transpose-par.pl: Parallelized transpose with paste.

This commit is contained in:
Ole Tange 2013-10-28 00:44:47 +01:00
parent 557e70fc58
commit fc350ac6cc
3 changed files with 293 additions and 0 deletions

37
transpose/transpose-par.pl Executable file
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#!/usr/bin/perl
#!/usr/local/bin/parallel --shebang-wrap --pipe --block 10m -k --files /usr/bin/perl | xargs paste
use Text::CSV;
use File::Temp qw(tempfile tempdir);
my $csv;
my (@table);
my $first_line = 1;
my $col = 0;
while(my $l = <>) {
if($first_line) {
my $csv_setting = guess_csv_setting($l);
$csv = Text::CSV->new($csv_setting)
or die "Cannot use CSV: ".Text::CSV->error_diag ();
$first_line = 0;
}
if(not $csv->parse($l)) {
die "CSV has unexpected format";
}
# append to each row
my $row = 0;
for($csv->fields()) {
$table[$row][$col] = defined($_) ? $_ : '';
$row++;
}
$col++;
}
print map { join("\t",@$_),"\n" } @table;
sub guess_csv_setting {
# Based on a single line guess the csv_setting
return { binary => 1 };
}

175
transpose/transpose.pod Normal file
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#!/usr/bin/perl
=head1 NAME
transpose - transpose CSV file
=head1 SYNOPSIS
B<transpose> [-d I<delim>] [I<input>]
=head1 DESCRIPTION
B<transpose> will read a CSV fie
=head1 OPTIONS
=over 9
=item I<input>
Input CSV file. If none is given reads from STDIN (standard input).
=item B<-d> I<delim> - not implemented
Use I<delim> as delimiter in input and output.
=back
=head1 EXAMPLES
=head2 EXAMPLE: Transpose a big CSV file
cat medium.csv | transpose > muidem.csv
=head1 DESIGN
B<transpose> is designed to deal efficiently with medium sized data
(up to 30 TB per file) on systems with 250 MB RAM per CPU core. It
works by chopping the input into 30 MB blocks. Each block is
transposed in parallel and saved to disk. Then these files are pasted
together and finally removed.
=head1 REPORTING BUGS
Report bugs to <tange@gnu.org>.
=head1 AUTHOR
Copyright (C) 2013 Ole Tange, http://ole.tange.dk and Free
Software Foundation, Inc.
=head1 LICENSE
Copyright (C) 2013 Free Software Foundation, Inc.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
at your option any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
=head2 Documentation license I
Permission is granted to copy, distribute and/or modify this documentation
under the terms of the GNU Free Documentation License, Version 1.3 or
any later version published by the Free Software Foundation; with no
Invariant Sections, with no Front-Cover Texts, and with no Back-Cover
Texts. A copy of the license is included in the file fdl.txt.
=head2 Documentation license II
You are free:
=over 9
=item B<to Share>
to copy, distribute and transmit the work
=item B<to Remix>
to adapt the work
=back
Under the following conditions:
=over 9
=item B<Attribution>
You must attribute the work in the manner specified by the author or
licensor (but not in any way that suggests that they endorse you or
your use of the work).
=item B<Share Alike>
If you alter, transform, or build upon this work, you may distribute
the resulting work only under the same, similar or a compatible
license.
=back
With the understanding that:
=over 9
=item B<Waiver>
Any of the above conditions can be waived if you get permission from
the copyright holder.
=item B<Public Domain>
Where the work or any of its elements is in the public domain under
applicable law, that status is in no way affected by the license.
=item B<Other Rights>
In no way are any of the following rights affected by the license:
=over 2
=item *
Your fair dealing or fair use rights, or other applicable
copyright exceptions and limitations;
=item *
The author's moral rights;
=item *
Rights other persons may have either in the work itself or in
how the work is used, such as publicity or privacy rights.
=back
=back
=over 9
=item B<Notice>
For any reuse or distribution, you must make clear to others the
license terms of this work.
=back
A copy of the full license is included in the file as cc-by-sa.txt.
=head1 DEPENDENCIES
B<transpose> uses Perl, B<paste>, B<bash> and B<parallel>.
=head1 SEE ALSO
B<bash>(1), B<parallel>(1), B<paste>(1)
=cut

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transpose/transposewrap.pl Executable file
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#!/usr/bin/perl
use File::Temp qw(tempfile tempdir);
#$Global::debug = 1;
my $block = "30m";
debug("parallel --pipe --block $block -k --files -j150% transpose-par.pl\n");
my @files = `parallel --pipe --block $block -k --files -j150% transpose-par.pl`;
chomp(@files);
my $tmp = File::Temp::tempdir(CLEANUP => 0);
my $fifo = "$tmp/0000000";
my $cmd = "mkfifo $fifo; paste > $fifo ";
my (@fifos, @args);
my $args_len = 0;
my $max_line_length_allowed = `parallel --max-line-length-allowed`;
while(@files) {
push @args, shift @files;
$args_len += length $args[$#args] + 1;
if(length $cmd + $args_len > $max_line_length_allowed) {
unshift @files, pop @args;
push @fifos, $fifo;
if(fork()) {
} else {
debug("($cmd @args &)\n");
`($cmd @args &)`;
exit($?);
}
$fifo++;
$cmd = "mkfifo $fifo; paste > $fifo ";
@args = ();
$args_len = 0;
}
}
if(@args) {
push @fifos, $fifo;
if(fork()) {
} else {
debug("($cmd @args &)\n");
`($cmd @args &)`;
exit($?);
}
}
# make sure all fifos are created by the spawned shells
my @non_existing_fifos = @fifos;
while(@non_existing_fifos) {
if(not -e $non_existing_fifos[0]) {
usleep(1);
} else {
shift @non_existing_fifos;
}
}
debug("paste @fifos\n");
system("paste @fifos");
unlink(@fifos);
rmdir($tmp);
sub usleep {
# Sleep this many milliseconds.
my $secs = shift;
::debug(int($secs),"ms ");
select(undef, undef, undef, $secs/1000);
}
sub debug {
# Returns: N/A
$Global::debug or return;
@_ = grep { defined $_ ? $_ : "" } @_;
if($Global::fd{1}) {
# Original stdout was saved
my $stdout = $Global::fd{1};
print $stdout @_;
} else {
print @_;
}
}