Mercurial > repos > bgruening > text_processing
view sort-header @ 13:0a8c6b61f0f4 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 4f79443517baf378fbfe1f81be361d97f2938601
author | bgruening |
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date | Wed, 03 Apr 2019 13:56:01 -0400 |
parents | 5314e5d6f040 |
children |
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#!/usr/bin/env perl ## ## Sort-header - wrapper for GNU sort with header-line support ## ## Copyright(C) A. Gordon ## license AGPLv3+ ## use strict; use warnings; use Data::Dumper; use IO::Handle; use Getopt::Long qw(:config bundling no_ignore_case_always); ## Forward declarations sub add_standard_sort_param(@); sub add_standard_sort_param_value(@); sub forbidden_sort_param(@); sub show_help(); sub show_version(); sub show_examples(); sub parse_commandline_options(); sub reassign_input_output(); sub process_header_lines(); sub run_sort(); sub read_line_non_buffered(); ## ## Runtime options ## my $PROGRAM="sort-header"; my $VERSION=0.4; my $check_only=undef; my $input_file=undef; my $output_file=undef; my $field_separator=undef; my $header_lines =1 ; my $debug=undef; my $sort_exit_code=1; #by default, assume some error my @sort_options; ## ## Program Start ## parse_commandline_options(); reassign_input_output(); process_header_lines(); run_sort(); exit($sort_exit_code); ## ## Program End ## sub show_examples() { print<<EOF; Sorting a file with a header line: \$ cat input.txt Fruit Color Price Banana Yellow 4.1 Avocado Green 8.0 Apple Red 3.0 Melon Green 6.1 # By default, 'sort-header' assumes 1 header line # (no need to use --header in this case). \$ sort-header -k3,3nr input.txt Fruit Color Price Avocado Green 8.0 Melon Green 6.1 Banana Yellow 4.1 Apple Red 3.0 EOF exit(0); } sub show_help() { print<<EOF; ${PROGRAM}: Wrapper for GNU sort, allowing sorting files with header lines. Usage: $PROGRAM [HEADER-OPTIONS] [GNU sort Options] [INPUT-FILE] HEADER-OPTIONS: the following options are supported by '${PROGRAM}': --header N = Treat the first N lines as header lines. These line will NOT be sorted. They will be passed directly to the output file. (default: 1) --version = Print ${PROGRAM}'s version. --debugheader = Print debug messages (relating to ${PROGRAM}'s operation). --help = Show this help screen. --examples = Show usage examples. GNU sort options: Most of the standard GNU sort options are supported and passed to GNU sort. The following options can not be used with '${PROGRAM}': -m --merge => ${PROGRAM} can only sort one file, not merge multiple files. -c -C --check => Currently not supported --files0-from => Currently not supported -z --zero-terminated => Currently not supported INPUT-FILE: If INPUT-FILE is not specified, $PROGRAM will use STDIN (just like GNU sort). 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 sort version, run: sort --version EOF exit(0); } sub parse_commandline_options() { my $rc = GetOptions( "ignore-leading-blanks|b" => \&add_standard_sort_param, "dictionary-order|d" => \&add_standard_sort_param, "ignore-case|f" => \&add_standard_sort_param, "general-numeric-sort|g" => \&add_standard_sort_param, "ignore-nonprinting|i" => \&add_standard_sort_param, "month-sort|M" => \&add_standard_sort_param, "human-numeric-sort|h" => \&add_standard_sort_param, "numeric-sort|n" => \&add_standard_sort_param, "random-source=s" => \&add_standard_sort_param_value, "random-sort|R" => \&add_standard_sort_param, "reverse|r" => \&add_standard_sort_param, "sort=s" => \&add_standard_sort_param_value, "version-sort|V" => \&add_standard_sort_param, "check|c" => \&forbidden_sort_param, "C" => \&forbidden_sort_param, "compress-program=s" => \&add_standard_sort_param_value, "debug" => \&add_standard_sort_param, "files0-from=s" => \&forbidden_sort_param, "key|k=s" => \&add_standard_sort_param_value, "merge|m" => \&forbidden_sort_param, "batch-size=i" => \&forbidden_sort_param, "parallel=i" => \&add_standard_sort_param_value, "output|o=s" => \$output_file, "stable|s" => \&add_standard_sort_param, "buffer-size|S=s" => \&add_standard_sort_param_value, "field-separator|t=s" => \&add_standard_sort_param_value, "temporary-directory|T=s" => \&add_standard_sort_param_value, "unique|u" => \&add_standard_sort_param, "zero-terminated|z" => \&forbidden_sort_param, "help" => \&show_help, "version" => \&show_version, "examples" => \&show_examples, "header=i" => \$header_lines, "debugheader" => \$debug, ); exit 1 unless $rc; my @INPUT_FILES = @ARGV; die "$PROGRAM: error: invalid number of header lines ($header_lines)\n" unless $header_lines>=0; die "$PROGRAM: error: Multiple input files specified. This program can sort only a signle file.\n" if (scalar(@INPUT_FILES)>1); $input_file = shift @INPUT_FILES if scalar(@INPUT_FILES)==1; if ($debug) { warn "$PROGRAM: number of header lines = $header_lines\n"; warn "$PROGRAM: PASS-to-Sort options:\n", Dumper(\@sort_options), "\n"; } } sub reassign_input_output() { if ($output_file) { warn "$PROGRAM: Re-assigning STDOUT to '$output_file'\n" if $debug; open OUTPUT, '>', $output_file or die "$PROGRAM: Error: failed to create output file '$output_file': $!\n"; STDOUT->fdopen(\*OUTPUT, 'w') or die "$PROGRAM: Error: failed to reassign STDOUT to '$output_file': $!\n"; } if ($input_file) { warn "$PROGRAM: Re-assigning STDIN to '$input_file'\n" if $debug; open INPUT, '<', $input_file or die "$PROGRAM: Error: failed to open input file '$input_file': $!\n"; STDIN->fdopen(\*INPUT, 'r') or die "$PROGRAM: Error: failed to reassign STDIN to '$input_file': $!\n"; } } sub process_header_lines() { warn "$PROGRAM: Reading $header_lines header lines...\n" if $debug; for (my $i=0; $i<$header_lines; $i++) { my $line = read_line_non_buffered(); exit unless defined $line; print $line; } } sub run_sort() { warn "$PROGRAM: Running GNU sort...\n" if $debug; system('sort', @sort_options); if ($? == -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); } } sub add_standard_sort_param(@) { my ($obj)= @_; add_standard_sort_param_value($obj, undef); } sub add_standard_sort_param_value(@) { my ($obj,$value)= @_; my $option = "" . $obj ; #stringify the optino object, get the option name. if (length($option)==1) { $option = "-" . $option ; } else { $option = "--" . $option ; } push @sort_options, $option ; push @sort_options, $value if $value; } sub forbidden_sort_param(@) { my ($obj,$value)= @_; my $option = "" . $obj ; #stringify the optino object, get the option name. die "$PROGRAM: Error: option '$option' can not be used with this program. If you must use it, run GNU sort directly. see --help for more details.\n"; } sub read_line_non_buffered() { my $line = ''; while ( 1 ) { my $c; my $rc = sysread STDIN, $c, 1; die "$PROGRAM: STDIN Read error: $!" unless defined $rc; return $line if $rc==0 && $line; return undef if $rc==0 && (!$line); $line .= $c ; return $line if ( $c eq "\n"); } }