cgi-bin/tools/align_viewer/index.pl

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