annotate easyjoin @ 21:86755160afbf draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7

#!/usr/bin/env perl
## EASY Join -
## Join with automatic pre-sorting of both files
## Copyright (C) 2010 A. Gordon ([e-mail])
## license: AGPLv3+
use strict;
use warnings;
use Data::Dumper;
use Getopt::Long qw(:config bundling no_ignore_case_always);
use File::Temp qw/tempfile/;
use POSIX qw(locale_h);

sub show_help();
sub show_version();
sub show_examples();
sub parse_commandline_options();
sub sort_file($$$);
sub join_files($$);
sub cleanup_files(@);


my $PROGRAM="easyjoin";
my $VERSION="0.6.1";

my $debug=undef;
my $HEADER=undef;
my $IGNORE_CASE=undef;
my $FIELD_SEP=undef;
my $FILE1_KEY_COLUMN=1;
my $FILE2_KEY_COLUMN=1;
my @OUTPUT_SPECIFIERS=();
my $OUTPUT_FORMAT=undef;
my $EMPTY_FILLER=undef;
my $SORT_BUFFER_SIZE=undef;
my $SORT_TEMP_DIR=undef;
my $input_filename1;
my $input_filename2;

##
## Program Start
##
$ENV{'LANG'}="C";## "C" locale is critical for sorting and joining correctly
parse_commandline_options();
my (undef, $tmp_filename1) = tempfile(OPEN=>0);
my (undef, $tmp_filename2) = tempfile(OPEN=>0);
sort_file($input_filename1, $tmp_filename1, $FILE1_KEY_COLUMN);
sort_file($input_filename2, $tmp_filename2, $FILE2_KEY_COLUMN);
my $join_exit_code = join_files($tmp_filename1, $tmp_filename2);
cleanup_files($tmp_filename1, $tmp_filename2);
exit($join_exit_code);

##
## Program end
##


sub show_help()
{
print<<EOF;
${PROGRAM}: Wrapper for GNU join+sort, automaticalyl sorts files before joining them.

Usage: $PROGRAM [OPTIONS] [JOIN-OPTIONS] [SORT-OPTIONS] FILE1 FILE2

OPTIONS: Options specific to this program:

   --header      =  Both input files have a header line as the first line.
                    The header line will be joined properly, without being sorted.

   --version     =  Print ${PROGRAM}'s version.

   --debug       =  Print debug messages (relating to ${PROGRAM}'s operation).

   --help        =  Show this help screen.

   --example     =  Show usage examples.

   --all         =  Short-cut for:
                      -a 1 -a 2 -o auto -e . -t <TAB>
                    This will show all values (paired and unpared) from both files,
		    Automatically formatting the columns, and using TAB as field separator.
		    You can override the empty filler (-e X) on the command line.

   --allh        =  Short-cut for:
                       -a 1 -a 2 -o auto -e . -t <TAB> --header
		    Same as above, but will also respect the header line from both input files.

JOIN-OPTIONS:
   All of GNU join options are supported.
   Run:
       join --help
   To see all possible joining options.

SORT-OPTIONS:
   The following options are supported for the intermediate sorting step:

   -S SIZE
   --buffer-size SIZE   = GNU sort's --buffer-size option.

   -T DIR
   --temporary-directory DIR = GNU sort's --temporary-directory option.

   Run:
      sort --help
   To learn about these options. They might improve sorting performances for big files.

FILE1 FILE2:
   The two input files to be sorted, joined.
   Unlike GNU join,  joining STDIN is not supported. Both files must be real files.


NOTE About "--header" and "--auto-format":
   The "--header" feature requires GNU coreutils version 8.6 or later.
   The "-o auto" feature requires GNU coreutils version 8.10 or later.

EOF
	exit(0);
}

sub show_version()
{
print<<EOF;
$PROGRAM $VERSION
Copyright (C) 2010 A. Gordon (gordon\@cshl.edu)
License AGPLv3+: Affero GPL version 3 or later (http://www.gnu.org/licenses/agpl.html)

To see the GNU's join version, run:
	join --version
EOF
	exit(0);
}

sub show_examples()
{
print<<EOF;
Example of joining two unsorted files (each file having a header line):

\$ cat input1.txt
Fruit	Color
Apple	red
Banana	yellow
Orange	orange
Melon	green

\$ cat input2.txt
Fruit	Price
Orange	7
Avocado	8
Apple	4
Banana	3

\$ easyjoin -j 1 -a 1 -a 2 --header -e . -o auto input1.txt input2.txt
Fruit   Color   Price
Apple   red     4
Avocado .       8
Banana  yellow  3
Melon   green   .
Orange  orange  7

## A short-cut for all the options above:
\$ easyjoin --allh input1.txt input2.txt
Fruit   Color   Price
Apple   red     4
Avocado .       8
Banana  yellow  3
Melon   green   .
Orange  orange  7

EOF
	exit(0);
}

sub parse_commandline_options()
{
	##
	## Parse command line
	##
	my $rc = GetOptions(
			"a=i" => sub { push @OUTPUT_SPECIFIERS, '-a', $_[1] },
			"e=s" => \$EMPTY_FILLER,
			"ignore-case|i" => \$IGNORE_CASE,
			"j=i" => sub { $FILE1_KEY_COLUMN = $_[1] ; $FILE2_KEY_COLUMN = $_[1] ; },
			"o=s" => \$OUTPUT_FORMAT,
			"t=s" => \$FIELD_SEP,
			"v=i" => sub { push @OUTPUT_SPECIFIERS, '-v', $_[1] },
			"1=i" => \$FILE1_KEY_COLUMN,
			"2=i" => \$FILE2_KEY_COLUMN,
			"debug" => \$debug,
			"header" => \$HEADER,
			"help" => \&show_help,
			"version" => \&show_version,
			"examples" => \&show_examples,
			"buffer-size|S=s" => \$SORT_BUFFER_SIZE,
			"temporary-directory|T=s" => \$SORT_TEMP_DIR,
			"all" => sub {
					push @OUTPUT_SPECIFIERS, "-a", 1, "-a", 2;
					$FIELD_SEP = "\t";
					$OUTPUT_FORMAT = "auto";
					$EMPTY_FILLER = "." unless defined $EMPTY_FILLER;
				},
			"allh" => sub {
					push @OUTPUT_SPECIFIERS, "-a", 1, "-a", 2;
					$FIELD_SEP = "\t";
					$OUTPUT_FORMAT = "auto";
					$HEADER=1;
					$EMPTY_FILLER = "." unless defined $EMPTY_FILLER;
				},
		);
	die "$PROGRAM: invalid command-line arguments.\n" unless $rc;

	## We need two file names to join
	my @INPUT_FILES = @ARGV;
	die "$PROGRAM: missing operand: two file names to join\n" if (scalar(@INPUT_FILES)<2);
	die "$PROGRAM: error: too many files specified (can only join two files)\n" if (scalar(@INPUT_FILES)>2);
	die "$PROGRAM: error: input file can't be STDIN, please use a real file name.\n" if $INPUT_FILES[0] eq "-" || $INPUT_FILES[1] eq "-";
	die "$PROGRAM: error: input file 1 '" . $INPUT_FILES[0] . "' not found!" unless -e $INPUT_FILES[0];
	die "$PROGRAM: error: input file 2 '" . $INPUT_FILES[1] . "' not found!" unless -e $INPUT_FILES[1];

	$input_filename1 = $INPUT_FILES[0];
	$input_filename2 = $INPUT_FILES[1];
}

sub sort_file($$$)
{
	my ($input_filename, $output_filename, $key_column) = @_;

	my @SORT_COMMAND;
	push @SORT_COMMAND, $HEADER ? "./sort-header" : "sort" ;
	push @SORT_COMMAND, "-f" if $IGNORE_CASE;
	push @SORT_COMMAND, "-k${key_column},${key_column}" ;
	push @SORT_COMMAND, "--buffer-size", $SORT_BUFFER_SIZE if $SORT_BUFFER_SIZE;
	push @SORT_COMMAND, "--temporary-directory", $SORT_TEMP_DIR if $SORT_TEMP_DIR;
	push @SORT_COMMAND, "--output", $output_filename;
	push @SORT_COMMAND, "--debugheader" if $debug && $HEADER;
	push @SORT_COMMAND, "-t", $FIELD_SEP if $FIELD_SEP;
	push @SORT_COMMAND, $input_filename;

	if ($debug) {
		warn "$PROGRAM: Running sort on '$input_filename' => '$output_filename'\n";
		warn "$PROGRAM: Sort command line:\n";
		print STDERR Dumper(\@SORT_COMMAND), "\n";
	}

	my $sort_exit_code=1;
	system(@SORT_COMMAND);
	if ($? == -1) {
		die "$PROGRAM: Error: failed to execute 'sort': $!\n";
	}
	elsif ($? & 127) {
		my $signal = ($? & 127);
		kill 2, $$ if $signal == 2; ##if sort was interrupted (CTRL-C) - just pass it on and commit suicide
		die "$PROGRAM: Error: 'sort' child-process died with signal $signal\n";
	}
	else {
		$sort_exit_code = ($? >> 8);
	}
	die "$PROGRAM: Error: 'sort' process failed, exit code $sort_exit_code\n" if $sort_exit_code!=0;
}

sub join_files($$)
{
	my ($file1, $file2) = @_;

	my @join_command = qw/join/;
	push @join_command, "--header" if $HEADER;
	push @join_command, "--ignore-case" if $IGNORE_CASE;
	push @join_command, "-t", $FIELD_SEP if $FIELD_SEP;
	push @join_command, "-1", $FILE1_KEY_COLUMN if $FILE1_KEY_COLUMN;
	push @join_command, "-2", $FILE2_KEY_COLUMN if $FILE2_KEY_COLUMN;
	push @join_command, "-e", $EMPTY_FILLER if defined $EMPTY_FILLER;
	push @join_command, "-o", $OUTPUT_FORMAT if $OUTPUT_FORMAT;
	push @join_command, @OUTPUT_SPECIFIERS;
	push @join_command, $file1, $file2;

	if ($debug) {
		warn "$PROGRAM: Running join on '$file1'  and '$file2'\n";
		warn "$PROGRAM: join command line:\n";
		print STDERR Dumper(\@join_command), "\n";
	}

	my $join_exit_code=1;
	system(@join_command);
	if ($? == -1) {
		die "$PROGRAM: Error: failed to execute 'join': $!\n";
	}
	elsif ($? & 127) {
		my $signal = ($? & 127);
		kill 2, $$ if $signal == 2; ##if join was interrupted (CTRL-C) - just pass it on and commit suicide
		die "$PROGRAM: Error: 'join' child-process died with signal $signal\n";
	}
	else {
		$join_exit_code = ($? >> 8);
	}
	return $join_exit_code;
}

sub cleanup_files(@)
{
	my (@files) = @_;

	foreach my $file (@files) {
		if ($debug) {
			warn "$PROGRAM: debug mode, not deleting temporary file '$file'\n";
		} else {
			my $count = unlink $file;
			warn "$PROGRAM: Error: failed to delete temporary file '$file': $!\n" if ($count != 1);
		}
	}
}