cgi-bin/tools/align_viewer/index.pl

   1 use strict;
   2 use CXGN::Page;
   3 use CXGN::Page::FormattingHelpers qw/  page_title_html
   4                                        blue_section_html  /;
   5 use HTML::Entities;
   6 #Get input, if this page is loaded from find_caps.pl
   7 our $page = CXGN::Page->new( "Align Browser", "Chenwei");
   8 my ($seq_data, $id_data, $format, $title, $type,
   9         $show_prot_example, $show_cds_example, $show_id_example,
  10         $temp_file, $maxiters
  11         ) =
  12         $page->get_arguments(
  13         "seq_data", "id_data", "format", "title", "type",
  14         "show_prot_example", "show_cds_example", "show_id_example",
  15         "temp_file", "maxiters"
  16         );
  17
  18 my ($intro_content, $input_content);
  19
  20 my $vhost_conf = CXGN::VHost->new();
  21 our $HTML_ROOT = $vhost_conf->get_conf('basepath');
  22 our $DOC_PATH =  $vhost_conf->get_conf('tempfiles_subdir').'/align_viewer';
  23 our $PATH = $HTML_ROOT . $DOC_PATH;
  24 unless($temp_file =~ /\//){
  25         $temp_file = $PATH . "/" . $temp_file;
  26 }
  27
  28 if(-f $temp_file){
  29         open(FH, $temp_file);
  30         $seq_data .= $_ while (<FH>);
  31         close(FH);
  32 }
  33
  34
  35 #############################################################
  36 #Create introduction content'
  37 $intro_content = <<HTML;
  38 <p>This tool analyzes sequence alignment.  Please input <b>aligned sequences only</b>, in either fasta or clustal format.</p>
  39 Its functionality includes:
  40 <ol>
  41 <li>Image display.</li>
  42 <li>Calculation and output of pairwise similaity and putative splice variant or allelle pairs based on overlap and similarity between sequence pairs in an alignment.</li>
  43 <li>Provides the user with options to hide some alignment sequences so that they are not included in the analysis.</li>
  44 <li>Select a range of sequences to be analyzed.</li>
  45 <li>Assess how an alignment member overlap with other members.</li>
  46 <li>Calculate the non-gap mid point of each align sequence and group the sequences according to their overlap.</li>
  47 </ol>
  48 HTML
  49
  50 $title||="";
  51
  52 #############################################################
  53 #Create input content
  54 $input_content = <<HTML;
  55 <form method="post" action="show_align.pl" name="aligninput" enctype="multipart/form-data">
  56
  57 <input type="submit" name="submit" value="Analyze Alignment" /><br /><br />
  58 <b>Title (optional): </b>&nbsp;&nbsp;
  59 <input type="textbox" name="title" size="16" value="$title">
  60 <br /><br />
  61 HTML
  62
  63 #Alignment type
  64 if(!$type) { $type = "pep" }
  65 my %type_checked = ( pep => "", nt => "", cds => "" );
  66 $type_checked{$type} = "checked=\"checked\"";
  67 my ($tcn, $tcp, $tcc) = map { $type_checked{$_} } qw/ nt pep cds /;
  68
  69 $input_content .= <<HTML;
  70 <b>Type</b>&nbsp;&nbsp;
  71 <input id="aligninput.radio.nt" type="radio" name="type" value="nt" $tcn/>nucleotide &nbsp;&nbsp;
  72 <input id="aligninput.radio.pep" type="radio" name="type" value="pep" $tcp/>peptide &nbsp;&nbsp;
  73 <input id="aligninput.radio.pep" type="radio" name="type" value="cds" $tcc/>CDS (most powerful)
  74 <br /><br />
  75 HTML
  76
  77 #############################
  78 #Input format let it be unaligned by default
  79 if (!$format) { $format="fasta_unaligned"; }
  80
  81 my %format_checked = ( clustalw => "",
  82                 fasta => "",
  83                 fasta_unaligned => "",
  84                 );
  85
  86 $format_checked{$format}="checked=\"checked\"";
  87 $maxiters ||= 2;
  88 my ($fcw, $fcf, $fcu) = map { $format_checked{$_} } qw/clustalw fasta fasta_unaligned/;
  89
  90 $input_content .= <<HTML;
  91 <b>Input format</b><br />
  92 You may specify the species of the sequence with a forward slash, e.g. "AT1G01010.1/Arabidopsis" <br />
  93 Make sure all the spaces in the id and species are replaced by '_'.<br />
  94 <input type="radio" name="format" value="clustalw" $fcw/>Clustal Alignment<a target="blank" href="/about/clustal_file.pl"> [What is this?]</a><br />
  95 <input type="radio" name="format" value="fasta" $fcf/>Fasta Alignment (With Gaps)<br /><br />
  96 <input type="radio" name="format" value="fasta_unaligned" $fcu/>Fasta Unaligned (Will be aligned with <a href="http://www.drive5.com/muscle/">Muscle 3.6</a>, Limited to 200 Sequences)<br />
  97
  98 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Max Iterations
  99 <input type="text" name="maxiters" value=$maxiters>
 100  Use more iterations for greater accuracy. The maximum is 1000.<br /><br />
 101 <!--
 102 <input type="radio" name="run" value="cluster" checked="1">run on cluster (preferred)<br />
 103 <input type="radio" name="run" value="local">run on localhost<br /><br />
 104 -->
 105 HTML
 106
 107 if($show_prot_example){
 108         $seq_data = seq_from_file($page->path_to("cgi-bin/tools/align_viewer/data/prot_example.txt"));
 109 }
 110 elsif($show_cds_example){
 111         $seq_data = seq_from_file($page->path_to("cgi-bin/tools/align_viewer/data/cds_example.txt"));
 112 }
 113 elsif($show_id_example){
 114         $id_data = <<HEREDOC;
 115 SGN-U282881 SGN-U228103 At1g09155.1 At1g56240.1 At1g56250.1 NP_178331.2 At2g02350.1 At2g02320.1 At2g02340.1 At2g02360.1 At2g02250.1 At2g02240.1 At2g02300.1 At2g02310.1 SGN-U211584 SGN-U219097 SGN-U219098 SGN-U311800 SGN-U218282 SGN-U218283 At5g24560.1 SGN-U204215 SGN-U221580 SGN-U282885 SGN-U234276 SGN-U220091 SGN-U305684 SGN-U219720
 116 HEREDOC
 117 }
 118
 119 $seq_data ||= '';
 120 ###############################
 121 #Text area for input sequences
 122 $input_content .= <<HTML;
 123 <b>Input fasta/clustal sequences</b>
 124 &nbsp;&nbsp;
 125 <a href="index.pl" onclick="
 126         document.getElementById('textarea_seq_data').value = '';
 127         return false">(x) Clear</a><br />
 128 <textarea id="textarea_seq_data" name="seq_data" rows="12" cols="80">$seq_data</textarea><br /><br />
 129 <b>Or use identifiers, separated by spaces</b><br />
 130  Supports TAIR AGI [AT1G01010.1], SGN Unigene [SGN-U332332], or any NCBI/Entrez identifier<br />
 131 <textarea id="textarea_id_data" name="id_data" rows="2" cols="80">$id_data</textarea><br /><br />
 132 <b>Or upload a fasta/clustal file</b> <input type="file" name="upload" /><br />
 133 <br /><br />
 134
 135
 136 <input type="submit" name="submit" value="Analyze Alignment" />
 137 </form>
 138
 139 HTML
 140
 141
 142 # Print Page
 143
 144 $page->header();
 145
 146
 147 my $example_link = <<HTML;
 148 &nbsp;&nbsp;&nbsp;<span style="color:#669">
 149 <a href="index.pl?&format=fasta&title=Alignment%20Example&type=pep&show_prot_example=1">
 150 Aligned Example</a>
 151 &nbsp;|&nbsp;
 152 <a href="index.pl?&format=fasta_unaligned&maxiters=300&title=CDS%20Example&type=cds&show_cds_example=1">Unaligned Example</a>
 153 &nbsp;|&nbsp;
 154 <a href="index.pl?&maxiters=10&title=ID%20Input%20Example&&type=pep&format=fasta_unaligned&show_id_example=1">ID Input Example</a>
 155 </span>
 156 HTML
 157
 158 print page_title_html("Alignment Analyzer");
 159
 160 #print blue_section_html('Introduction','<table width="100%" cellpadding="5" cellspacing="0" border="0" summary=""><tr><td>' . $intro_content . '</td></tr></table>');
 161
 162 print blue_section_html(
 163         "<span style=\"white-space:nowrap\">Query Input &nbsp;&nbsp;&nbsp;&nbsp;$example_link</span>",
 164         '<table width="100%" cellpadding="5" cellspacing="0" border="0" summary=""><tr><td>' . $input_content . '</td></tr></table>');
 165
 166
 167 $page->footer();
 168
 169
 170 sub seq_from_file {
 171         my $file = shift;
 172         my $seq = "";
 173         open(FH, $file) or return "File not found";
 174         $seq .= $_ while(<FH>);
 175         close FH;
 176         return $seq;
 177 }