annotate multijoin @ 7:01ca80da2266 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6

#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case);
use Data::Dumper;
use Carp;
use File::Basename;

my $version = "0.1.1";
my $field_sep = "\t";
my $key_column;
my @values_columns;
my $max_value_column;
my @input_files;
my $input_headers ;
my $output_headers;
my $filler = "0";
my $filler_string ;
my $ignore_duplicates;
my $debug = 0 ;
my %input_headers;
my $have_file_labels;
my %file_labels;

sub parse_command_line_parameters();
sub show_help();
sub read_input_file($);
sub print_combined_data();
sub sanitize_filename($);
sub print_output_header();
sub show_examples();

##
## Program Start
##

parse_command_line_parameters();

my %data;
foreach my $file (@input_files) {
	read_input_file($file);
}
#print STDERR Dumper(\%input_headers),"\n";
#print STDERR Dumper(\%data) if $debug;
print_output_header() if $output_headers;
print_combined_data();


##
## Program End
##
sub print_output_header()
{
	my @output = ("key");
	foreach my $file ( @input_files ) {
		foreach my $column ( @values_columns ) {
			my $column_name = ( exists $input_headers{$file}->{$column} ) ?
				$input_headers{$file}->{$column} :
				"V$column" ;

			push @output, $file_labels{$file} . "_" . $column_name;
		}
	}
	print join($field_sep,@output),"\n"
		or die "Output error: can't write output line: $!\n";
}

sub print_combined_data()
{
	my @keys = sort keys %data ;

	foreach my $key ( @keys ) {
		my @outputs;

		foreach my $file (@input_files) {
			push @outputs,
				(exists $data{$key}->{$file}) ? $data{$key}->{$file} : $filler_string;
		}

		print join($field_sep,$key,@outputs),"\n"
			or die "Output error: can't write output line: $!\n";
	}
}

sub sanitize_filename($)
{
	my ($filename) = shift or croak "missing file name";
	my $file_ID = basename($filename);
	$file_ID =~ s/\.\w+$//; # remove extension
	$file_ID =~ s/^[^\w\.\-]+//;
	$file_ID =~ s/[^\w\.\-]+$//;
	$file_ID =~ s/[^\w\.\-]+/_/g; # sanitize bad characters
	return $file_ID;
}

sub read_input_file($)
{
	my ($filename) = shift or croak "Missing input file name";

	my @value_indexes = map { $_-1 } @values_columns; #zero-based indexes for value columns

	open FILE, "<", $filename
		or die "Error: can't open file '$filename': $!\n";

	## Read file's header
	if ($input_headers) {
		my $line = <FILE>;
		chomp $line;
		my @fields = split $field_sep, $line;

		my $num_input_fields = scalar(@fields);
		die "Input error: file '$filename' line $. doesn't have enough columns (value column = $max_value_column, line has only $num_input_fields columns)\n" if $num_input_fields < $max_value_column ;

		foreach my $col (@values_columns) {
			$input_headers{$filename}->{$col} = $fields[$col-1] ;
		}
	}


	## Read file's data
	while ( my $line = <FILE> ) {
		chomp $line;
		my @fields = split $field_sep, $line;

		my $num_input_fields = scalar(@fields);
		die "Input error: file '$filename' line $. doesn't have enough columns (key column = $key_column, line has only $num_input_fields columns)\n" if $num_input_fields < $key_column ;
		die "Input error: file '$filename' line $. doesn't have enough columns (value column = $max_value_column, line has only $num_input_fields columns)\n" if $num_input_fields < $max_value_column ;


		my $key = $fields[$key_column-1];
		my $value = join($field_sep, @fields[@value_indexes]);

		die "Input error: file '$filename' line $. have duplicated key '$key'.\n"
			if (exists $data{$key}->{$filename} && !$ignore_duplicates) ;
		$data{$key}->{$filename} = $value;
	}
	close FILE
		or die "Error: can't write and close file '$filename': $!\n";
}

sub parse_command_line_parameters()
{
	my $values_columns_string;

	my $rc = GetOptions("help" => \&show_help,
			    "key|k=i" => \$key_column,
			    "values|v=s" => \$values_columns_string,
		            "t=s" => \$field_sep,
		            "in-header" => \$input_headers,
		            "out-header|h" => \$output_headers,
		            "H" => sub { $input_headers = 1 ; $output_headers = 1 ; },
			    "ignore-dups" => \$ignore_duplicates,
		            "filler|f=s" => \$filler,
		            "examples"   => \&show_examples,
			    "labels" => \$have_file_labels,
			);
	die "Error: inalid command-line parameters.\n" unless $rc;

	die "Error: missing key column. use --key N. see --help for more details.\n" unless defined $key_column;
	die "Error: Invalid key column ($key_column). Must be bigger than zero. see --help for more details.\n" if $key_column <= 0 ;

	die "Error: missing values column. use --values V1,V2,Vn. See --help for more details.\n" unless defined $values_columns_string;
	@values_columns = split(/\s*,\s*/, $values_columns_string);

	die "Error: missing values column. use --values N,N,N. see --help for more details.\n" unless scalar(@values_columns)>0;
	foreach my $v (@values_columns) {
		die "Error: invalid value column ($v), please use only numbers>=1. see --help for more details.\n"
			unless $v =~ /^\d+$/ && $v>=1;

		$max_value_column = $v unless defined $max_value_column && $max_value_column>$v;
	}

	$filler_string = join($field_sep, map { $filler } @values_columns);


	if ($have_file_labels) {
		## have file labels - each pair of parameters is a file/label pair.
		die "Error: missing input files and labels\n" if scalar(@ARGV)==0;
		die "Error: when using --labels, a pair of file names + labels is required (got odd number of argiments)\n" unless scalar(@ARGV)%2==0;

		while (@ARGV) {
			my $filename = shift @ARGV;
			my $label = shift @ARGV;
			$label =~ s/^[^\.\w\-]+//;
			$label =~ s/[^\.\w\-]+$//g;
			$label =~ s/[^\.\w\-]+/_/g;

			my $file_ID = sanitize_filename($filename);
			$file_labels{$filename} = $label;
			push @input_files, $filename;
		}
	} else {
		## no file labels - the rest of the arguments are just file names;
		@input_files = @ARGV;
		die "Error: missing input files\n" if scalar(@input_files)==0;
		die "Error: need more than one input file to join.\n" if scalar(@input_files)==1;

		foreach my $file (@input_files) {
			my $file_ID = sanitize_filename($file);
			$file_labels{$file} = $file_ID;
		}
	}

}

sub show_help()
{
	print<<EOF;
Multi-File join, version $version
Copyright (C) 2012 - A. Gordon (gordon at cshl dot edu)
License AGPLv3+: Affero GPL version 3 or later (http://www.gnu.org/licenses/agpl.html)

Usage:
 multijoin [OPTIONS] -k N -v V1,V2,Vn,..  FILE1  FILE2  ... FILEn

Options:

 --help         This helpful help screen.

  -k N
  --key N       Use column N as key column.

  -v V1,V2,Vn
  --values V1,V2,Vn
                 Use columns V1,V2,Vn as value columns - those will be joined
                According to the Key column.
		Multiple columns can be specified.

  -t SEP        Use SEP as field separator character (default: tab).

  -h
  --out-header  Add a header line to the output file.

  --in-header   The input files have a header line.
                The first line will not be joined.
		if '--out-header' is also used, the output column headers will
		be constructed based on the input header column names.

  -H
  --headers     Same as '--in-header --out-header' combined.

  --ignore-dups   Ignore duplicated keys (within a file).
                By default, duplicated keys cause an error.

 -f X
 --filler X     Fill missing values with X.
                (Default: '$filler').

 --labels       When printing output headers with '-h', instead of using the file name,
                use specific labels.
		Each file name must be followed by a name.

		example (without labels):
		 \$ multijoin -h -k 1 -v 2 A.TXT B.TXT C.TXT

		example (with labels):
                 \$ multijoin -h --labels -k 1 -v 2 A.TXT Sample1 B.TXT SampleB C.TXT SampleC

 --examples     Show detailed examples.

EOF
	exit(0);
}

sub show_examples()
{
	print<<EOF;

To join three files, based on the 4th column, and keeping the 7th,8th,9th columns:

\$ head *.txt
==> AAA.txt <==
chr4	888449	890171	FBtr0308778	0	+	266	1527	1722
chr4	972167	979017	FBtr0310651	0	-	3944	6428	6850
chr4	972186	979017	FBtr0089229	0	-	3944	6428	6831
chr4	972186	979017	FBtr0089231	0	-	3944	6428	6831
chr4	972186	979017	FBtr0089233	0	-	3944	6428	6831
chr4	995793	996435	FBtr0111046	0	+	7	166	642
chr4	995793	997931	FBtr0111044	0	+	28	683	2138
chr4	995793	997931	FBtr0111045	0	+	28	683	2138
chr4	1034029	1047719	FBtr0089223	0	-	5293	13394	13690

==> BBB.txt <==
chr4	90286	134453	FBtr0309803	0	+	657	29084	44167
chr4	251355	266499	FBtr0089116	0	+	56	1296	15144
chr4	252050	266506	FBtr0308086	0	+	56	1296	14456
chr4	252050	266506	FBtr0308087	0	+	56	1296	14456
chr4	252053	266528	FBtr0300796	0	+	56	1296	14475
chr4	252053	266528	FBtr0300800	0	+	56	1296	14475
chr4	252055	266528	FBtr0300798	0	+	56	1296	14473
chr4	252055	266528	FBtr0300799	0	+	56	1296	14473
chr4	252541	266528	FBtr0300797	0	+	56	1296	13987

==> CCC.txt <==
chr4	972167	979017	FBtr0310651	0	-	9927	6738	6850
chr4	972186	979017	FBtr0089229	0	-	9927	6738	6831
chr4	972186	979017	FBtr0089231	0	-	9927	6738	6831
chr4	972186	979017	FBtr0089233	0	-	9927	6738	6831
chr4	995793	996435	FBtr0111046	0	+	5	304	642
chr4	995793	997931	FBtr0111044	0	+	17	714	2138
chr4	995793	997931	FBtr0111045	0	+	17	714	2138
chr4	1034029	1047719	FBtr0089223	0	-	17646	13536	13690

\$ multijoin -h --key 4 --values 7,8,9 *.txt | head -n 10
key           AAA__V7   AAA__V8   AAA__V9   BBB__V7    BBB__V8    BBB__V9    CCC__V7   CCC__V8   CCC__V9
FBtr0089116         0         0         0        56       1296      15144          0         0         0
FBtr0089223      5293     13394     13690         0          0          0      17646     13536     13690
FBtr0089229      3944      6428      6831         0          0          0       9927      6738      6831
FBtr0089231      3944      6428      6831         0          0          0       9927      6738      6831
FBtr0089233      3944      6428      6831         0          0          0       9927      6738      6831
FBtr0111044        28       683      2138         0          0          0         17       714      2138
FBtr0111045        28       683      2138         0          0          0         17       714      2138
FBtr0111046         7       166       642         0          0          0          5       304       642
FBtr0300796         0         0         0        56       1296      14475          0         0         0



EOF
	exit(0);
}