install is from the future,
# then make will detect this and cause it to re-run over and over
# again. This is bad. Rather than taking action to touch it (which
# is unreliable on some platforms and requires write permissions)
# for now we should catch this and refuse to run.
if ( -f $0 and (stat($0))[9] > time ) {
	die << "END_DIE";
Your installer $0 has a modification time in the future.

This is known to create infinite loops in make.

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t/Blio/run.t  view on Meta::CPAN

file_exists_ok( $blio->output_dir->file('movies.html') );
file_exists_ok( $blio->output_dir->file('books.html') );
file_exists_ok( $blio->output_dir->file('books/un_lun_dun.html') );
file_exists_ok( $blio->output_dir->file('books/artemis_fowl.html') );

my $un_lun_dun_mtime = (stat($blio->output_dir->file('books/un_lun_dun.html')->stringify))[9];
my $books_mtime = (stat($blio->output_dir->file('books.html')->stringify))[9];
is($un_lun_dun_mtime,$books_mtime,'books.html mtime = books/un_lun_dun.html');

done_testing();

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lib/Blog/Blosxom.pm  view on Meta::CPAN

    my ($self, $fn) = @_;

    my $dop;
    return $dop if $dop = $self->_check_plugins("date_of_post", @_);

    return stat($fn)->mtime;
}

=head2 filter (@entries)

This function returns only the desired entries from the array passed in. By

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inc/Module/Install.pm  view on Meta::CPAN

# If the script that is loading Module::Install is from the future,
# then make will detect this and cause it to re-run over and over
# again. This is bad. Rather than taking action to touch it (which
# is unreliable on some platforms and requires write permissions)
# for now we should catch this and refuse to run.
if ( -f $0 and (stat($0))[9] > time ) {
	die << "END_DIE";
Your installer $0 has a modification time in the future.

This is known to create infinite loops in make.

 view release on metacpan or  search on metacpan

inc/Module/Install.pm  view on Meta::CPAN

# If the script that is loading Module::Install is from the future,
# then make will detect this and cause it to re-run over and over
# again. This is bad. Rather than taking action to touch it (which
# is unreliable on some platforms and requires write permissions)
# for now we should catch this and refuse to run.
if ( -f $0 and (stat($0))[9] > time ) {
	die << "END_DIE";
Your installer $0 has a modification time in the future.

This is known to create infinite loops in make.

 view release on metacpan or  search on metacpan

inc/Module/Install.pm  view on Meta::CPAN

	# then make will detect this and cause it to re-run over and over
	# again. This is bad. Rather than taking action to touch it (which
	# is unreliable on some platforms and requires write permissions)
	# for now we should catch this and refuse to run.
	if ( -f $0 ) {
		my $s = (stat($0))[9];

		# If the modification time is only slightly in the future,
		# sleep briefly to remove the problem.
		my $a = $s - time;
		if ( $a > 0 and $a < 5 ) { sleep 5 }

 view release on metacpan or  search on metacpan

inc/Module/Install.pm  view on Meta::CPAN

	# then make will detect this and cause it to re-run over and over
	# again. This is bad. Rather than taking action to touch it (which
	# is unreliable on some platforms and requires write permissions)
	# for now we should catch this and refuse to run.
	if ( -f $0 ) {
		my $s = (stat($0))[9];

		# If the modification time is only slightly in the future,
		# sleep briefly to remove the problem.
		my $a = $s - time;
		if ( $a > 0 and $a < 5 ) { sleep 5 }

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include/boost/spirit/iterator/impl/file_iterator.ipp  view on Meta::CPAN

            return;

        // call fstat to find get information about the file just
        // opened (size and file type)
        struct stat stat_buf;
        if ((fstat(fd, &stat_buf) != 0) || !S_ISREG(stat_buf.st_mode))
        {   // if fstat returns an error or if the file isn't a
            // regular file we give up.
            close(fd);
            return;
        }

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lib/Bootylicious/Plugin/Gallery.pm  view on Meta::CPAN

sub _cache_image {
    my ($self, $c, $opts) = @_;

    return
      if (-e $opts->{cached_file})
      && ((stat($opts->{source_file}))[9] < (stat($opts->{cached_file}))[9]);


    return $self->_create_thubnail($c, $opts);
}

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lib/Bootylicious/Comment.pm  view on Meta::CPAN

    return $self;
}

sub created {
    Bootylicious::Timestamp->new(epoch => stat(shift->path)->mtime);
}
sub email { shift->metadata(email => @_) }
sub url   { shift->metadata(url   =>) }

sub content { shift->inner(content => @_) }

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inc/Module/Install.pm  view on Meta::CPAN

# then make will detect this and cause it to re-run over and over
# again. This is bad. Rather than taking action to touch it (which
# is unreliable on some platforms and requires write permissions)
# for now we should catch this and refuse to run.
if ( -f $0 ) {
	my $s = (stat($0))[9];

	# If the modification time is only slightly in the future,
	# sleep briefly to remove the problem.
	my $a = $s - time;
	if ( $a > 0 and $a < 5 ) { sleep 5 }

 view release on metacpan or  search on metacpan

inc/Module/Install.pm  view on Meta::CPAN

# If the script that is loading Module::Install is from the future,
# then make will detect this and cause it to re-run over and over
# again. This is bad. Rather than taking action to touch it (which
# is unreliable on some platforms and requires write permissions)
# for now we should catch this and refuse to run.
if ( -f $0 and (stat($0))[9] > time ) { die <<"END_DIE" }

Your installer $0 has a modification time in the future.

This is known to create infinite loops in make.

 view release on metacpan or  search on metacpan

lib/Bot/BasicBot/Pluggable/Module/Crontab.pm  view on Meta::CPAN

    my $self = shift;

    my $fn = $self->store->get( 'crontab', 'file' ) or return 0;
    return 0 unless(-r $fn); # file must be readable

    my $mod = (stat($fn))[9];
    return 1 if($mod <= $load_time); # don't reload if not modified

    @crontab = ();

    my $fh = IO::File->new($fn,'r') or die "Cannot load file [$fn]: $!\n";

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inc/Module/Install.pm  view on Meta::CPAN

# then make will detect this and cause it to re-run over and over
# again. This is bad. Rather than taking action to touch it (which
# is unreliable on some platforms and requires write permissions)
# for now we should catch this and refuse to run.
if ( -f $0 ) {
	my $s = (stat($0))[9];

	# If the modification time is only slightly in the future,
	# sleep briefly to remove the problem.
	my $a = $s - time;
	if ( $a > 0 and $a < 5 ) { sleep 5 }

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lib/Bot/BasicBot/Pluggable/Module/Notify.pm  view on Meta::CPAN

    my $self = shift;

    my $fn = $self->store->get( 'notify', 'notifications' ) or return 0;
    return 0 unless(-r $fn); # file must be readable

    my $mod = (stat($fn))[9];
    return 1 if($mod <= $load_time && keys %emails); # don't reload if not modified

    my $fh = IO::File->new($fn,'r') or return 0;
    (%settings,%emails) = ();
    while(<$fh>) {

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inc/Module/Install.pm  view on Meta::CPAN

# If the script that is loading Module::Install is from the future,
# then make will detect this and cause it to re-run over and over
# again. This is bad. Rather than taking action to touch it (which
# is unreliable on some platforms and requires write permissions)
# for now we should catch this and refuse to run.
if ( -f $0 and (stat($0))[9] > time ) { die <<"END_DIE" }

Your installer $0 has a modification time in the future.

This is known to create infinite loops in make.

 view release on metacpan or  search on metacpan

inc/Module/Install.pm  view on Meta::CPAN

# If the script that is loading Module::Install is from the future,
# then make will detect this and cause it to re-run over and over
# again. This is bad. Rather than taking action to touch it (which
# is unreliable on some platforms and requires write permissions)
# for now we should catch this and refuse to run.
if ( -f $0 and (stat($0))[9] > time ) { die <<"END_DIE" }

Your installer $0 has a modification time in the future.

This is known to create infinite loops in make.

 view release on metacpan or  search on metacpan

inc/Module/Install.pm  view on Meta::CPAN

# If the script that is loading Module::Install is from the future,
# then make will detect this and cause it to re-run over and over
# again. This is bad. Rather than taking action to touch it (which
# is unreliable on some platforms and requires write permissions)
# for now we should catch this and refuse to run.
if ( -f $0 and (stat($0))[9] > time ) {
	die << "END_DIE";
Your installer $0 has a modification time in the future.

This is known to create infinite loops in make.