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diff variant_effect_predictor/Bio/Tools/Blast/HTML.pm @ 0:1f6dce3d34e0
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| author | mahtabm |
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| date | Thu, 11 Apr 2013 02:01:53 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/Tools/Blast/HTML.pm Thu Apr 11 02:01:53 2013 -0400 @@ -0,0 +1,754 @@ +#------------------------------------------------------------------------------- +# PACKAGE : Bio::Tools::Blast::HTML +# PURPOSE : To encapsulate code for HTML formatting BLAST reports. +# AUTHOR : Steve Chervitz (sac@bioperl.org) +# CREATED : 28 Apr 1998 +# STATUS : Alpha +# REVISION: $Id: HTML.pm,v 1.15 2002/11/04 09:12:51 heikki Exp $ +# +# For the latest version and documentation, visit the distribution site: +# http://bio.perl.org/Projects/Blast/ +# +# To generate documentation, run this module through pod2html +# (preferably from Perl v5.004 or better). +# +# CUSTOMIZATION NOTE: +# +# If your Blast reports are not getting marked up correctly, add or +# modify the regexps in _markup_report() to accomodate the format of +# your reports. +# +# Copyright (c) 1996-98 Steve Chervitz. All Rights Reserved. +# This module is free software; you can redistribute it and/or +# modify it under the same terms as Perl itself. +#------------------------------------------------------------------------------- + +package Bio::Tools::Blast::HTML; +use strict; +use Exporter; + +use Bio::Tools::WWW qw(:obj); + +use vars qw( @ISA @EXPORT @EXPORT_OK %EXPORT_TAGS + $ID %DbUrl %SGDUrl $Revision + $Acc $Pir_acc $Word $Signif $Int $Descrip); + +@ISA = qw(Exporter); +@EXPORT = qw(); +@EXPORT_OK = qw(&get_html_func &strip_html); +%EXPORT_TAGS = ( std => [qw(&get_html_func &strip_html)] ); + +$ID = 'Bio::Tools::Blast::HTML'; +$Revision = '$Id: HTML.pm,v 1.15 2002/11/04 09:12:51 heikki Exp $'; #' + +my $_set_markup = 0; +my $_gi_link = ''; + + +## POD Documentation: + +=head1 NAME + +Bio::Tools::Blast::HTML - Bioperl Utility module for HTML formatting Blast reports + +=head1 SYNOPSIS + +=head2 Adding HTML-formatting + + use Bio::Tools::Blast::HTML qw(&get_html_func); + + $func = &get_html_func(); + + # Now as each line of the report is read, pass it to &$func($line). + +See L<get_html_func()|get_html_func> for details. +Also see B<Bio::Tools::Blast::to_html> for an example of usage. + + +=head2 Removing HTML-formatting + + use Bio::Tools::Blast::HTML qw(&strip_html); + + &strip_html(\$blast_report_string) + +See L<strip_html()|strip_html> for details. + + +=head1 INSTALLATION + +This module is included with the central Bioperl distribution: + + http://bio.perl.org/Core/Latest + ftp://bio.perl.org/pub/DIST + +Follow the installation instructions included in the README file. + +=head1 DESCRIPTION + +This module can be used to add HTML formatting to or remove HTML +formatting from a raw Blast sequence analysis report. Hypertext links +to the appropriate database are added for each hit sequence (GenBank, +Swiss-Prot, PIR, PDB, SGD). + +This module is intended for use by Bio::Tools::Blast.pm and related modules, +which provides a front-end to the methods in Bio::Tools::Blast::HTML.pm. + +=head1 DEPENDENCIES + +Bio::Tools::Blast::HTML.pm does not inherit from any other class +besides Exporter. It is used by B<Bio::Tools::Blast.pm> only. This +class relies on B<Bio::Tools::WWW.pm> to provide key URLS for adding +links in the Blast report to specific databases. + +The greatest dependency comes from the dynamic state of the web. URLs +are are likely to change in the future, so all links cannot be +guaranteed to work indefinitely. Feel free to report broken or +incorrect database links (L<FEEDBACK | FEEDBACK>). Thanks! + +=head1 SEE ALSO + + Bio::Tools::Blast.pm - Blast object. + Bio::Tools::WWW.pm - URL repository. + + http://bio.perl.org/Projects/modules.html - Online module documentation + http://bio.perl.org/Projects/Blast/ - Bioperl Blast Project + http://bio.perl.org/ - Bioperl Project Homepage + +=head1 FEEDBACK + +=head2 Mailing Lists + +User feedback is an integral part of the evolution of this and other +Bioperl modules. Send your comments and suggestions preferably to one +of the Bioperl mailing lists. Your participation is much appreciated. + + bioperl-l@bioperl.org - General discussion + http://bio.perl.org/MailList.html - About the mailing lists + +=head2 Reporting Bugs + +Report bugs to the Bioperl bug tracking system to help us keep +track the bugs and their resolution. Bug reports can be submitted +via email or the web: + + bioperl-bugs@bio.perl.org + http://bugzilla.bioperl.org/ + +=head1 AUTHOR + +Steve Chervitz, E<lt>sac@bioperl.orgE<gt> + +=head1 COPYRIGHT + +Copyright (c) 1998-2000 Steve Chervitz. All Rights Reserved. +This module is free software; you can redistribute it and/or +modify it under the same terms as Perl itself. + + +=cut + + +# +## +### +#### END of main POD documentation. +### +## +#' + + +###################### BEGIN FUNCTIONS ######################## + +=head1 APPENDIX + +Methods beginning with a leading underscore are considered private +and are intended for internal use by this module. They are +B<not> considered part of the public interface and are described here +for documentation purposes only. + + + +=head2 get_html_func + + Usage : $func_ref = &get_html_func( [array_ref] ); + : This method is exported. + Purpose : Provides a function that adds HTML formatting to a + : raw Blast report line-by-line. + : Utility method used by to_html() in Bio::Tools::Blast.pm. + Returns : Reference to an anonymous function to be used while reading in + : the raw report. + : The function itself operates on the Blast report line-by-line + : HTML-ifying it and printing it to STDOUT (or saving in the supplied + : array ref) as it goes: + : foreach( @raw_report ) { &$func_ref($_); } + Argument : array ref (optional) for storing the HTML-formatted report. + : If no argument is supplied, HTML output is sent to STDOUT. + Throws : Croaks if an argument is supplied and is not an array ref. + : The anonymous function returned by this method croaks if + : the Blast output appears to be HTML-formatted already. + Comments : Adapted from a script by Keith Robison November 1993 + : krobison@nucleus.harvard.edu; http://golgi.harvard.edu/gilbert.html + : Modified extensively by Steve Chervitz and Mike Cherry. + : Some modifications are customizations for BLAST reports served up + : by the Saccharomyces Genome Database. + : Feel free to modify or replace portions of this code as necessary + : to accomodate new BLAST datasets or changes to the Blast format. + +See Also : B<Bio::Tools::Blast::to_html()> + +=cut + +#-------------------- +sub get_html_func { +#-------------------- + my ($out_aref) = @_; + + ## Key booleans used in parsing. + my $found_table = 0; # Located the table at top of report (a.k.a. 'descriptions'). + my $found_data = 0; # Nothing is done until this is true + my $skip = 0; # Skipping various items in the report header + my $ref_skip = 0; # so we can include nice HTML versions + # (e.g., references for the BLAST program). + my $getNote = 0; + my $getGenBankAlert = 0; + my $str = ''; + my $gi_link = \$_gi_link; + my $prog = ''; + + if( defined($out_aref) and not ref($out_aref) eq 'ARRAY') { + croak("Argument must be an ARRAY ref not a ${\ref $out_aref}."); + } + + my $refs = &_prog_ref_html; + + &_set_markup_data() if not $_set_markup; + + return sub { + # $_ contains a single line from a Blast report. + local $_ = shift; + + croak("Report appears to be HTML formatted already.") if m/<HTML>|<TITLE>|<PRE>/i; + + if(not $found_table) { + if($ref_skip) { + # Replacing an reference data with special HTML. + $ref_skip = 0 if /^\s+$/; + } + if($getNote) { + ## SAC: created this test since we are no longer reading from STDIN. + $out_aref ? push(@$out_aref, $_) : print $_; + $getNote = 0 if m/^\s+$/; + } elsif( m/(.*), Up \d.*/ or /Date: +(.+)/ or /Start: +(.+?) +End:/ ) { + ### Network BLAST reports from NCBI are time stamped as follows: + #Fri Apr 18 15:55:41 EDT 1997, Up 1 day, 19 mins, 1 user, load: 19.54, 19.13, 17.77 + my $date = "<b>BLASTed on:</b> $1<p>\n"; + $out_aref ? push(@$out_aref, $date) : print $date; + } elsif ( /^(<\w+>)?(T?BLAST[NPX])\s+(.*?)/ ) { + $found_data = 1; + local($^W) = 0; + s#(\S+)\s+(.*)#<P><B>Program:</B> $1 $2 $3<br>#o; + $out_aref ? push(@$out_aref, $_) : print $_; + $skip = 1; + $prog = $2; + if($prog =~ /BLASTN/) { + ## Prevent the error at Entrez when you ask for a nucl + ## entry with a protein GI number. + $$gi_link = $DbUrl{'gb_n'}; # nucleotide + } else { + $$gi_link = $DbUrl{'gb_p'}; # protein + } + } elsif ( m/^Query=/ ) { + # Keeping the "Query=" format to keep it parsable by Blast.pm + # (after stripping HTML). + s#Query= *(.*)#<title>$1</title>\n<p><b>Query=</b> $1#o; + $out_aref ? push(@$out_aref, $_) : print $_; + $skip = 1; + } elsif ( /Reference:/) { + $ref_skip = 1; + } elsif ( /^Database:/ ) { + &_markup_database(\$_); + $out_aref ? push(@$out_aref, $_) : print $_; + if ( /non-redundant genbank/i and $prog =~ /TBLAST[NX]/i) { + $getGenBankAlert = 1; + } + $skip = 1; + } elsif ( /sequences;/ ) { + $str = "$_<p>"; + $out_aref ? push(@$out_aref, $str) : print $str; + } elsif ( /^\s+\(\d+ letters\)\s+/ ) { + $str = "<br>    $_"; + $out_aref ? push(@$out_aref, $str) : print $str; + } elsif ( /^(WARNING|NOTICE):/i ) { + s#WARNING: *(.*)#<p><b><font color="red">$1:</font></b> $1#o; + $out_aref ? push(@$out_aref, $_) : print $_; + $getNote = 1; + } elsif ( /Score +E\s*$/ or /Probability\s*$/ ) { + # Put the last HTML-formatted lines before the main body of report. + $found_table = 1; + $skip = 0; + $out_aref ? push(@$out_aref, $refs) : print $refs; + if($getGenBankAlert) { + $str = &_genbank_alert; + $out_aref ? push(@$out_aref, $str) : print $str; + } + $str = "\n<p><pre>"; + $out_aref ? push(@$out_aref, $str) : print $str; + } + + } else { + &_markup_report(\$_); + } + + if ($found_data and not($skip or $ref_skip)) { + $out_aref ? push(@$out_aref, $_) : print $_; + } + 1; + } # end sub {} +} + + + + +=head2 _set_markup_data + + Usage : n/a; utility method used by get_html_func() + Purpose : Sets various hashes and regexps used for adding HTML + : to raw Blast output. + Returns : n/a + Comments : These items need be set only once. + +See Also : L<get_html_func()|get_html_func> + +=cut + +#------------------- +sub _set_markup_data { +#------------------- + %DbUrl = $BioWWW->search_url('all'); + %SGDUrl = $BioWWW->sgd_url('all'); + + $Signif = '[\de.-]{3,}'; # Regexp for a P-value or Expect value. + $Int = ' *\d\d*'; # Regexp for an integer. + $Descrip = ' +.* {2,}?'; # Regexp for a description line. + $Acc = '[A-Z][\d.]+'; # Regexp for GB/EMBL/DDJB/SP accession number + $Pir_acc = '[A-Z][A-Z0-9]{5,}'; # Regexp for PIR accession number + $Word = '[\w_.]+'; # Regexp for a word. Include dot for version. + + $_set_markup = 1; +} + + +=head2 _markup_database + + Usage : n/a; utility method used by get_html_func() + Purpose : Converts a cryptic database ID into a readable name. + Returns : n/a + Comments : This is used for converting local database IDs into + : understandable terms. At present, it only recognizes + : databases used locally at SGD. + +See Also : L<get_html_func()|get_html_func> + +=cut + +#--------------------- +sub _markup_database { +#--------------------- + my $line_ref = shift; + local $_ = $$line_ref; + + $_ =~ s#YeastN#<i>S. cerevisiae</i> GenBank Data Set; #; + $_ =~ s#YeastP#Non-Redundant <i>S. cerevisiae</i> Protein Data Set; #; + $_ =~ s#genoSC#Complete DNA Sequence for the S. cerevisiae Genome; #; + $_ =~ s#YeastORF-P#Translation of all Standard S.c. ORFs; #; + $_ =~ s#YeastORF-N#Coding Sequence of all Standard S.c. ORFs; #; + s#Database: *(.*)#<p><b>Database:</b> $1#o; + + $$line_ref = $_; +} + + +=head2 _markup_report + + Usage : n/a; utility function used by get_html_func() + Purpose : Adds HTML links to aid navigation of raw Blast output. + Returns : n/a + Comments : HTML-formatting is dependent on the Blast server that + : provided the Blast report. Currently, this function can handle reports + : produced by NCBI and SGD. Feel free to modify this function + : to accomodate reports produced by other servers/sites. + : + : This function is simply a collection of substitution regexps + : that recognize and modify the relevant lines of the Blast report. + : All non-header lines of the report are passed through this function, + : only the ones that match will get modified. + : + : The general scheme for adding links is as follows: + : (Some of the SGD markups do not follow this scheme precisely + : but this is the general trend.) + : + : For description lines in the summary table at the top of report: + : + : DB:SEQUENCE_ID DESCRIPTION SIGNIF_VAL + : DB = links to the indicated database (if not Gen/Embl/Ddbj). + : SEQUENCE_ID = links to GenBank entry for the sequence. + : SIGNIF_VAL = internal link to relevant alignment section. + : + : For the alignment sections in the body of the report: + : + : DB:SEQUENCE_ID (Back | Top) DESCRIPTION + : DB = links to the indicated database (if not Gen/Embl/Ddbj). + : SEQUENCE_ID = links to GenBank entry for the sequence. + : SIGNIF_VAL = internal link to alignment section. + : Back = internal link to description line in summary section. + : Top = internal link to top of page. + : + : 'DB' links are created for PDB, PIR, and SwissProt sequences. + : + : RE_PARSING HTML-FOMRATTED REPORTS: + : ---------------------------------- + : HTML-formatted reports generated by this module, as well as reports + : obtained from the NCBI servers, should be parsable + : by Bio::Tools::Blast.pm. Parsing HTML-formatted reports is + : slow, however, since the HTML must be removed prior to parsing. + : Parsing HTML-formatted reports is dependent on the specific structure + : of the HTML and is generally not recommended. + : + : Note that since URLs can change without notice, links will need updating. + : The links are obtained from Bio::Tools::WWW.pm updating that module + : will update this as well. + : + Bugs : Some links to external databases are incorrect + : (in particular, for 'bbs' and 'prf' databases on NCBI Blast reports. + : Some links may fail as a result of the dynamic nature of the web. + : Hypertext links are not added to hits without database ids. + +See Also : L<get_html_func()|get_html_func>, B<Bio::Tools::WWW.pm>, L<strip_html>() + +=cut + +#-------------------- +sub _markup_report { +#-------------------- + my $line_ref = shift; + local $_ = $$line_ref; +## +## REGEXPS FOR ALIGNMENT SECTIONS (within the body of the report, +## the text above the list of HSPs). +## +## If the HSP alignment sections don't start with a '>' we have no way +## of finding them. This occurs with reports saved from HTML-formatted +## web pages, which we shouldn't be processing here anyway. + +## To facilitate parsing of HTML-formatted reports by Bio::Tools::Blast.pm, +## the <a name=...> anchors should be added at the BEGINNING of the HSP +## alignment section lines and at the END of the description section lines. + + # Removing " ! " addded by GCG. + s/ ! / /; + + ### NCBI-specific markups for HSP alignment section lines: + + local($^W) = 0; + + # GenBank/EMBL, DDBJ hits (GenBank Format): + s@^>(gb|emb|dbj|ref)\|($Word)(\|$Word)?(.*)$@<a name=$2_A></a><b>$1:<a href="$_gi_link$2">$2$3</a></b>$4<br>(<a href="\#$2_H">Back|<a href="\#top">Top</a>)@o; + + s@^>(gb|emb|dbj|ref)\|($Word)(\| \(?$Word\)?)(.*)$@<a name=$2_A></a><b>$1:<a href="$_gi_link$2">$2</a></b>$3$4<br>(<a href="\#$2_H">Back|<a href="\#top">Top</a>)@o; + + # PIR hits + s@^>pir\|\|($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="\#$1_H">Back|<a href="\#top">Top</a>)@o; + + # GI hits (GenBank Format): using a nested (()) + s@^>(gi)\|($Word)( +\(($Word)\))( .*)$@<a name=$4_A></a><b>$1:<a href="$_gi_link$4">$2</a></b>$3$5<br>(<a href="\#$4_H">Back|<a href="\#top">Top</a>)@o; + + # GNL PID hits (GenBank Format): + s@^>(gnl)\|($Word)?(\|$Word) +\(($Word)\)( .*)$@<a name=$4_A></a><b>$1:<a href="$_gi_link$4">$2$3</a></b>($4)$5<br>(<a href="\#$4_H">Back|<a href="\#top">Top</a>)@o; + + # BBS and PRF hits (what db?) (GenBank Format): + s@^>(bbs|prf)\|\|?($Word)( .*)$@<a name=$2_A></a><b>$1:<a href="$_gi_link$2">$2</a></b>$3<br>(<a href="\#$2_H">Back|<a href="\#top">Top</a>)@o; + + # SwissProt hits: + s@^>sp\|($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="\#$1_H">Back|<a href="\#top">Top</a>)@o; + + + ## PDB ids with or without a chain identifier (GenBank format) + s@^>pdb\|(\d\w{3})\|[\w ] (.*)$@<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>) $2@o; + + + ### SGD-specific markups for HSP alignment section lines: + + ## PDB ids without chain identifier + s@^>PDB_UNIQUEP:(\d\w{3})_ (.*)$@<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>) $2@o; + + ## PDB ids with chain identifier + s@^>PDB_UNIQUEP:(\d\w{3})_([\w ]{1})(.*)$@<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>) $3@o; + + s@^>($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; + + # The gcg blast dataset generating tools up-case all sbjct sequence IDs. + # This is fine for yeast but not worm. This is considered a hack here. + s@WORMPEPT:(\w+\.)(\S+)@WORMPEPT:$1\L$2\E@; + + s@^>WORMPEPT:(\S+)(.*)$@<a name=$1_A></a><b>WORMPEP:<A HREF="$DbUrl{'wormace'}$1">$1</a></b> $2 <br>(<a href="\#$1_H">Back|<a href="\#top">Top</a>)@o; + + s#^>(GB_$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'}$2\*\">SGD</A>]</b> #o; + + # Sac's version: ORF name is an external link into SGD: + s@^>ORFP:(\S*) +([\w-]+)(.*$)@<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="\#$1_H">Back</a>|<a href="\#top">Top</a>@o; + +# Mike's version: +# s#^>ORFP:(\S*) (.*$)#<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'}$1\">ORF Map</a>]</b> #o; + + s#^>ORFN:(\S*) (.*$)#<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'}$1\">ORF Map</a></b> #o; + + s#^>NR_SC:GP-\S* gi\|(\w+)([\w\|]*) (.*$)#<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'}$1\*\">SGD</A>]</b> #o; + + s#^>NR_SC:SW-$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'}$2>Entrez</A>]</b>#o; + + s#^>NR_SC:PIR-$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'}$1>Entrez</A>]</b>#o; + + s#^>CHRS:([A-Z][0-9]*) (.*)$#<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'}$1\">ORF Map</a></b>]#o; + + s#^>NOT:([A-Z]_[0-9]*-[0-9]*)( *)Chromosome ([0-9]*) from ([0-9]*) to ([0-9]*)$#<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=$5\">Retrieve DNA</a></b>]#o; + + s#^>UTR5_SC_[0-9]*:(\S*) 5' untranslated region, chr(\S*) ([0-9]*) - ([0-9]*)(.*$)#<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=$4\">ORF Map</a>]</b>#o; + + # Hits without a db identifier. + # If any of the previous regexps succeed, the leading '>' will be removed. + # Otherwise, this regexp could cause trouble. + s@^>($Word)(.*)$@<a name=$1_A></a>$1 $2<br>(<a href="\#$1_H">Back|<a href="\#top">Top</a>)@o; + +## +## REGEXPS FOR SUMMARY TABLE LINES AT TOP OF REPORT (a.k.a. 'descriptions') +## (table of sequence id, description, score, P/Expect value, n) +## +## Not using bold face to highlight the sequence id's since this can throw off +## off formatting of the line when the IDs are different lengths. This lead to +## the scores and P/Expect values not lining up properly. + + ### NCBI-specific markups for description lines: + + # GenBank/EMBL, DDBJ hits (GenBank Format): + s@^ ?(gb|emb|dbj|ref)\|($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="$2_H"></a>@o; + + s@^ ?(gb|emb|dbj|ref)\|($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="$2_H"></a>@o; + + # Missing inner ID + s@^ ?pir\|\|($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="$1_H"></a>@o; + + # GI hits (GenBank Format): using a nested (()) + s@^ ?gi\|($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="$3_H"></a>@o; + + s@^ ?(gnl)\|($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="$4_H"></a>@o; + + + s@^ ?(bbs|prf)\|\|?($Word)($Descrip)($Int) ($Signif)(.*)$@$1:<a href="$_gi_link$2">$2</a> $3$4 <A href="\#$2_A">$5</a>$6<a name="$2_H"></a>@o; + + + ## SwissProt accessions (GenBank format) + s@^ ?sp\|($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="$1_H"></a>@o; + + ## PDB ids with or without a chain ID (GenBank format) + s@^ ?pdb\|($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="$1_H"></a>@o; + + + ### SGD-specific markups for description lines: + + ## PDB ids without chain identifier + s@^ ?PDB_UNIQUEP:(\d\w{3})_($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="$1_H"></a>@o; + + + ## PDB ids with chain identifier + s@^ ?PDB_UNIQUEP:(\d\w{3})_(\w)($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="$1_H"></a>@o; + + + s@^ ?($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="$2_H"></a>@o; + + s@^ *WORMPEPT:(\S+)($Descrip)($Int) ($Signif)(.*)$@WORMPEP:<A HREF="$DbUrl{'wormace'}$1">$1</a> $2 $3 <a href="\#$1_A">$4</a>$5<a name="$1_H"></a>@o; + + ## Mike Cherry's markups. SAC note: added back database name to allow + ## the HTML-formatted version to be parsable by Blast.pm. + + s#^ ?(GB_$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_$4_H"></A>#o; + +# Mike's version: +# s#^ ?(ORFP:)(\S*)($Descrip)($Int) ($Signif) ($Int)$#$1<b>$2</b> $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o; + +# My modification: + s@^ ?ORFP:(\S*) +([\w-]+)(.*[ ]{2,3})($Int) ($Signif) ($Int)$@ORFP:<A HREF=\"$SGDUrl{'locus'}$2\">$1 $2</A>$3$4 <a href="\#$1_A">$5</a> $6<a name="$1_H"></a>@o; + + s#^ ?(ORFN:)(\S*)($Descrip)($Int) ($Signif) ($Int)$#$1$2 $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o; + + s#^ ?(NR_SC:GP-)(\S*) ( *)gi\|(\w+)([\w\|]*)($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="$4_H"></A>#o; + + s#^ ?(NR_SC:SW-)$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="$3_H"></A>#o; + + s#^ ?(NR_SC:PIR-)$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="$3_H"></A>#o; + + s#^ ?(CHRS:)([A-Z][0-9]*)($Descrip)($Int) ($Signif) ($Int)$#$1Segment:$2 $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o; + + s#^ ?(CHR[0-9]*)($Descrip)($Int) ($Signif) ($Int)$#$1 $2 $3 <a href="\#$1_A">$4</a> $5<a name="$1_H"></a>#o; + + s#^ ?(NOT:)([A-Z]_[0-9]*-[0-9]*)($Descrip)($Int) ($Signif) ($Int)$#$1$2 $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o; + + s#^ ?(UTR5_SC_[0-9]*:)(\S*)($Descrip)($Int) ($Signif) ($Int)$#UTR5:$2 $3 $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o; + + # Hits without a db identifier. + s@^ ?($Word)($Descrip)($Int) ($Signif)(.*)$@$1$2$3 <A href="\#$1_A">$4</a>$5<a name="$1_H"></a>@o; + + $$line_ref = $_; +} + + + + +=head2 _prog_ref_html + + Usage : n/a; utility method used by get_html_func(). + Purpose : Get a special alert for BLAST reports against all of GenBank/EMBL. + Returns : string with HTML + +See Also : L<get_html_func()|get_html_func> + +=cut + +#------------------ +sub _prog_ref_html { +#------------------ + return <<"QQ_REF_QQ"; +<p> +<small> +<b>References:</b> +<ol> +<li>Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990). +Basic local alignment search tool. +<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>. +<li>Altschul et al. (1997), Gapped BLAST and PSI-BLAST: +a new generation of protein database search programs. +<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>. +<li><b>Program Descriptions</b>: +<a href="http://www.ncbi.nlm.nih.gov/BLAST/newblast.html">BLAST2</a> | +<a href="http://blast.wustl.edu/">WU-BLAST2</a> | +<a href="http://www.ncbi.nlm.nih.gov/BLAST/blast_help.html">Help Manual</a> +</ol> +<small> +HTML formatting provided by the <a href="${\$BioWWW->home_url('bioperl')}Projects/Blast/">Bioperl Blast module</a>. +</small> +</small> +<p> + +QQ_REF_QQ + +# Not really a reference for the Blast algorithm itself but an interesting usage. +#<li>Gish, Warren, and David J. States (1993). Identification of protein coding regions by database similarity search. +#<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>. + +} + + +=head2 _genbank_alert + + Usage : n/a; utility method used by get_html_func(). + Purpose : Get a special alert for BLAST reports against all of GenBank/EMBL. + Returns : string with HTML + +See Also : L<get_html_func()|get_html_func> + +=cut + +#------------------ +sub _genbank_alert { +#------------------ + return << "QQ_GENBANK_QQ"; +<p><b><font color="red">CAUTION: Hits reported on this page may be derived from DNA sequences + that contain more than one gene. + </font>To avoid mis-interpretation, always check database entries + for any sequence of interest to verify that the similarity + occurs within the described sequence. (E.g., A DNA sequence + for gene X as reported in GenBank may contain a 5' or 3' + fragment of coding sequence for a neighboring gene Y, yet will + be listed as gene X, since gene Y had not yet been identified). </b> +QQ_GENBANK_QQ +} + + + +=head2 strip_html + + Usage : $boolean = &strip_html( string_ref ); + : This method is exported. + Purpose : Removes HTML formatting from a supplied string. + : Attempts to restore the Blast report to enable + : parsing by Bio::Tools::Blast.pm. + Returns : Boolean: true if string was stripped, false if not. + Argument : string_ref = reference to a string containing the whole Blast + : report. + Throws : Croaks if the argument is not a scalar reference. + Comments : Based on code originally written by Alex Dong Li + : (ali@genet.sickkids.on.ca). + : This method does some Blast-specific stripping + : (adds back a '>' character in front of each HSP + : alignment listing). + : + : THIS METHOD IS HIGHLY ERROR-PRONE! + : + : Removal of the HTML tags and accurate reconstitution of the + : non-HTML-formatted report is highly dependent on structure of + : the HTML-formatted version. For example, it assumes that first + : line of each alignment section (HSP listing) starts with a + : <a name=..> anchor tag. This permits the reconstruction of the + : original report in which these lines begin with a ">". + : This is required for parsing. + : + : If the structure of the Blast report itself is not intended to + : be a standard, the structure of the HTML-formatted version + : is even less so. Therefore, the use of this method to + : reconstitute parsable Blast reports from HTML-format versions + : should be considered a temorary solution. + +See Also : B<Bio::Tools::Blast::parse()> + +=cut + +#--------------- +sub strip_html { +#--------------- + # This may not best way to remove html tags. However, it is simple. + # it won't work under following conditions: + # 1) if quoted > appears in a tag (does this ever happen?) + # 2) if a tag is split over multiple lines and this method is + # used to process one line at a time. + + my $string_ref = shift; + + ref $string_ref eq 'SCALAR' or + croak ("Can't strip HTML: ". + "Argument is should be a SCALAR reference not a ${\ref $string_ref}"); + + my $str = $$string_ref; + my $stripped = 0; + + # Removing "<a name =...>" and adding the '>' character for + # HSP alignment listings. + $str =~ s/(\A|\n)<a name ?=[^>]+> ?/>/sgi and $stripped = 1; + + # Removing all "<>" tags. + $str =~ s/<[^>]+>| //sgi and $stripped = 1; + + # Re-uniting any lone '>' characters. + $str =~ s/(\A|\n)>\s+/\n\n>/sgi and $stripped = 1; + + $$string_ref = $str; + $stripped; +} + +1; +__END__ + +##################################################################################### +# END OF CLASS # +##################################################################################### + + +