Mercurial > repos > bgruening > text_processing
view multijoin @ 16:ddf54b12c295 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit ded469a802a0496c9a6a2daee7b9505bd8698802-dirty"
author | bgruening |
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date | Tue, 06 Oct 2020 09:47:04 +0000 |
parents | 20344ce0c811 |
children |
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#!/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); }