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Re: Parse XML with Perl regex

by rowdog (Curate)
on Jul 07, 2010 at 23:44 UTC ( #848574=note: print w/replies, xml ) Need Help??

in reply to Parse XML with Perl regex

You're pretty close. In a scalar context a regex returns the number of matches. In a list context, it returns the list of matches.

my ($info_name) = $line =~ /\<info_name\>(\S+)\<\/info_name\>/i;

And now for some notes...

  • DON'T DO THAT! Using regexs on XML is fragile.
  • Use something like XML::LibXML
  • I see fasta in there so you may like Perl and Bioinformatics
  • use strict;
  • use warnings;
  • XML element names should always be lower case, so you don't need to ignore the case in your regex.
  • Your example XML has 3 copies of the same structure so you will end up with one unique key in your hash.
  • Unless this is the beginning of nested t_volumes, you missed the / in </t_volume>

For my example, I decided to rely on the fact that the interesting tags do not contain other tags. If that changes, my code breaks. I also rely on the order of the tags as shown in the example XML, which is generally a dumb assumption since things like XML::LibXML can reorder the elements.

#!/usr/bin/perl use strict; use warnings; my @files = glob('./*.xml'); my %results; foreach my $xmlname (@files) { open my $fh, '<', $xmlname or die "$xmlname: $!"; while ( my $line = <$fh> ) { my ($name) = $line =~ /\<info_name\>([^<]+)\<\/info_name\>/ or next; while ( my $l = <$fh> ) { $l =~ /\<it_size\>([^<]+)\<\/it_size\>/ or next; $results{$name} = $1; last; } } } print map { "$_ => $results{$_}\n" } keys %results;
jth@reina:~/tmp$ perl FZGA34177.b1 => 35000

And finally, my XML::LibXML alternative which does not rely on tag ordering or the content of the tag.

#!/usr/bin/perl use strict; use warnings; use XML::LibXML; my @files = glob('./*.xml'); my %results; foreach my $xmlname (@files) { my $dom = XML::LibXML->load_xml( location => $xmlname, recover => 1, # no </t_volume> in example ) or die $!; foreach my $node ( $dom->findnodes('//info') ) { $results{ $node->find('info_name') } = $node->find('it_size'); } } print map { "$_ => $results{$_}\n" } keys %results;
jth@reina:~/tmp$ perl ./848551.xml:55: parser error : Premature end of data in tag t_volume +line 54 ^ ./848551.xml:55: parser error : Premature end of data in tag t_volume +line 2 ^ FZGA34177.b1 => 35000

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