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1 #-------------------------------------------------------------------------------
2 # PACKAGE : Bio::Tools::Blast::HTML
3 # PURPOSE : To encapsulate code for HTML formatting BLAST reports.
4 # AUTHOR : Steve Chervitz (sac@bioperl.org)
5 # CREATED : 28 Apr 1998
6 # STATUS : Alpha
7 # REVISION: $Id: HTML.pm,v 1.15 2002/11/04 09:12:51 heikki Exp $
8 #
9 # For the latest version and documentation, visit the distribution site:
10 # http://bio.perl.org/Projects/Blast/
11 #
12 # To generate documentation, run this module through pod2html
13 # (preferably from Perl v5.004 or better).
14 #
15 # CUSTOMIZATION NOTE:
16 #
17 # If your Blast reports are not getting marked up correctly, add or
18 # modify the regexps in _markup_report() to accomodate the format of
19 # your reports.
20 #
21 # Copyright (c) 1996-98 Steve Chervitz. All Rights Reserved.
22 # This module is free software; you can redistribute it and/or
23 # modify it under the same terms as Perl itself.
24 #-------------------------------------------------------------------------------
25
26 package Bio::Tools::Blast::HTML;
27 use strict;
28 use Exporter;
29
30 use Bio::Tools::WWW qw(:obj);
31
32 use vars qw( @ISA @EXPORT @EXPORT_OK %EXPORT_TAGS
33 $ID %DbUrl %SGDUrl $Revision
34 $Acc $Pir_acc $Word $Signif $Int $Descrip);
35
36 @ISA = qw(Exporter);
37 @EXPORT = qw();
38 @EXPORT_OK = qw(&get_html_func &strip_html);
39 %EXPORT_TAGS = ( std => [qw(&get_html_func &strip_html)] );
40
41 $ID = 'Bio::Tools::Blast::HTML';
42 $Revision = '$Id: HTML.pm,v 1.15 2002/11/04 09:12:51 heikki Exp $'; #'
43
44 my $_set_markup = 0;
45 my $_gi_link = '';
46
47
48 ## POD Documentation:
49
50 =head1 NAME
51
52 Bio::Tools::Blast::HTML - Bioperl Utility module for HTML formatting Blast reports
53
54 =head1 SYNOPSIS
55
56 =head2 Adding HTML-formatting
57
58 use Bio::Tools::Blast::HTML qw(&get_html_func);
59
60 $func = &get_html_func();
61
62 # Now as each line of the report is read, pass it to &$func($line).
63
64 See L<get_html_func()|get_html_func> for details.
65 Also see B<Bio::Tools::Blast::to_html> for an example of usage.
66
67
68 =head2 Removing HTML-formatting
69
70 use Bio::Tools::Blast::HTML qw(&strip_html);
71
72 &strip_html(\$blast_report_string)
73
74 See L<strip_html()|strip_html> for details.
75
76
77 =head1 INSTALLATION
78
79 This module is included with the central Bioperl distribution:
80
81 http://bio.perl.org/Core/Latest
82 ftp://bio.perl.org/pub/DIST
83
84 Follow the installation instructions included in the README file.
85
86 =head1 DESCRIPTION
87
88 This module can be used to add HTML formatting to or remove HTML
89 formatting from a raw Blast sequence analysis report. Hypertext links
90 to the appropriate database are added for each hit sequence (GenBank,
91 Swiss-Prot, PIR, PDB, SGD).
92
93 This module is intended for use by Bio::Tools::Blast.pm and related modules,
94 which provides a front-end to the methods in Bio::Tools::Blast::HTML.pm.
95
96 =head1 DEPENDENCIES
97
98 Bio::Tools::Blast::HTML.pm does not inherit from any other class
99 besides Exporter. It is used by B<Bio::Tools::Blast.pm> only. This
100 class relies on B<Bio::Tools::WWW.pm> to provide key URLS for adding
101 links in the Blast report to specific databases.
102
103 The greatest dependency comes from the dynamic state of the web. URLs
104 are are likely to change in the future, so all links cannot be
105 guaranteed to work indefinitely. Feel free to report broken or
106 incorrect database links (L<FEEDBACK | FEEDBACK>). Thanks!
107
108 =head1 SEE ALSO
109
110 Bio::Tools::Blast.pm - Blast object.
111 Bio::Tools::WWW.pm - URL repository.
112
113 http://bio.perl.org/Projects/modules.html - Online module documentation
114 http://bio.perl.org/Projects/Blast/ - Bioperl Blast Project
115 http://bio.perl.org/ - Bioperl Project Homepage
116
117 =head1 FEEDBACK
118
119 =head2 Mailing Lists
120
121 User feedback is an integral part of the evolution of this and other
122 Bioperl modules. Send your comments and suggestions preferably to one
123 of the Bioperl mailing lists. Your participation is much appreciated.
124
125 bioperl-l@bioperl.org - General discussion
126 http://bio.perl.org/MailList.html - About the mailing lists
127
128 =head2 Reporting Bugs
129
130 Report bugs to the Bioperl bug tracking system to help us keep
131 track the bugs and their resolution. Bug reports can be submitted
132 via email or the web:
133
134 bioperl-bugs@bio.perl.org
135 http://bugzilla.bioperl.org/
136
137 =head1 AUTHOR
138
139 Steve Chervitz, E<lt>sac@bioperl.orgE<gt>
140
141 =head1 COPYRIGHT
142
143 Copyright (c) 1998-2000 Steve Chervitz. All Rights Reserved.
144 This module is free software; you can redistribute it and/or
145 modify it under the same terms as Perl itself.
146
147
148 =cut
149
150
151 #
152 ##
153 ###
154 #### END of main POD documentation.
155 ###
156 ##
157 #'
158
159
160 ###################### BEGIN FUNCTIONS ########################
161
162 =head1 APPENDIX
163
164 Methods beginning with a leading underscore are considered private
165 and are intended for internal use by this module. They are
166 B<not> considered part of the public interface and are described here
167 for documentation purposes only.
168
169
170
171 =head2 get_html_func
172
173 Usage : $func_ref = &get_html_func( [array_ref] );
174 : This method is exported.
175 Purpose : Provides a function that adds HTML formatting to a
176 : raw Blast report line-by-line.
177 : Utility method used by to_html() in Bio::Tools::Blast.pm.
178 Returns : Reference to an anonymous function to be used while reading in
179 : the raw report.
180 : The function itself operates on the Blast report line-by-line
181 : HTML-ifying it and printing it to STDOUT (or saving in the supplied
182 : array ref) as it goes:
183 : foreach( @raw_report ) { &$func_ref($_); }
184 Argument : array ref (optional) for storing the HTML-formatted report.
185 : If no argument is supplied, HTML output is sent to STDOUT.
186 Throws : Croaks if an argument is supplied and is not an array ref.
187 : The anonymous function returned by this method croaks if
188 : the Blast output appears to be HTML-formatted already.
189 Comments : Adapted from a script by Keith Robison November 1993
190 : krobison@nucleus.harvard.edu; http://golgi.harvard.edu/gilbert.html
191 : Modified extensively by Steve Chervitz and Mike Cherry.
192 : Some modifications are customizations for BLAST reports served up
193 : by the Saccharomyces Genome Database.
194 : Feel free to modify or replace portions of this code as necessary
195 : to accomodate new BLAST datasets or changes to the Blast format.
196
197 See Also : B<Bio::Tools::Blast::to_html()>
198
199 =cut
200
201 #--------------------
202 sub get_html_func {
203 #--------------------
204 my ($out_aref) = @_;
205
206 ## Key booleans used in parsing.
207 my $found_table = 0; # Located the table at top of report (a.k.a. 'descriptions').
208 my $found_data = 0; # Nothing is done until this is true
209 my $skip = 0; # Skipping various items in the report header
210 my $ref_skip = 0; # so we can include nice HTML versions
211 # (e.g., references for the BLAST program).
212 my $getNote = 0;
213 my $getGenBankAlert = 0;
214 my $str = '';
215 my $gi_link = \$_gi_link;
216 my $prog = '';
217
218 if( defined($out_aref) and not ref($out_aref) eq 'ARRAY') {
219 croak("Argument must be an ARRAY ref not a ${\ref $out_aref}.");
220 }
221
222 my $refs = &_prog_ref_html;
223
224 &_set_markup_data() if not $_set_markup;
225
226 return sub {
227 # $_ contains a single line from a Blast report.
228 local $_ = shift;
229
230 croak("Report appears to be HTML formatted already.") if m/<HTML>|<TITLE>|<PRE>/i;
231
232 if(not $found_table) {
233 if($ref_skip) {
234 # Replacing an reference data with special HTML.
235 $ref_skip = 0 if /^\s+$/;
236 }
237 if($getNote) {
238 ## SAC: created this test since we are no longer reading from STDIN.
239 $out_aref ? push(@$out_aref, $_) : print $_;
240 $getNote = 0 if m/^\s+$/;
241 } elsif( m/(.*), Up \d.*/ or /Date: +(.+)/ or /Start: +(.+?) +End:/ ) {
242 ### Network BLAST reports from NCBI are time stamped as follows:
243 #Fri Apr 18 15:55:41 EDT 1997, Up 1 day, 19 mins, 1 user, load: 19.54, 19.13, 17.77
244 my $date = "<b>BLASTed on:</b> $1<p>\n";
245 $out_aref ? push(@$out_aref, $date) : print $date;
246 } elsif ( /^(<\w+>)?(T?BLAST[NPX])\s+(.*?)/ ) {
247 $found_data = 1;
248 local($^W) = 0;
249 s#(\S+)\s+(.*)#<P><B>Program:</B> $1 $2 $3<br>#o;
250 $out_aref ? push(@$out_aref, $_) : print $_;
251 $skip = 1;
252 $prog = $2;
253 if($prog =~ /BLASTN/) {
254 ## Prevent the error at Entrez when you ask for a nucl
255 ## entry with a protein GI number.
256 $$gi_link = $DbUrl{'gb_n'}; # nucleotide
257 } else {
258 $$gi_link = $DbUrl{'gb_p'}; # protein
259 }
260 } elsif ( m/^Query=/ ) {
261 # Keeping the "Query=" format to keep it parsable by Blast.pm
262 # (after stripping HTML).
263 s#Query= *(.*)#<title>$1</title>\n<p><b>Query=</b> $1#o;
264 $out_aref ? push(@$out_aref, $_) : print $_;
265 $skip = 1;
266 } elsif ( /Reference:/) {
267 $ref_skip = 1;
268 } elsif ( /^Database:/ ) {
269 &_markup_database(\$_);
270 $out_aref ? push(@$out_aref, $_) : print $_;
271 if ( /non-redundant genbank/i and $prog =~ /TBLAST[NX]/i) {
272 $getGenBankAlert = 1;
273 }
274 $skip = 1;
275 } elsif ( /sequences;/ ) {
276 $str = "$_<p>";
277 $out_aref ? push(@$out_aref, $str) : print $str;
278 } elsif ( /^\s+\(\d+ letters\)\s+/ ) {
279 $str = "<br>&nbsp&nbsp&nbsp&nbsp$_";
280 $out_aref ? push(@$out_aref, $str) : print $str;
281 } elsif ( /^(WARNING|NOTICE):/i ) {
282 s#WARNING: *(.*)#<p><b><font color="red">$1:</font></b> $1#o;
283 $out_aref ? push(@$out_aref, $_) : print $_;
284 $getNote = 1;
285 } elsif ( /Score +E\s*$/ or /Probability\s*$/ ) {
286 # Put the last HTML-formatted lines before the main body of report.
287 $found_table = 1;
288 $skip = 0;
289 $out_aref ? push(@$out_aref, $refs) : print $refs;
290 if($getGenBankAlert) {
291 $str = &_genbank_alert;
292 $out_aref ? push(@$out_aref, $str) : print $str;
293 }
294 $str = "\n<p><pre>";
295 $out_aref ? push(@$out_aref, $str) : print $str;
296 }
297
298 } else {
299 &_markup_report(\$_);
300 }
301
302 if ($found_data and not($skip or $ref_skip)) {
303 $out_aref ? push(@$out_aref, $_) : print $_;
304 }
305 1;
306 } # end sub {}
307 }
308
309
310
311
312 =head2 _set_markup_data
313
314 Usage : n/a; utility method used by get_html_func()
315 Purpose : Sets various hashes and regexps used for adding HTML
316 : to raw Blast output.
317 Returns : n/a
318 Comments : These items need be set only once.
319
320 See Also : L<get_html_func()|get_html_func>
321
322 =cut
323
324 #-------------------
325 sub _set_markup_data {
326 #-------------------
327 %DbUrl = $BioWWW->search_url('all');
328 %SGDUrl = $BioWWW->sgd_url('all');
329
330 $Signif = '[\de.-]{3,}'; # Regexp for a P-value or Expect value.
331 $Int = ' *\d\d*'; # Regexp for an integer.
332 $Descrip = ' +.* {2,}?'; # Regexp for a description line.
333 $Acc = '[A-Z][\d.]+'; # Regexp for GB/EMBL/DDJB/SP accession number
334 $Pir_acc = '[A-Z][A-Z0-9]{5,}'; # Regexp for PIR accession number
335 $Word = '[\w_.]+'; # Regexp for a word. Include dot for version.
336
337 $_set_markup = 1;
338 }
339
340
341 =head2 _markup_database
342
343 Usage : n/a; utility method used by get_html_func()
344 Purpose : Converts a cryptic database ID into a readable name.
345 Returns : n/a
346 Comments : This is used for converting local database IDs into
347 : understandable terms. At present, it only recognizes
348 : databases used locally at SGD.
349
350 See Also : L<get_html_func()|get_html_func>
351
352 =cut
353
354 #---------------------
355 sub _markup_database {
356 #---------------------
357 my $line_ref = shift;
358 local $_ = $$line_ref;
359
360 $_ =~ s#YeastN#<i>S. cerevisiae</i> GenBank Data Set; #;
361 $_ =~ s#YeastP#Non-Redundant <i>S. cerevisiae</i> Protein Data Set; #;
362 $_ =~ s#genoSC#Complete DNA Sequence for the S. cerevisiae Genome; #;
363 $_ =~ s#YeastORF-P#Translation of all Standard S.c. ORFs; #;
364 $_ =~ s#YeastORF-N#Coding Sequence of all Standard S.c. ORFs; #;
365 s#Database: *(.*)#<p><b>Database:</b> $1#o;
366
367 $$line_ref = $_;
368 }
369
370
371 =head2 _markup_report
372
373 Usage : n/a; utility function used by get_html_func()
374 Purpose : Adds HTML links to aid navigation of raw Blast output.
375 Returns : n/a
376 Comments : HTML-formatting is dependent on the Blast server that
377 : provided the Blast report. Currently, this function can handle reports
378 : produced by NCBI and SGD. Feel free to modify this function
379 : to accomodate reports produced by other servers/sites.
380 :
381 : This function is simply a collection of substitution regexps
382 : that recognize and modify the relevant lines of the Blast report.
383 : All non-header lines of the report are passed through this function,
384 : only the ones that match will get modified.
385 :
386 : The general scheme for adding links is as follows:
387 : (Some of the SGD markups do not follow this scheme precisely
388 : but this is the general trend.)
389 :
390 : For description lines in the summary table at the top of report:
391 :
392 : DB:SEQUENCE_ID DESCRIPTION SIGNIF_VAL
393 : DB = links to the indicated database (if not Gen/Embl/Ddbj).
394 : SEQUENCE_ID = links to GenBank entry for the sequence.
395 : SIGNIF_VAL = internal link to relevant alignment section.
396 :
397 : For the alignment sections in the body of the report:
398 :
399 : DB:SEQUENCE_ID (Back | Top) DESCRIPTION
400 : DB = links to the indicated database (if not Gen/Embl/Ddbj).
401 : SEQUENCE_ID = links to GenBank entry for the sequence.
402 : SIGNIF_VAL = internal link to alignment section.
403 : Back = internal link to description line in summary section.
404 : Top = internal link to top of page.
405 :
406 : 'DB' links are created for PDB, PIR, and SwissProt sequences.
407 :
408 : RE_PARSING HTML-FOMRATTED REPORTS:
409 : ----------------------------------
410 : HTML-formatted reports generated by this module, as well as reports
411 : obtained from the NCBI servers, should be parsable
412 : by Bio::Tools::Blast.pm. Parsing HTML-formatted reports is
413 : slow, however, since the HTML must be removed prior to parsing.
414 : Parsing HTML-formatted reports is dependent on the specific structure
415 : of the HTML and is generally not recommended.
416 :
417 : Note that since URLs can change without notice, links will need updating.
418 : The links are obtained from Bio::Tools::WWW.pm updating that module
419 : will update this as well.
420 :
421 Bugs : Some links to external databases are incorrect
422 : (in particular, for 'bbs' and 'prf' databases on NCBI Blast reports.
423 : Some links may fail as a result of the dynamic nature of the web.
424 : Hypertext links are not added to hits without database ids.
425
426 See Also : L<get_html_func()|get_html_func>, B<Bio::Tools::WWW.pm>, L<strip_html>()
427
428 =cut
429
430 #--------------------
431 sub _markup_report {
432 #--------------------
433 my $line_ref = shift;
434 local $_ = $$line_ref;
435 ##
436 ## REGEXPS FOR ALIGNMENT SECTIONS (within the body of the report,
437 ## the text above the list of HSPs).
438 ##
439 ## If the HSP alignment sections don't start with a '>' we have no way
440 ## of finding them. This occurs with reports saved from HTML-formatted
441 ## web pages, which we shouldn't be processing here anyway.
442
443 ## To facilitate parsing of HTML-formatted reports by Bio::Tools::Blast.pm,
444 ## the <a name=...> anchors should be added at the BEGINNING of the HSP
445 ## alignment section lines and at the END of the description section lines.
446
447 # Removing " ! " addded by GCG.
448 s/ ! / /;
449
450 ### NCBI-specific markups for HSP alignment section lines:
451
452 local($^W) = 0;
453
454 # GenBank/EMBL, DDBJ hits (GenBank Format):
455 s@^>(gb|emb|dbj|ref)\|($Word)(\|$Word)?(.*)$@<a name=$2_A></a><b>$1:<a href="$_gi_link$2">$2$3</a></b>$4<br>(<a href="\#$2_H">Back|<a href="\#top">Top</a>)@o;
456
457 s@^>(gb|emb|dbj|ref)\|($Word)(\| \(?$Word\)?)(.*)$@<a name=$2_A></a><b>$1:<a href="$_gi_link$2">$2</a></b>$3$4<br>(<a href="\#$2_H">Back|<a href="\#top">Top</a>)@o;
458
459 # PIR hits
460 s@^>pir\|\|($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="\#$1_H">Back|<a href="\#top">Top</a>)@o;
461
462 # GI hits (GenBank Format): using a nested (())
463 s@^>(gi)\|($Word)( +\(($Word)\))( .*)$@<a name=$4_A></a><b>$1:<a href="$_gi_link$4">$2</a></b>$3$5<br>(<a href="\#$4_H">Back|<a href="\#top">Top</a>)@o;
464
465 # GNL PID hits (GenBank Format):
466 s@^>(gnl)\|($Word)?(\|$Word) +\(($Word)\)( .*)$@<a name=$4_A></a><b>$1:<a href="$_gi_link$4">$2$3</a></b>($4)$5<br>(<a href="\#$4_H">Back|<a href="\#top">Top</a>)@o;
467
468 # BBS and PRF hits (what db?) (GenBank Format):
469 s@^>(bbs|prf)\|\|?($Word)( .*)$@<a name=$2_A></a><b>$1:<a href="$_gi_link$2">$2</a></b>$3<br>(<a href="\#$2_H">Back|<a href="\#top">Top</a>)@o;
470
471 # SwissProt hits:
472 s@^>sp\|($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="\#$1_H">Back|<a href="\#top">Top</a>)@o;
473
474
475 ## PDB ids with or without a chain identifier (GenBank format)
476 s@^>pdb\|(\d\w{3})\|[\w ] (.*)$@<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>) $2@o;
477
478
479 ### SGD-specific markups for HSP alignment section lines:
480
481 ## PDB ids without chain identifier
482 s@^>PDB_UNIQUEP:(\d\w{3})_ (.*)$@<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>) $2@o;
483
484 ## PDB ids with chain identifier
485 s@^>PDB_UNIQUEP:(\d\w{3})_([\w ]{1})(.*)$@<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>) $3@o;
486
487 s@^>($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;
488
489 # The gcg blast dataset generating tools up-case all sbjct sequence IDs.
490 # This is fine for yeast but not worm. This is considered a hack here.
491 s@WORMPEPT:(\w+\.)(\S+)@WORMPEPT:$1\L$2\E@;
492
493 s@^>WORMPEPT:(\S+)(.*)$@<a name=$1_A></a><b>WORMPEP:<A HREF="$DbUrl{'wormace'}$1">$1</a></b> $2 <br>(<a href="\#$1_H">Back|<a href="\#top">Top</a>)@o;
494
495 s#^>(GB_$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'}$2\*\">SGD</A>]</b> #o;
496
497 # Sac's version: ORF name is an external link into SGD:
498 s@^>ORFP:(\S*) +([\w-]+)(.*$)@<a name=$1_A></A>ORFP:<a href=\"$SGDUrl{'locus'}$2\">$1 $2</A>$3<br>&nbsp&nbsp&nbsp&nbsp&nbsp<b>[<A HREF=\"$SGDUrl{'seq_an'}$2\">Gene/Sequence Resources</a> / <a href=\"$SGDUrl{'map_orf'}$2\">ORF Map</a></b>] <a href="\#$1_H">Back</a>|<a href="\#top">Top</a>@o;
499
500 # Mike's version:
501 # s#^>ORFP:(\S*) (.*$)#<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'}$1\">ORF Map</a>]</b> #o;
502
503 s#^>ORFN:(\S*) (.*$)#<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'}$1\">ORF Map</a></b> #o;
504
505 s#^>NR_SC:GP-\S* gi\|(\w+)([\w\|]*) (.*$)#<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'}$1\*\">SGD</A>]</b> #o;
506
507 s#^>NR_SC:SW-$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'}$2>Entrez</A>]</b>#o;
508
509 s#^>NR_SC:PIR-$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'}$1>Entrez</A>]</b>#o;
510
511 s#^>CHRS:([A-Z][0-9]*) (.*)$#<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'}$1\">ORF Map</a></b>]#o;
512
513 s#^>NOT:([A-Z]_[0-9]*-[0-9]*)( *)Chromosome ([0-9]*) from ([0-9]*) to ([0-9]*)$#<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=$5\">Retrieve DNA</a></b>]#o;
514
515 s#^>UTR5_SC_[0-9]*:(\S*) 5' untranslated region, chr(\S*) ([0-9]*) - ([0-9]*)(.*$)#<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=$4\">ORF Map</a>]</b>#o;
516
517 # Hits without a db identifier.
518 # If any of the previous regexps succeed, the leading '>' will be removed.
519 # Otherwise, this regexp could cause trouble.
520 s@^>($Word)(.*)$@<a name=$1_A></a>$1 $2<br>(<a href="\#$1_H">Back|<a href="\#top">Top</a>)@o;
521
522 ##
523 ## REGEXPS FOR SUMMARY TABLE LINES AT TOP OF REPORT (a.k.a. 'descriptions')
524 ## (table of sequence id, description, score, P/Expect value, n)
525 ##
526 ## Not using bold face to highlight the sequence id's since this can throw off
527 ## off formatting of the line when the IDs are different lengths. This lead to
528 ## the scores and P/Expect values not lining up properly.
529
530 ### NCBI-specific markups for description lines:
531
532 # GenBank/EMBL, DDBJ hits (GenBank Format):
533 s@^ ?(gb|emb|dbj|ref)\|($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="$2_H"></a>@o;
534
535 s@^ ?(gb|emb|dbj|ref)\|($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="$2_H"></a>@o;
536
537 # Missing inner ID
538 s@^ ?pir\|\|($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="$1_H"></a>@o;
539
540 # GI hits (GenBank Format): using a nested (())
541 s@^ ?gi\|($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="$3_H"></a>@o;
542
543 s@^ ?(gnl)\|($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="$4_H"></a>@o;
544
545
546 s@^ ?(bbs|prf)\|\|?($Word)($Descrip)($Int) ($Signif)(.*)$@$1:<a href="$_gi_link$2">$2</a> $3$4 <A href="\#$2_A">$5</a>$6<a name="$2_H"></a>@o;
547
548
549 ## SwissProt accessions (GenBank format)
550 s@^ ?sp\|($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="$1_H"></a>@o;
551
552 ## PDB ids with or without a chain ID (GenBank format)
553 s@^ ?pdb\|($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="$1_H"></a>@o;
554
555
556 ### SGD-specific markups for description lines:
557
558 ## PDB ids without chain identifier
559 s@^ ?PDB_UNIQUEP:(\d\w{3})_($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="$1_H"></a>@o;
560
561
562 ## PDB ids with chain identifier
563 s@^ ?PDB_UNIQUEP:(\d\w{3})_(\w)($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="$1_H"></a>@o;
564
565
566 s@^ ?($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="$2_H"></a>@o;
567
568 s@^ *WORMPEPT:(\S+)($Descrip)($Int) ($Signif)(.*)$@WORMPEP:<A HREF="$DbUrl{'wormace'}$1">$1</a> $2 $3 <a href="\#$1_A">$4</a>$5<a name="$1_H"></a>@o;
569
570 ## Mike Cherry's markups. SAC note: added back database name to allow
571 ## the HTML-formatted version to be parsable by Blast.pm.
572
573 s#^ ?(GB_$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_$4_H"></A>#o;
574
575 # Mike's version:
576 # s#^ ?(ORFP:)(\S*)($Descrip)($Int) ($Signif) ($Int)$#$1<b>$2</b> $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o;
577
578 # My modification:
579 s@^ ?ORFP:(\S*) +([\w-]+)(.*[ ]{2,3})($Int) ($Signif) ($Int)$@ORFP:<A HREF=\"$SGDUrl{'locus'}$2\">$1 $2</A>$3$4 <a href="\#$1_A">$5</a> $6<a name="$1_H"></a>@o;
580
581 s#^ ?(ORFN:)(\S*)($Descrip)($Int) ($Signif) ($Int)$#$1$2 $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o;
582
583 s#^ ?(NR_SC:GP-)(\S*) ( *)gi\|(\w+)([\w\|]*)($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="$4_H"></A>#o;
584
585 s#^ ?(NR_SC:SW-)$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="$3_H"></A>#o;
586
587 s#^ ?(NR_SC:PIR-)$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="$3_H"></A>#o;
588
589 s#^ ?(CHRS:)([A-Z][0-9]*)($Descrip)($Int) ($Signif) ($Int)$#$1Segment:$2 $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o;
590
591 s#^ ?(CHR[0-9]*)($Descrip)($Int) ($Signif) ($Int)$#$1 $2 $3 <a href="\#$1_A">$4</a> $5<a name="$1_H"></a>#o;
592
593 s#^ ?(NOT:)([A-Z]_[0-9]*-[0-9]*)($Descrip)($Int) ($Signif) ($Int)$#$1$2 $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o;
594
595 s#^ ?(UTR5_SC_[0-9]*:)(\S*)($Descrip)($Int) ($Signif) ($Int)$#UTR5:$2 $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o;
596
597 # Hits without a db identifier.
598 s@^ ?($Word)($Descrip)($Int) ($Signif)(.*)$@$1$2$3 <A href="\#$1_A">$4</a>$5<a name="$1_H"></a>@o;
599
600 $$line_ref = $_;
601 }
602
603
604
605
606 =head2 _prog_ref_html
607
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
611
612 See Also : L<get_html_func()|get_html_func>
613
614 =cut
615
616 #------------------
617 sub _prog_ref_html {
618 #------------------
619 return <<"QQ_REF_QQ";
620 <p>
621 <small>
622 <b>References:</b>
623 <ol>
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>
634 </ol>
635 <small>
636 HTML formatting provided by the <a href="${\$BioWWW->home_url('bioperl')}Projects/Blast/">Bioperl Blast module</a>.
637 </small>
638 </small>
639 <p>
640
641 QQ_REF_QQ
642
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>.
646
647 }
648
649
650 =head2 _genbank_alert
651
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
655
656 See Also : L<get_html_func()|get_html_func>
657
658 =cut
659
660 #------------------
661 sub _genbank_alert {
662 #------------------
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>
672 QQ_GENBANK_QQ
673 }
674
675
676
677 =head2 strip_html
678
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
686 : report.
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).
693 :
694 : THIS METHOD IS HIGHLY ERROR-PRONE!
695 :
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.
703 :
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.
709
710 See Also : B<Bio::Tools::Blast::parse()>
711
712 =cut
713
714 #---------------
715 sub strip_html {
716 #---------------
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.
722
723 my $string_ref = shift;
724
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}");
728
729 my $str = $$string_ref;
730 my $stripped = 0;
731
732 # Removing "<a name =...>" and adding the '>' character for
733 # HSP alignment listings.
734 $str =~ s/(\A|\n)<a name ?=[^>]+> ?/>/sgi and $stripped = 1;
735
736 # Removing all "<>" tags.
737 $str =~ s/<[^>]+>|&nbsp//sgi and $stripped = 1;
738
739 # Re-uniting any lone '>' characters.
740 $str =~ s/(\A|\n)>\s+/\n\n>/sgi and $stripped = 1;
741
742 $$string_ref = $str;
743 $stripped;
744 }
745
746 1;
747 __END__
748
749 #####################################################################################
750 # END OF CLASS #
751 #####################################################################################
752
753
754