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#-------------------------------------------------------------------------------
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# PACKAGE : Bio::Tools::Blast::HTML
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# PURPOSE : To encapsulate code for HTML formatting BLAST reports.
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# AUTHOR : Steve Chervitz (sac@bioperl.org)
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# CREATED : 28 Apr 1998
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# REVISION: $Id: HTML.pm,v 1.15 2002/11/04 09:12:51 heikki Exp $
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# For the latest version and documentation, visit the distribution site:
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# http://bio.perl.org/Projects/Blast/
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# To generate documentation, run this module through pod2html
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# (preferably from Perl v5.004 or better).
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# If your Blast reports are not getting marked up correctly, add or
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# modify the regexps in _markup_report() to accomodate the format of
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# Copyright (c) 1996-98 Steve Chervitz. All Rights Reserved.
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# This module is free software; you can redistribute it and/or
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# modify it under the same terms as Perl itself.
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#-------------------------------------------------------------------------------
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package Bio::Tools::Blast::HTML;
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use Bio::Tools::WWW qw(:obj);
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use vars qw( @ISA @EXPORT @EXPORT_OK %EXPORT_TAGS
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$ID %DbUrl %SGDUrl $Revision
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$Acc $Pir_acc $Word $Signif $Int $Descrip);
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@EXPORT_OK = qw(&get_html_func &strip_html);
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%EXPORT_TAGS = ( std => [qw(&get_html_func &strip_html)] );
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$ID = 'Bio::Tools::Blast::HTML';
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$Revision = '$Id: HTML.pm,v 1.15 2002/11/04 09:12:51 heikki Exp $'; #'
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Bio::Tools::Blast::HTML - Bioperl Utility module for HTML formatting Blast reports
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=head2 Adding HTML-formatting
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use Bio::Tools::Blast::HTML qw(&get_html_func);
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$func = &get_html_func();
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# Now as each line of the report is read, pass it to &$func($line).
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See L<get_html_func()|get_html_func> for details.
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Also see B<Bio::Tools::Blast::to_html> for an example of usage.
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=head2 Removing HTML-formatting
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use Bio::Tools::Blast::HTML qw(&strip_html);
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&strip_html(\$blast_report_string)
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See L<strip_html()|strip_html> for details.
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This module is included with the central Bioperl distribution:
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http://bio.perl.org/Core/Latest
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ftp://bio.perl.org/pub/DIST
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Follow the installation instructions included in the README file.
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This module can be used to add HTML formatting to or remove HTML
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formatting from a raw Blast sequence analysis report. Hypertext links
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to the appropriate database are added for each hit sequence (GenBank,
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Swiss-Prot, PIR, PDB, SGD).
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This module is intended for use by Bio::Tools::Blast.pm and related modules,
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which provides a front-end to the methods in Bio::Tools::Blast::HTML.pm.
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Bio::Tools::Blast::HTML.pm does not inherit from any other class
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besides Exporter. It is used by B<Bio::Tools::Blast.pm> only. This
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class relies on B<Bio::Tools::WWW.pm> to provide key URLS for adding
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links in the Blast report to specific databases.
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The greatest dependency comes from the dynamic state of the web. URLs
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are are likely to change in the future, so all links cannot be
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guaranteed to work indefinitely. Feel free to report broken or
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incorrect database links (L<FEEDBACK | FEEDBACK>). Thanks!
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Bio::Tools::Blast.pm - Blast object.
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Bio::Tools::WWW.pm - URL repository.
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http://bio.perl.org/Projects/modules.html - Online module documentation
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http://bio.perl.org/Projects/Blast/ - Bioperl Blast Project
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http://bio.perl.org/ - Bioperl Project Homepage
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User feedback is an integral part of the evolution of this and other
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Bioperl modules. Send your comments and suggestions preferably to one
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of the Bioperl mailing lists. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bio.perl.org/MailList.html - About the mailing lists
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=head2 Reporting Bugs
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Report bugs to the Bioperl bug tracking system to help us keep
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track the bugs and their resolution. Bug reports can be submitted
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via email or the web:
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bioperl-bugs@bio.perl.org
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http://bugzilla.bioperl.org/
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Steve Chervitz, E<lt>sac@bioperl.orgE<gt>
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Copyright (c) 1998-2000 Steve Chervitz. All Rights Reserved.
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This module is free software; you can redistribute it and/or
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modify it under the same terms as Perl itself.
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#### END of main POD documentation.
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###################### BEGIN FUNCTIONS ########################
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Methods beginning with a leading underscore are considered private
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and are intended for internal use by this module. They are
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B<not> considered part of the public interface and are described here
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for documentation purposes only.
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Usage : $func_ref = &get_html_func( [array_ref] );
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: This method is exported.
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Purpose : Provides a function that adds HTML formatting to a
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: raw Blast report line-by-line.
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: Utility method used by to_html() in Bio::Tools::Blast.pm.
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Returns : Reference to an anonymous function to be used while reading in
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: The function itself operates on the Blast report line-by-line
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: HTML-ifying it and printing it to STDOUT (or saving in the supplied
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: array ref) as it goes:
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: foreach( @raw_report ) { &$func_ref($_); }
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Argument : array ref (optional) for storing the HTML-formatted report.
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: If no argument is supplied, HTML output is sent to STDOUT.
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Throws : Croaks if an argument is supplied and is not an array ref.
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: The anonymous function returned by this method croaks if
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: the Blast output appears to be HTML-formatted already.
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Comments : Adapted from a script by Keith Robison November 1993
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: krobison@nucleus.harvard.edu; http://golgi.harvard.edu/gilbert.html
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: Modified extensively by Steve Chervitz and Mike Cherry.
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: Some modifications are customizations for BLAST reports served up
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: by the Saccharomyces Genome Database.
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: Feel free to modify or replace portions of this code as necessary
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: to accomodate new BLAST datasets or changes to the Blast format.
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See Also : B<Bio::Tools::Blast::to_html()>
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#--------------------
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#--------------------
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## Key booleans used in parsing.
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my $found_table = 0; # Located the table at top of report (a.k.a. 'descriptions').
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my $found_data = 0; # Nothing is done until this is true
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my $skip = 0; # Skipping various items in the report header
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my $ref_skip = 0; # so we can include nice HTML versions
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# (e.g., references for the BLAST program).
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my $getGenBankAlert = 0;
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my $gi_link = \$_gi_link;
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if( defined($out_aref) and not ref($out_aref) eq 'ARRAY') {
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croak("Argument must be an ARRAY ref not a ${\ref $out_aref}.");
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my $refs = &_prog_ref_html;
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&_set_markup_data() if not $_set_markup;
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# $_ contains a single line from a Blast report.
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croak("Report appears to be HTML formatted already.") if m/<HTML>|<TITLE>|<PRE>/i;
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if(not $found_table) {
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# Replacing an reference data with special HTML.
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$ref_skip = 0 if /^\s+$/;
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## SAC: created this test since we are no longer reading from STDIN.
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$out_aref ? push(@$out_aref, $_) : print $_;
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$getNote = 0 if m/^\s+$/;
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} elsif( m/(.*), Up \d.*/ or /Date: +(.+)/ or /Start: +(.+?) +End:/ ) {
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### Network BLAST reports from NCBI are time stamped as follows:
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#Fri Apr 18 15:55:41 EDT 1997, Up 1 day, 19 mins, 1 user, load: 19.54, 19.13, 17.77
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my $date = "<b>BLASTed on:</b> $1<p>\n";
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$out_aref ? push(@$out_aref, $date) : print $date;
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} elsif ( /^(<\w+>)?(T?BLAST[NPX])\s+(.*?)/ ) {
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s#(\S+)\s+(.*)#<P><B>Program:</B> $1 $2 $3<br>#o;
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$out_aref ? push(@$out_aref, $_) : print $_;
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if($prog =~ /BLASTN/) {
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## Prevent the error at Entrez when you ask for a nucl
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## entry with a protein GI number.
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$$gi_link = $DbUrl{'gb_n'}; # nucleotide
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$$gi_link = $DbUrl{'gb_p'}; # protein
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} elsif ( m/^Query=/ ) {
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# Keeping the "Query=" format to keep it parsable by Blast.pm
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# (after stripping HTML).
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s#Query= *(.*)#<title>$1</title>\n<p><b>Query=</b> $1#o;
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$out_aref ? push(@$out_aref, $_) : print $_;
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} elsif ( /Reference:/) {
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} elsif ( /^Database:/ ) {
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&_markup_database(\$_);
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$out_aref ? push(@$out_aref, $_) : print $_;
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if ( /non-redundant genbank/i and $prog =~ /TBLAST[NX]/i) {
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$getGenBankAlert = 1;
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} elsif ( /sequences;/ ) {
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$out_aref ? push(@$out_aref, $str) : print $str;
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} elsif ( /^\s+\(\d+ letters\)\s+/ ) {
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$str = "<br>    $_";
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$out_aref ? push(@$out_aref, $str) : print $str;
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} elsif ( /^(WARNING|NOTICE):/i ) {
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s#WARNING: *(.*)#<p><b><font color="red">$1:</font></b> $1#o;
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$out_aref ? push(@$out_aref, $_) : print $_;
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} elsif ( /Score +E\s*$/ or /Probability\s*$/ ) {
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# Put the last HTML-formatted lines before the main body of report.
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$out_aref ? push(@$out_aref, $refs) : print $refs;
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if($getGenBankAlert) {
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$str = &_genbank_alert;
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$out_aref ? push(@$out_aref, $str) : print $str;
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$out_aref ? push(@$out_aref, $str) : print $str;
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&_markup_report(\$_);
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if ($found_data and not($skip or $ref_skip)) {
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$out_aref ? push(@$out_aref, $_) : print $_;
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=head2 _set_markup_data
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Usage : n/a; utility method used by get_html_func()
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Purpose : Sets various hashes and regexps used for adding HTML
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: to raw Blast output.
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Comments : These items need be set only once.
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See Also : L<get_html_func()|get_html_func>
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sub _set_markup_data {
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%DbUrl = $BioWWW->search_url('all');
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%SGDUrl = $BioWWW->sgd_url('all');
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$Signif = '[\de.-]{3,}'; # Regexp for a P-value or Expect value.
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$Int = ' *\d\d*'; # Regexp for an integer.
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$Descrip = ' +.* {2,}?'; # Regexp for a description line.
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$Acc = '[A-Z][\d.]+'; # Regexp for GB/EMBL/DDJB/SP accession number
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$Pir_acc = '[A-Z][A-Z0-9]{5,}'; # Regexp for PIR accession number
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$Word = '[\w_.]+'; # Regexp for a word. Include dot for version.
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=head2 _markup_database
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Usage : n/a; utility method used by get_html_func()
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Purpose : Converts a cryptic database ID into a readable name.
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Comments : This is used for converting local database IDs into
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: understandable terms. At present, it only recognizes
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: databases used locally at SGD.
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See Also : L<get_html_func()|get_html_func>
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#---------------------
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sub _markup_database {
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#---------------------
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my $line_ref = shift;
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local $_ = $$line_ref;
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$_ =~ s#YeastN#<i>S. cerevisiae</i> GenBank Data Set; #;
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$_ =~ s#YeastP#Non-Redundant <i>S. cerevisiae</i> Protein Data Set; #;
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$_ =~ s#genoSC#Complete DNA Sequence for the S. cerevisiae Genome; #;
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$_ =~ s#YeastORF-P#Translation of all Standard S.c. ORFs; #;
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$_ =~ s#YeastORF-N#Coding Sequence of all Standard S.c. ORFs; #;
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s#Database: *(.*)#<p><b>Database:</b> $1#o;
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=head2 _markup_report
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Usage : n/a; utility function used by get_html_func()
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Purpose : Adds HTML links to aid navigation of raw Blast output.
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Comments : HTML-formatting is dependent on the Blast server that
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: provided the Blast report. Currently, this function can handle reports
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: produced by NCBI and SGD. Feel free to modify this function
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: to accomodate reports produced by other servers/sites.
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: This function is simply a collection of substitution regexps
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: that recognize and modify the relevant lines of the Blast report.
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: All non-header lines of the report are passed through this function,
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: only the ones that match will get modified.
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: The general scheme for adding links is as follows:
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: (Some of the SGD markups do not follow this scheme precisely
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: but this is the general trend.)
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: For description lines in the summary table at the top of report:
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: DB:SEQUENCE_ID DESCRIPTION SIGNIF_VAL
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: DB = links to the indicated database (if not Gen/Embl/Ddbj).
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: SEQUENCE_ID = links to GenBank entry for the sequence.
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: SIGNIF_VAL = internal link to relevant alignment section.
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: For the alignment sections in the body of the report:
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: DB:SEQUENCE_ID (Back | Top) DESCRIPTION
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: DB = links to the indicated database (if not Gen/Embl/Ddbj).
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: SEQUENCE_ID = links to GenBank entry for the sequence.
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: SIGNIF_VAL = internal link to alignment section.
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: Back = internal link to description line in summary section.
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: Top = internal link to top of page.
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: 'DB' links are created for PDB, PIR, and SwissProt sequences.
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: RE_PARSING HTML-FOMRATTED REPORTS:
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: ----------------------------------
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: HTML-formatted reports generated by this module, as well as reports
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: obtained from the NCBI servers, should be parsable
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: by Bio::Tools::Blast.pm. Parsing HTML-formatted reports is
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: slow, however, since the HTML must be removed prior to parsing.
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: Parsing HTML-formatted reports is dependent on the specific structure
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: of the HTML and is generally not recommended.
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: Note that since URLs can change without notice, links will need updating.
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: The links are obtained from Bio::Tools::WWW.pm updating that module
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: will update this as well.
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Bugs : Some links to external databases are incorrect
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: (in particular, for 'bbs' and 'prf' databases on NCBI Blast reports.
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: Some links may fail as a result of the dynamic nature of the web.
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: Hypertext links are not added to hits without database ids.
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See Also : L<get_html_func()|get_html_func>, B<Bio::Tools::WWW.pm>, L<strip_html>()
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#--------------------
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#--------------------
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my $line_ref = shift;
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local $_ = $$line_ref;
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## REGEXPS FOR ALIGNMENT SECTIONS (within the body of the report,
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## the text above the list of HSPs).
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## If the HSP alignment sections don't start with a '>' we have no way
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## of finding them. This occurs with reports saved from HTML-formatted
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## web pages, which we shouldn't be processing here anyway.
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## To facilitate parsing of HTML-formatted reports by Bio::Tools::Blast.pm,
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## the <a name=...> anchors should be added at the BEGINNING of the HSP
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## alignment section lines and at the END of the description section lines.
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# Removing " ! " addded by GCG.
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### NCBI-specific markups for HSP alignment section lines:
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# GenBank/EMBL, DDBJ hits (GenBank Format):
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s@^>(gb|emb|dbj|ref)\|($Word)(\|$Word)?(.*)$@<a name=$2_A></a><b>$1:<a href="$_gi_link$2">$2$3</a></b>$4<br>(<a href="\#$2_H">Back|<a href="\#top">Top</a>)@o;
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s@^>(gb|emb|dbj|ref)\|($Word)(\| \(?$Word\)?)(.*)$@<a name=$2_A></a><b>$1:<a href="$_gi_link$2">$2</a></b>$3$4<br>(<a href="\#$2_H">Back|<a href="\#top">Top</a>)@o;
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s@^>pir\|\|($Word)( .*)$@<a name=$1_A></a><b><a href=\"$DbUrl{'pir_acc'}$1\">pir</a>:<a href="$DbUrl{'gb_p'}$1">$1</a></b> $2 <br>(<a href="\#$1_H">Back|<a href="\#top">Top</a>)@o;
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# GI hits (GenBank Format): using a nested (())
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s@^>(gi)\|($Word)( +\(($Word)\))( .*)$@<a name=$4_A></a><b>$1:<a href="$_gi_link$4">$2</a></b>$3$5<br>(<a href="\#$4_H">Back|<a href="\#top">Top</a>)@o;
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# GNL PID hits (GenBank Format):
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s@^>(gnl)\|($Word)?(\|$Word) +\(($Word)\)( .*)$@<a name=$4_A></a><b>$1:<a href="$_gi_link$4">$2$3</a></b>($4)$5<br>(<a href="\#$4_H">Back|<a href="\#top">Top</a>)@o;
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# BBS and PRF hits (what db?) (GenBank Format):
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s@^>(bbs|prf)\|\|?($Word)( .*)$@<a name=$2_A></a><b>$1:<a href="$_gi_link$2">$2</a></b>$3<br>(<a href="\#$2_H">Back|<a href="\#top">Top</a>)@o;
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s@^>sp\|($Word)\|($Word)?( .*)$@<a name=$1_A></a><b><a href="$DbUrl{'swpr'}$1">sp</a>:<a href="$DbUrl{'gb_p'}$1">$1|$2</a></b>$3<br>(<a href="\#$1_H">Back|<a href="\#top">Top</a>)@o;
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## PDB ids with or without a chain identifier (GenBank format)
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s@^>pdb\|(\d\w{3})\|[\w ] (.*)$@<a name=$1_A></A><b><a href=\"$DbUrl{'3db'}$1\">pdb</A>:<a href="$DbUrl{'gb_struct'}$1">$1</a></b> (<a href="\#$1_H">Back</a>|<a href="\#top">Top</a>) $2@o;
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### SGD-specific markups for HSP alignment section lines:
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## PDB ids without chain identifier
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s@^>PDB_UNIQUEP:(\d\w{3})_ (.*)$@<a name=$1_A></A><b><A HREF="$DbUrl{'3db'}$1">PDB</a>:<A HREF="$DbUrl{'gb_struct'}$1">$1</A></b> (<a href="\#$1_H">Back</a>|<a href="\#top">Top</a>) $2@o;
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## PDB ids with chain identifier
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s@^>PDB_UNIQUEP:(\d\w{3})_([\w ]{1})(.*)$@<a name=$1_A></A><b><A HREF="$DbUrl{'3db'}$1">PDB</a>:<A HREF="$DbUrl{'gb_struct'}$1">$1</A></b> Chain:$2, (<a href="\#$1_H">Back</a>|<a href="\#top">Top</a>) $3@o;
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s@^>($Word)PEPT:GI_(\d+)(.*)$@<a name=$2_A></a><b>$1:<a href="$DbUrl{'gb_p'}$2">GI_$2</a></b> $3 <br>(<a href="\#$2_H">Back|<a href="\#top">Top</a>)@o;
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# The gcg blast dataset generating tools up-case all sbjct sequence IDs.
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# This is fine for yeast but not worm. This is considered a hack here.
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s@WORMPEPT:(\w+\.)(\S+)@WORMPEPT:$1\L$2\E@;
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s@^>WORMPEPT:(\S+)(.*)$@<a name=$1_A></a><b>WORMPEP:<A HREF="$DbUrl{'wormace'}$1">$1</a></b> $2 <br>(<a href="\#$1_H">Back|<a href="\#top">Top</a>)@o;
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s#^>(GB_$Word):($Word) ($Acc) (.*$)#<a name=$2_$3_A></A><a href=\#$2_$3_H>$2|$3</A>$4\t<b>[<A HREF=$_gi_link$3>GenBank</A> / <A HREF=$DbUrl{'embl'}$3>EMBL</A> / <A HREF=\"$SGDUrl{'seq_an'}$2\*\">SGD</A>]</b> #o;
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# Sac's version: ORF name is an external link into SGD:
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s@^>ORFP:(\S*) +([\w-]+)(.*$)@<a name=$1_A></A>ORFP:<a href=\"$SGDUrl{'locus'}$2\">$1 $2</A>$3<br>     <b>[<A HREF=\"$SGDUrl{'seq_an'}$2\">Gene/Sequence Resources</a> / <a href=\"$SGDUrl{'map_orf'}$2\">ORF Map</a></b>] <a href="\#$1_H">Back</a>|<a href="\#top">Top</a>@o;
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# s#^>ORFP:(\S*) (.*$)#<a name=$1_A></A><a href=\#$1_H>ORFP:$1</A> $2\t<b>[<A HREF=\"$SGDUrl{'seq_an'}$1\">Gene/Sequence Resources</a> / <a href=\"$SGDUrl{'map_orf'}$1\">ORF Map</a>]</b> #o;
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s#^>ORFN:(\S*) (.*$)#<a name=$1_A></A><a href=\#$1_H>ORFN:$1</A> $2\t<b>[<A HREF=\"$SGDUrl{'seq_an'}$1\">Gene/Sequence Resources</a>] / <a href=\"$SGDUrl{'map_orf'}$1\">ORF Map</a></b> #o;
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s#^>NR_SC:GP-\S* gi\|(\w+)([\w\|]*) (.*$)#<a name=$1_A></A><a href=\#$1_H>GenPept|$1</A> gp|$2 $3\t<b>[<A HREF=$DbUrl{'gb_p'}$1>GenPept</A> / <A HREF=\"$SGDUrl{'gi'}$1\*\">SGD</A>]</b> #o;
507
s#^>NR_SC:SW-$Word SW:($Word) ($Acc) (.*$)#<a name=$1_A></A><a href=\#$1_H>SWISS|$1 $2</A> $3\t<b>[<a href=$DbUrl{'swpr'}$2>SwissProt</a> / <A HREF=$DbUrl{'gb_p'}$2>Entrez</A>]</b>#o;
509
s#^>NR_SC:PIR-$Word PIR:($Word) (.*$)#<a name=$1_A> </A><a href=\#$1_H>PIR|$1</A> $2\t<b>[<a href=$DbUrl{'pir_uid'}$1>PIR</a> / <A HREF=$DbUrl{'gb_p'}$1>Entrez</A>]</b>#o;
511
s#^>CHRS:([A-Z][0-9]*) (.*)$#<a name=$1_A></a><a href=\#$1_H>$1</A> $2: [<b><a href=$SGDUrl{'seq_an'}$1>Gene/Sequence Resources</A> / <a href=\"$SGDUrl{'map_chr'}$1\">ORF Map</a></b>]#o;
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s#^>NOT:([A-Z]_[0-9]*-[0-9]*)( *)Chromosome ([0-9]*) from ([0-9]*) to ([0-9]*)$#<a name=$1_A></a><a href=\#$1_H>$1</A> $2Chromosome $3 from $4 to $5 [<b><a href=$SGDUrl{'chr'}$3\&beg=$4\&end=$5>Gene/Sequence Resources</a> / <a href=\"$SGDUrl{'map_chr'}$3\&beg=$4\&end=$5\">ORF Map</a> / <a href=\"$SGDUrl{'chr_old'}$3\&beg=$4\&end=$5\">Retrieve DNA</a></b>]#o;
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s#^>UTR5_SC_[0-9]*:(\S*) 5' untranslated region, chr(\S*) ([0-9]*) - ([0-9]*)(.*$)#<a name=$1_A></A><a href=\#$1_H>UTR5:$1</A> $1 5' untranslated region, chr$2 $3 - $4, $5\t<b>[<A HREF=\"$SGDUrl{'chr'}$2&beg=$3&end=$4\">Gene/Sequence Resources</A> / <a href=\"$SGDUrl{'map_chr'}$2\&beg=$3\&end=$4\">ORF Map</a>]</b>#o;
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# Hits without a db identifier.
518
# If any of the previous regexps succeed, the leading '>' will be removed.
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# Otherwise, this regexp could cause trouble.
520
s@^>($Word)(.*)$@<a name=$1_A></a>$1 $2<br>(<a href="\#$1_H">Back|<a href="\#top">Top</a>)@o;
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## REGEXPS FOR SUMMARY TABLE LINES AT TOP OF REPORT (a.k.a. 'descriptions')
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## (table of sequence id, description, score, P/Expect value, n)
526
## Not using bold face to highlight the sequence id's since this can throw off
527
## off formatting of the line when the IDs are different lengths. This lead to
528
## the scores and P/Expect values not lining up properly.
530
### NCBI-specific markups for description lines:
532
# GenBank/EMBL, DDBJ hits (GenBank Format):
533
s@^ ?(gb|emb|dbj|ref)\|($Word)(\|$Word)?($Descrip)($Int +)($Signif)(.*)$@$1:<a href="$_gi_link$2">$2$3</a>$4$5<A href="\#$2_A">$6</a>$7<a name="$2_H"></a>@o;
535
s@^ ?(gb|emb|dbj|ref)\|($Word)(\| \(?$Word\)?)($Descrip)($Int +)($Signif)(.*)$@$1:<a href="$_gi_link$2">$2</a>$3$4$5<A href="\#$2_A">$6</a>$7<a name="$2_H"></a>@o;
538
s@^ ?pir\|\|($Word)?($Descrip)($Int) ($Signif)(.*)$@<a href="$DbUrl{'pir_acc'}$1">pir</a>:<a href="$DbUrl{'gb_p'}$1">$1</a> $2$3 <A href="\#$1_A">$4</a>$5<a name="$1_H"></a>@o;
540
# GI hits (GenBank Format): using a nested (())
541
s@^ ?gi\|($Word)( +\(($Word)\))($Descrip)($Int) ($Signif)(.*)$@gi:<a href="$_gi_link$3">$1</a>$2$4$5 <A href="\#$3_A">$6</a>$7<a name="$3_H"></a>@o;
543
s@^ ?(gnl)\|($Word)?(\|$Word +)\(($Word)\)($Descrip)($Int) ($Signif)(.*)$@$1:<a href="$_gi_link$4">$2$3</a>($4)$5$6 <A href="\#$4_A">$7</a>$8<a name="$4_H"></a>@o;
546
s@^ ?(bbs|prf)\|\|?($Word)($Descrip)($Int) ($Signif)(.*)$@$1:<a href="$_gi_link$2">$2</a> $3$4 <A href="\#$2_A">$5</a>$6<a name="$2_H"></a>@o;
549
## SwissProt accessions (GenBank format)
550
s@^ ?sp\|($Word)(\|$Word)?($Descrip)($Int) ($Signif)(.*)$@<a href="$DbUrl{'swpr'}$1">sp</a>:<a href="$DbUrl{'gb_p'}$1">$1$2</a>$3$4 <a href="\#$1_A">$5</a>$6<a name="$1_H"></a>@o;
552
## PDB ids with or without a chain ID (GenBank format)
553
s@^ ?pdb\|($Word)\|($Word)?($Descrip)($Int) ($Signif)(.*)$@<a href="$DbUrl{'3db'}$1">pdb</a>:<a href="$DbUrl{'gb_struct'}$1">$1_$2</a>$3$4 <a href="\#$1_A">$5</a>$6<a name="$1_H"></a>@o;
556
### SGD-specific markups for description lines:
558
## PDB ids without chain identifier
559
s@^ ?PDB_UNIQUEP:(\d\w{3})_($Descrip)($Int) ($Signif)(.*)$@<a href="$DbUrl{'3db'}$1">PDB</a>:<A HREF="$DbUrl{'gb_struct'}$1">$1</A> $2$3 <a href="\#$1_A">$4</a>$5<a name="$1_H"></a>@o;
562
## PDB ids with chain identifier
563
s@^ ?PDB_UNIQUEP:(\d\w{3})_(\w)($Descrip)($Int) ($Signif)(.*)$@<a href="$DbUrl{'3db'}$1">PDB</a>:<A HREF="$DbUrl{'gb_struct'}$1">$1</A> Chain:$2$3$4 <a href="\#$1_A">$5</a>$6<a name="$1_H"></a>@o;
566
s@^ ?($Word)PEPT:GI_(\d+)($Descrip)($Int) ($Signif)(.*)$@$1:<A HREF="$DbUrl{'gb_p'}$2">GI_$2</A> $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>@o;
568
s@^ *WORMPEPT:(\S+)($Descrip)($Int) ($Signif)(.*)$@WORMPEP:<A HREF="$DbUrl{'wormace'}$1">$1</a> $2 $3 <a href="\#$1_A">$4</a>$5<a name="$1_H"></a>@o;
570
## Mike Cherry's markups. SAC note: added back database name to allow
571
## the HTML-formatted version to be parsable by Blast.pm.
573
s#^ ?(GB_$Word:)($Word)( *)($Acc)($Descrip)($Int) ( *$Signif) ( *\d*)$#GenBank\|<a href="$_gi_link$4">$2</A>\|$4 $3$5$6 <a href="\#$2_$4_A">$7</A> $8<a name="$2_$4_H"></A>#o;
576
# s#^ ?(ORFP:)(\S*)($Descrip)($Int) ($Signif) ($Int)$#$1<b>$2</b> $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o;
579
s@^ ?ORFP:(\S*) +([\w-]+)(.*[ ]{2,3})($Int) ($Signif) ($Int)$@ORFP:<A HREF=\"$SGDUrl{'locus'}$2\">$1 $2</A>$3$4 <a href="\#$1_A">$5</a> $6<a name="$1_H"></a>@o;
581
s#^ ?(ORFN:)(\S*)($Descrip)($Int) ($Signif) ($Int)$#$1$2 $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o;
583
s#^ ?(NR_SC:GP-)(\S*) ( *)gi\|(\w+)([\w\|]*)($Descrip)($Int) ($Signif) ($Int)$#GenPept\|<a href="$DbUrl{'gb_p'}$4">$4</A>$3 gp|$2 $5$6$7 <a href="\#$4_A">$8</A> $9<a name="$4_H"></A>#o;
585
s#^ ?(NR_SC:SW-)$Word ( *)SW:($Word) ($Acc)($Descrip)($Int) ($Signif) ($Int)$#SWISS\|<a href="$DbUrl{'swpr'}$4">$3</A> SW:$3 $4 $5$6 <a href="\#$3_A">$7</A> $8<a name="$3_H"></A>#o;
587
s#^ ?(NR_SC:PIR-)$Word ( *)PIR:($Word)($Descrip)($Int) ($Signif) ($Int)$#PIR\|<a href="$DbUrl{'pir_uid'}$3">$3</A> $2 PIR:$3 $4$5 <a href="\#$3_A">$6</A> $7<a name="$3_H"></A>#o;
589
s#^ ?(CHRS:)([A-Z][0-9]*)($Descrip)($Int) ($Signif) ($Int)$#$1Segment:$2 $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o;
591
s#^ ?(CHR[0-9]*)($Descrip)($Int) ($Signif) ($Int)$#$1 $2 $3 <a href="\#$1_A">$4</a> $5<a name="$1_H"></a>#o;
593
s#^ ?(NOT:)([A-Z]_[0-9]*-[0-9]*)($Descrip)($Int) ($Signif) ($Int)$#$1$2 $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o;
595
s#^ ?(UTR5_SC_[0-9]*:)(\S*)($Descrip)($Int) ($Signif) ($Int)$#UTR5:$2 $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o;
597
# Hits without a db identifier.
598
s@^ ?($Word)($Descrip)($Int) ($Signif)(.*)$@$1$2$3 <A href="\#$1_A">$4</a>$5<a name="$1_H"></a>@o;
606
=head2 _prog_ref_html
608
Usage : n/a; utility method used by get_html_func().
609
Purpose : Get a special alert for BLAST reports against all of GenBank/EMBL.
610
Returns : string with HTML
612
See Also : L<get_html_func()|get_html_func>
619
return <<"QQ_REF_QQ";
624
<li>Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990).
625
Basic local alignment search tool.
626
<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=2231712&form=6&db=m&Dopt=r">J. Mol. Biol. 215: 403-10</a>.
627
<li>Altschul et al. (1997), Gapped BLAST and PSI-BLAST:
628
a new generation of protein database search programs.
629
<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9254694&form=6&db=m&Dopt=r">Nucl. Acids Res. 25: 3389-3402</a>.
630
<li><b>Program Descriptions</b>:
631
<a href="http://www.ncbi.nlm.nih.gov/BLAST/newblast.html">BLAST2</a> |
632
<a href="http://blast.wustl.edu/">WU-BLAST2</a> |
633
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blast_help.html">Help Manual</a>
636
HTML formatting provided by the <a href="${\$BioWWW->home_url('bioperl')}Projects/Blast/">Bioperl Blast module</a>.
643
# Not really a reference for the Blast algorithm itself but an interesting usage.
644
#<li>Gish, Warren, and David J. States (1993). Identification of protein coding regions by database similarity search.
645
#<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=8485583&form=6&db=m&Dopt=r">Nature Genetics 3:266-72</a>.
650
=head2 _genbank_alert
652
Usage : n/a; utility method used by get_html_func().
653
Purpose : Get a special alert for BLAST reports against all of GenBank/EMBL.
654
Returns : string with HTML
656
See Also : L<get_html_func()|get_html_func>
663
return << "QQ_GENBANK_QQ";
664
<p><b><font color="red">CAUTION: Hits reported on this page may be derived from DNA sequences
665
that contain more than one gene.
666
</font>To avoid mis-interpretation, always check database entries
667
for any sequence of interest to verify that the similarity
668
occurs within the described sequence. (E.g., A DNA sequence
669
for gene X as reported in GenBank may contain a 5' or 3'
670
fragment of coding sequence for a neighboring gene Y, yet will
671
be listed as gene X, since gene Y had not yet been identified). </b>
679
Usage : $boolean = &strip_html( string_ref );
680
: This method is exported.
681
Purpose : Removes HTML formatting from a supplied string.
682
: Attempts to restore the Blast report to enable
683
: parsing by Bio::Tools::Blast.pm.
684
Returns : Boolean: true if string was stripped, false if not.
685
Argument : string_ref = reference to a string containing the whole Blast
687
Throws : Croaks if the argument is not a scalar reference.
688
Comments : Based on code originally written by Alex Dong Li
689
: (ali@genet.sickkids.on.ca).
690
: This method does some Blast-specific stripping
691
: (adds back a '>' character in front of each HSP
692
: alignment listing).
694
: THIS METHOD IS HIGHLY ERROR-PRONE!
696
: Removal of the HTML tags and accurate reconstitution of the
697
: non-HTML-formatted report is highly dependent on structure of
698
: the HTML-formatted version. For example, it assumes that first
699
: line of each alignment section (HSP listing) starts with a
700
: <a name=..> anchor tag. This permits the reconstruction of the
701
: original report in which these lines begin with a ">".
702
: This is required for parsing.
704
: If the structure of the Blast report itself is not intended to
705
: be a standard, the structure of the HTML-formatted version
706
: is even less so. Therefore, the use of this method to
707
: reconstitute parsable Blast reports from HTML-format versions
708
: should be considered a temorary solution.
710
See Also : B<Bio::Tools::Blast::parse()>
717
# This may not best way to remove html tags. However, it is simple.
718
# it won't work under following conditions:
719
# 1) if quoted > appears in a tag (does this ever happen?)
720
# 2) if a tag is split over multiple lines and this method is
721
# used to process one line at a time.
723
my $string_ref = shift;
725
ref $string_ref eq 'SCALAR' or
726
croak ("Can't strip HTML: ".
727
"Argument is should be a SCALAR reference not a ${\ref $string_ref}");
729
my $str = $$string_ref;
732
# Removing "<a name =...>" and adding the '>' character for
733
# HSP alignment listings.
734
$str =~ s/(\A|\n)<a name ?=[^>]+> ?/>/sgi and $stripped = 1;
736
# Removing all "<>" tags.
737
$str =~ s/<[^>]+>| //sgi and $stripped = 1;
739
# Re-uniting any lone '>' characters.
740
$str =~ s/(\A|\n)>\s+/\n\n>/sgi and $stripped = 1;
749
#####################################################################################
751
#####################################################################################
added
removed
Bio/Tools/Blast/HTML.pm
