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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/cif2csv $
#------------------------------------------------------------------------------
#*
#* Convert a CIF file into a CSV file.
#*
#* USAGE:
#* $0 --options input1.cif input*.cif
#**
use strict;
use warnings;
use COD::CIF::Parser qw( parse_cif );
use COD::SOptions qw( getOptions );
use COD::SUsage qw( usage options );
use COD::ErrorHandler qw( process_parser_messages report_message );
use COD::ToolsVersion qw( get_version_string );
sub csv_format($$$);
my $die_on_error_level = {
'ERROR' => 1,
'WARNING' => 0,
'NOTE' => 0
};
my $use_parser = 'c';
#* OPTIONS:
#* --use-perl-parser
#* Use Perl parser to parse CIF files.
#* --use-c-parser
#* Use C parser to parse CIF files (default).
#*
#* --help, --usage
#* Output a short usage message (this message) and exit.
#* --version
#* Output version information and exit.
#**
@ARGV = getOptions(
'--use-perl-parser' => sub { $use_parser = 'perl' },
'--use-c-parser' => sub { $use_parser = 'c' },
'--options' => sub { options; exit },
'--help,--usage' => sub { usage; exit },
'--version' => sub { print get_version_string(), "\n"; exit }
);
@ARGV = ('-') unless @ARGV;
binmode STDOUT, ':encoding(UTF-8)';
binmode STDERR, ':encoding(UTF-8)';
my $fields_separator = ','; # as per section 1.4 of RFC 4180
my $lines_separator = "\r\n"; # as per section 4.1.1 of RFC 2046
for my $filename (@ARGV) {
my $options = { 'parser' => $use_parser, 'no_print' => 1 };
my ( $data, $err_count, $messages ) = parse_cif( $filename, $options );
process_parser_messages( $messages, $die_on_error_level );
if( !@{$data} || !defined $data->[0] || !defined $data->[0]{name} ) {
report_message( {
'program' => $0,
'filename' => $filename,
'err_level' => 'WARNING',
'message' => 'file seems to be empty'
}, $die_on_error_level->{WARNING} );
next;
}
for my $datablock (@{$data}) {
print {*STDERR} $datablock->{name} . "\n";
print 'data_'
. $fields_separator . $datablock->{name}
. $lines_separator;
# print stray values
for my $tagName (sort keys %{$datablock->{values}}) {
if(defined $datablock->{inloop}->{$tagName}) {
next; # print loops after stray values
}
my $precision = undef;
if(defined $datablock->{precisions}{$tagName}[0]) {
$precision = $datablock->{precisions}{$tagName}[0];
}
print $tagName . $fields_separator;
print csv_format($datablock->{values}{$tagName}[0],
$datablock->{types}{$tagName}[0],
$precision);
print $lines_separator;
}
# and print loop values
for my $loop (@{$datablock->{loops}}) {
local $, = $fields_separator;
print @{$loop};
print $lines_separator;
my $loop_value_length = $#{$datablock->{values}{$loop->[0]}};
for my $line(0..$loop_value_length) {
for my $tagName (@{$loop}) {
my $precision = undef;
if(defined $datablock->{precisions}{$tagName}[0]) {
$precision = $datablock->{precisions}{$tagName}[0];
}
print csv_format($datablock->{values}{$tagName}[$line],
$datablock->{types}{$tagName}[$line],
$precision);
if($tagName ne $loop->[$#{$loop}]) { # do not print field separator
print $fields_separator; # after last element
}
}
print $lines_separator;
}
}
}
}
sub csv_format($$$)
{
my ($value, $type, $precision) = @_;
if(0 == length $value) {
return '';
}
my $result = '';
my %formats = ('SQSTRING' => '"%s"',
'DQSTRING' => '"%s"',
'UQSTRING' => '"%s"',
'TEXTFIELD' => '"%s"',
'INT' => '%d',
'FLOAT' => '%f');
return unless defined $formats{$type} && defined $value;
my $format = $formats{$type};
if('INT' eq $type || 'FLOAT' eq $type) {
if ( $value =~ m/([+-]?[0-9]*(?:[.][0-9]+)?)(?:[(]([0-9]+)[)])?/ ) {
$precision = $2;
$value = $1;
}
}
if($value =~ m/,/ && $format !~ m/"/) {
$format = '"' . $format . '"';
}
if($format =~ m/"/) {
$value =~ s/"/""/g; # as per sections 2.6 & 2.7 of RFC 4180
}
$result = sprintf $format, $value;
if(defined $precision) {
$result .= '(' . $precision . ')';
}
return $result;
}
|
