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|
#!/bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
if 0;
#-----------------------------------------------------------------------
#$Author: antanas $
#$Date: 2021-04-28 19:35:53 +0300 (Wed, 28 Apr 2021) $
#$Revision: 8738 $
#$URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/tags/v3.7.0/scripts/cif_split_primitive $
#------------------------------------------------------------------------
#*
#* Split CIF files into separate files with one data_ section each.
#*
#* This is a very naive and primitive version of the splitter, which
#* expects each data_... section to start on a new line. It may fail on
#* some CIF files that do not follow such convention. For splitting of
#* any correctly formatted CIF files, one must do full CIF parsing
#* using CIF grammar and tokenisation of the file.
#*
#* USAGE:
#* $0 --options input1.cif input*.cif
#**
use strict;
use warnings;
use File::Basename qw( basename );
use COD::SOptions qw( getOptions );
use COD::SUsage qw( usage options );
use COD::ErrorHandler qw( report_message );
use COD::ToolsVersion qw( get_version_string );
my $die_on_error_level = {
ERROR => 1,
WARNING => 0,
NOTE => 0
};
my $verbose = 1;
my $output_dir = '';
#* OPTIONS:
#* -o, --output-dir out/
#* Put all split files into the directory out/
#* (default: './').
#* -v, --verbose
#* Print names of the generated files to STDERR.
#* -q, --quiet
#* Do not print file names to STDERR.
#* --help, --usage
#* Output a short usage message (this message) and exit.
#* --version
#* Output version information and exit.
#**
@ARGV = getOptions(
'-o,--output-dir' => \$output_dir,
'-v,--verbose' => sub { $verbose = 1 },
'-q,--quiet' => sub { $verbose = 0 },
'--options' => sub { options; exit },
'--help,--usage' => sub { usage; exit },
'--version' => sub { print get_version_string(), "\n"; exit }
);
$output_dir =~ s./+$..;
my $output_file;
my $output_handle;
my @initial_comments = ();
my @data_global = ();
my %files = ();
my %has_end = ();
my $global = 0;
my $skip = 1;
my $initial_comments = 1;
my $data_id;
while(<>) {
if( /^\s*\#|^\s*$/ && $initial_comments ) {
push @initial_comments, $_;
next;
}
$initial_comments = 0;
if( /^\s*data_global\s*$/ || /^\s*data_global\s+/ ) {
if( int(@data_global) == 0 ) {
push @data_global, $_;
$global = 1;
$skip = 0;
} else {
report_message( {
'program' => $0,
'err_level' => 'WARNING',
'message' => 'second data_global encountered -- skipping'
}, $die_on_error_level->{'WARNING'} );
$global = 1;
$skip = 1;
}
next;
}
if( /^\s*data_([^\s]+)/ ) {
$data_id = $1;
$data_id =~ s/^data_//;
$global = 0;
$skip = 0;
close $output_handle if $output_handle;
my $suffix = $data_id;
$suffix =~ s/[^-+._a-zA-Z0-9]/_/g;
my $basename = basename( $ARGV, '.cif' );
if( $basename ne '-' ) {
$output_file = basename( $ARGV, '.cif' ) . "_${suffix}" . '.cif';
} else {
$output_file = $suffix . '.cif';
}
if( $output_dir ne '' ) {
$output_file = $output_dir . '/' . $output_file;
}
if( !exists $files{$output_file} ) {
open $output_handle, '>', $output_file or
die "$0: $output_file: ERROR, could not open file for "
. 'writing -- ' . lcfirst($!) . "\n";
$files{$output_file} = $output_file;
print "$output_file\n" if $verbose;
for ( @initial_comments, @data_global ) {
print $output_handle $_;
}
} else {
open $output_handle, '>>', $output_file or
die "$0: $output_file: ERROR, could not open file for"
. 'appending -- ' . lcfirst($!) . "\n";
print "$output_file (appending)\n" if $verbose;
}
}
if( /^\s*\#=+END/ ) {
$has_end{$output_file} = 1;
}
if( $global == 1 && $skip == 0 ) {
push @data_global, $_;
next;
}
next if $skip;
print $output_handle $_;
if( eof ARGV ) {
$output_file = undef;
close $output_file if $output_file;
@data_global = ();
@initial_comments = ();
$global = 0;
$skip = 1;
$initial_comments = 1;
}
}
close $output_file if $output_file;
|
