cgi-bin/bulk/input.pl

   1
   2 =head1 NAME
   3
   4   /bulk/input.pl
   5
   6 =head1 DESCRIPTION
   7
   8   This perl script is used on the bulk download page. It structures the tabs on
   9   the main download page and determines the mode of each tab, as well as what
  10   information fields are available in each mode. It does this by accepting the
  11   mode parameter and displaying its corresponding input form. Legal values for
  12   mode are clone_search, array_search, unigene_search, bac_search,
  13   bac_end_search, unigene_convert and ftp. Other values have undefined results but will
  14   probably default to clone_search.It also accepts a debug parameter, which when
  15   set to 1 will add a 'print debug info' checkbox to the input forms. This
  16   parameter will be used by download.pl to display debug information.
  17
  18 =cut
  19
  20 use Modern::Perl;
  21 use CXGN::Page;
  22 use CXGN::Page::FormattingHelpers
  23   qw/page_title_html modesel simple_selectbox_html/;
  24 use CXGN::DB::Connection;
  25
  26 our $page = CXGN::Page->new( "Bulk download",
  27     "Lukas Mueller, Caroline Nyenke, Rob Buels" );
  28 my $db = CXGN::DB::Connection->new();
  29
  30 my ( $mode, $debug ) =
  31   $page->get_arguments(qw/mode debug/);  #determine mode and whether debug is on
  32
  33 $page->header( "Bulk download", 'Bulk download' )
  34   ;                                      #print page header and text below
  35 print <<EOH;
  36 <div style="margin-bottom: 1em">Download Unigene or BAC information using a list of identifiers, or complete datasets with FTP.</div>
  37 EOH
  38
  39 # create tab categories
  40 my @mode_funcs = (
  41     \&clone_search,   \&array_search, \&unigene_search, \&bac_search,
  42     \&bac_end_search, \&ftp_site,     \&unigene_convert,
  43 );
  44
  45 # define urls of modes
  46 my @mode_links = (
  47     [ '?mode=clone_search',    'Clone&nbsp;name<br />(SGN-C)' ],
  48     [ '?mode=microarray',      'Array&nbsp;spot&nbsp;ID<br />(SGN-S)' ],
  49     [ '?mode=unigene',         'Unigene&nbsp;ID<br />(SGN-U)' ],
  50     [ '?mode=bac',             'BACs' ],
  51     [ '?mode=bac_end',         'BAC&nbsp;ends' ],
  52     [ '?mode=ftp',             'Full&nbsp;datasets<br />(FTP)' ],
  53     [ '?mode=unigene_convert', 'Unigene ID Converter<br />(SGN-U)' ],
  54     [ '/bulk/feature',         'Features' ],
  55     [ '/bulk/gene',            'Genes' ],
  56 );
  57
  58 ### figure out which mode we're in ###
  59 my $modenum =
  60     $mode =~ /clone_search/i    ? 0
  61   : $mode =~ /array/i           ? 1
  62   : $mode =~ /unigene_convert/i ? 6
  63   : $mode =~ /unigene/i         ? 2
  64   : $mode =~ /bac_end/i         ? 4
  65   : $mode =~ /bac/i             ? 3
  66   : $mode =~ /ftp/i             ? 5
  67   : $mode =~ /feature/i         ? 7
  68   :                               0;    #clone search is default
  69
  70 ### print out the mode selection buttons at the top of the page ###
  71 ### prints out all @mode_links buttons, highlighting the current selected one###
  72 print modesel( \@mode_links, $modenum );
  73 print qq|<div class="indentedcontent">\n|;
  74
  75 ### call the appropriate function from the $mode_funcs list to print###
  76 ### out the download form, passing the $page object                      ###
  77 $mode_funcs[$modenum]( $page, $db, $debug );
  78
  79 print <<EOH;
  80 </div>
  81         <i><b>Note:</b> The SGN bulk download is limited to 10,000 identifiers per request.  If you need more, please either split your query into multiple parts, download a full dataset from the FTP site, or <a href="mailto:sgn-feedback\@sgn.cornell.edu">email us</a> and we will be happy to generate a custom dataset for you.</i>
  82 EOH
  83 $page->footer();
  84
  85 ###end of webpage###
  86
  87 =head2 DEBUG
  88
  89   Desc: sub DEBUG
  90   Args: string;
  91   Ret : n/a
  92
  93   Print debug information fed to it by download.pl when set to 1. (see also
  94   debug() in download.pl).
  95
  96 =cut
  97
  98 #one parameter: a string to print, or not, as desired
  99 sub DEBUG {
 100     print shift(@_);
 101 }
 102
 103 sub ug_build_selectbox {
 104     my ( $db, $filter_sub ) = @_;
 105     my %builds;
 106     my $sth = $db->prepare(
 107         q|SELECT        ub.unigene_build_id,
 108                                         ub.organism_group_id,
 109                                         ub.build_nr,
 110                                         g.group_id,
 111                                         g.comment
 112                                 FROM    sgn.unigene_build as ub, sgn.groups as g
 113                                 WHERE   ub.organism_group_id=g.group_id
 114                                   AND   g.type=1
 115                                   AND   ub.status='C'
 116                          |
 117     );
 118     $sth->execute();
 119     while ( my @row = $sth->fetchrow_array() ) {
 120         if ($filter_sub) {
 121             next unless $filter_sub->(@row);
 122         }
 123
 124         my ( $unigene_build_id, $organism_group_id, $build_nr, $group_id,
 125             $species )
 126           = @row;
 127         $species =~ s/(\S)[a-z]+\s([a-z]+)/uc($1).'. '.$2/ei
 128           ;    #< abbreviate the species names
 129         $builds{$unigene_build_id} = "$species (build $build_nr)";
 130     }
 131
 132     return simple_selectbox_html(
 133         name    => 'build_id',
 134         label   => 'Only include unigene build:',
 135         choices => [
 136             [ all => 'include all' ],
 137             ( map [ $_, $builds{$_} ], keys %builds ),
 138         ],
 139     );
 140
 141 }
 142
 143 =head2 clone_search
 144
 145   Desc: sub clone_search
 146   Args: n/a
 147   Ret : clone tab format
 148
 149   Defines the format of the clone tab using html, perl and perl dbi. Speicfies
 150   information fields available for searching clones. Also, this and all other
 151   tabs print the debug checkbox when debug parameter is set to one.
 152
 153 =cut
 154
 155 sub clone_search {
 156
 157     # displays the clone search input form
 158     #
 159     my ( $page, $db, $debug ) = @_;
 160
 161     my $content         = "";
 162     my $ug_build_select = ug_build_selectbox($db);
 163     print <<HTML;
 164 <form name="bulkform" action="download.pl" method="post" enctype="multipart/form-data">
 165
 166 <br />
 167 <table summary="" cellpadding="10" width="100%"><tr><td valign="top" bgcolor="#EEEEEE" width="320">
 168
 169 $ug_build_select
 170 <br />
 171
 172 Enter a list of identifiers or upload a file containing identifers, one per line:<br />
 173 <table summary="" width="100%"><tr><td>
 174 <textarea name="ids" rows="5" cols="20"></textarea>
 175 </td>
 176 <td>
 177 <i>Example:</i> #example box
 178 <pre style="border: 1px solid gray; width: 10em; height: 5em">
 179 cLEB-1-A2
 180 cLEB-1-A3
 181 cLEB-1-A4
 182 </pre>
 183 </td></tr></table>
 184
 185 <br />
 186 <br />
 187 And/or upload list file: <br /><input type="file" name="file" />
 188 <br />
 189 <br />
 190
 191 HTML
 192
 193     print qq|</td><td valign="top" bgcolor="#EEEEEE" width="320">\n|;
 194     output_list();    #print out checkboxes
 195
 196     print <<HTML;
 197
 198 </td></tr></table>
 199
 200 HTML
 201
 202     if ( $debug eq "1" ) {
 203         print
 204 qq|<input type="checkbox" checked="checked" name="debug" /> print debug statements<br /><br />\n|;
 205     }
 206
 207     print <<HTML;
 208
 209         <input type="hidden" name="idType" value="clone" />
 210         <input type="reset" />&nbsp;&nbsp;
 211         <input type="submit" value="Submit" /><br />
 212    </form>
 213
 214 HTML
 215
 216 }
 217
 218 =head2 array_search
 219
 220   Desc: sub array_search
 221   Args: n/a
 222   Ret : array tab format
 223
 224   Defines the format of the array tab using html, perl and perl dbi. Specifies
 225   information fields available for searching microarrays. Prints the debug
 226   checkbox when debug parameter is set to one.
 227
 228 =cut
 229
 230 sub array_search {
 231
 232     #
 233     # displays the array search input form
 234     #
 235     my ( $page, $db, $debug ) = @_;
 236
 237     my $content = "";
 238
 239     $page = CXGN::Page->new( "Bulk download", "Lukas Mueller" );
 240
 241     my $ug_select = ug_build_selectbox(
 242         $db,
 243         sub {
 244             ( $_[4] =~ /lycopersicon|tomato/i && $_[4] !~ /demethylated/i )
 245               ? 1
 246               : 0;
 247         }
 248     );
 249     print <<HTML;
 250
 251 <form name="bulkform" action="download.pl" method="post" enctype="multipart/form-data">
 252 <br />
 253 <table summary="" cellpadding="10" width="100%"><tr><td valign="top" bgcolor="#EEEEEE" width="320">
 254
 255 $ug_select
 256 <br /><br />
 257         <br />
 258 Enter a list of identifiers or upload a file containing one identifier:<br />
 259 <table summary="" width="100%"><tr><td>
 260 <textarea name="ids" rows="5" cols="20"></textarea>
 261 </td>
 262 <td>
 263 <i>Example:</i>
 264 <pre style="border: 1px solid gray; width: 10em; height: 5em">
 265 1-1-1.2.3.4
 266 1-1-1.2.4.5
 267 1-1-1.5.3.6
 268 </pre>
 269 </td></tr></table>
 270 <br />
 271 <br />
 272 And/or upload list file: <br /><input type="file" name="file" />
 273 <br />
 274 <br />
 275
 276  </td><td valign="top" bgcolor="#EEEEEE" width="320">
 277
 278 HTML
 279
 280     output_list();
 281
 282     print "</td></tr></table>\n";
 283
 284     if ( $debug eq "1" ) {
 285         print
 286 qq|<input type="checkbox" checked="checked" name="debug" /> print debug statements<br /><br />\n|;
 287     }
 288
 289     print <<HTML
 290
 291 <input type="hidden" name="idType" value="microarray" />
 292         <input type="reset" />&nbsp;&nbsp;
 293 <input type="submit" value="Submit" /><br />
 294 </form>
 295
 296 HTML
 297
 298       ;
 299
 300 }
 301
 302 =head2 unigene_search
 303
 304   Desc: sub unigene_search
 305   Args: n/a
 306   Ret : unigene tab format
 307
 308   Defines the format of the unigene tab using html, perl and perl dbi. Speicfies
 309   information fields available for searching unigenes. Prints the debug
 310   checkbox when debug parameter is set to one.
 311
 312 =cut
 313
 314 sub unigene_search {
 315
 316 #
 317 # displays the unigene input form
 318 #
 319 # Note: the unigene input form does not display the drop down of unigene builds, because a unigene ID is by definition mapped to a
 320 # given build.
 321 #
 322 # This form supports to different types of unigene queries: getting information pertaining to unigenes themselves (annotations and seq)
 323 # and unigene membership information. The two queries are distinguished by the unigene_mode radio control. Some adjustments have to
 324 # be made in the download.pl program when distinguishing the two modes.
 325 #
 326     my ( $page, $db, $debug ) = @_;
 327
 328     my $content   = "";
 329     my $ug_select = ug_build_selectbox($db);
 330
 331     print <<HTML;
 332
 333 <form name="bulkform" action="download.pl" method="post" enctype="multipart/form-data">
 334
 335 <br />
 336 <table summary="" cellpadding="10" width="100%"><tr><td valign="top" bgcolor="#EEEEEE" width="320">
 337
 338 HTML
 339
 340     print <<HTML1
 341
 342 <br />
 343 Enter a list of identifiers or upload a file containing one identifer separated by whitespace (returns, spaces or tabs):<br />
 344
 345
 346 <table summary="" width="100%" cellpadding="0"><tr><td>
 347 <textarea name="ids" rows="5" cols="20"></textarea>
 348 </td>
 349 <td>
 350 <i>Example:</i>
 351 <pre style="border: 1px solid gray; width: 10em; height: 5em">
 352 SGN-U268057
 353 SGN-U562661
 354 SGN-U196026
 355 </pre>
 356 </td></tr></table>
 357 <br />
 358 <br />
 359
 360 And/or upload list file: <br /><input type="file" name="file" />
 361 <br />
 362 <br />
 363
 364 </td><td valign="top" bgcolor="#EEEEEE" width="320">
 365
 366  <input type="checkbox" name="convert_to_current" checked="checked" /><label for="convert_to_current"><a class="stealth" title="Check this box to convert each unigene in the list to its equivalent in the most current corresponding unigene build(s), if available"><img src="/documents/img/new.gif" />convert unigene list to current build</a></label>
 367
 368  <hr />
 369
 370 <input type="radio" name="unigene_mode" value="unigene_info" checked="checked" /> <b>Download unigene information</b>:<br />
 371 <!-- SGN_U for Unigene Info -->
 372 <div style="padding-left: 1em">
 373     <input type="checkbox" name="SGN_U_U" checked="checked" /> unigene id (SGN-U)<br />
 374     <input type="checkbox" name="automatic_annotation" checked="checked" /> automatic (BLAST) annotation<br />
 375     <input type="checkbox" name="best_genbank_match" checked="checked" /> best genbank match<br />
 376     <input type="checkbox" name="best_arabidopsis_match" checked="checked" /> best arabidopsis match<br />
 377     <input type="checkbox" name="associated_loci" checked="checked" /> associated loci<br />
 378     <input type="checkbox" name = "uni_seq" checked="checked" onclick="check_fasta_option()"/> sequence<br />
 379     <div style="padding-left: 1em">
 380          <input type="radio" name="seq_mode" value="unigene_seq" checked="checked" /> unigene nucleotide sequence<br />
 381          <input type="radio" name="seq_mode" value="estscan_seq" /> estscan predicted proteins<br />
 382          <input type="radio" name="seq_mode" value="longest6frame_seq" /> longest ORF from 6-frame translation<br />
 383          <input type="radio" name="seq_mode" value="preferred_protein_seq" /> preferred sequence<br />
 384     </div>
 385 </div>
 386
 387 <input type="radio" name="unigene_mode" value="member_info" /> <b>Download member information</b>:
 388 <div style="padding-left: 1em">
 389     <input type="checkbox" name="clone_name" checked="checked" /> clone name<br />
 390     <input type="checkbox" name="SGN_C" checked="checked" /> clone id (SGN-C)<br />
 391     <input type="checkbox" name="SGN_T" checked="checked" /> sequence read id (SGN-T)<br />
 392     <input type="checkbox" name="SGN_E" checked="checked" /> est id (SGN-E)<br />
 393     <input type="checkbox" name="build_nr" checked="checked" /> unigene build number<br />
 394     <!-- SGN_U for Member Info -->
 395     <input type="checkbox" name="SGN_U_M" checked="checked" /> unigene id (SGN-U)<br />
 396     <input type="checkbox" name="chipname" checked="checked" /> chipname<br />
 397     <input type="checkbox" name="SGN_S" checked="checked" /> microarray spot id (SGN-S)<br />
 398     <input type="checkbox" name="TUS" checked="checked" /> TUS number<br />
 399     <input type="checkbox" name="manual_annotation" /> manual annotation<br />
 400     <input type="checkbox" name="est_seq" checked="checked" /> EST sequence<br />
 401 </div>
 402 </td></tr></table>
 403
 404 HTML1
 405
 406       ;
 407
 408     if ( $debug eq "1" ) {
 409         print
 410 qq|<input type="checkbox" checked="checked" name=debug /> print debug statements<br /><br />\n|;
 411     }
 412
 413     print <<HTML2
 414
 415         <input type=hidden name="idType" value="unigene" />
 416         <input type="reset" />&nbsp;&nbsp;
 417 <input type="submit" value="Submit" /><br />
 418 </form>
 419
 420 HTML2
 421
 422       ;
 423
 424 }
 425
 426 =head2 unigene_convert
 427
 428   Desc: sub unigene_convert
 429   Args: n/a
 430   Ret : unigene tab format
 431
 432   Defines the format of the unigene conversion tab using html, perl and perl dbi. Speicfies
 433   information fields available for searching unigenes. Prints the debug
 434   checkbox when debug parameter is set to one.
 435
 436 =cut
 437
 438 sub unigene_convert {
 439
 440 #
 441 # displays the unigene converter input form
 442 #
 443 # Note: the unigene input form does not display the drop down of unigene builds, because a unigene ID is by definition mapped to a
 444 # given build.
 445
 446     my ( $page, $db, $debug ) = @_;
 447
 448     my $content = "";
 449
 450     print <<HTML;
 451
 452 <form name="bulkform" action="download.pl" method="post" enctype="multipart/form-data">
 453
 454 <br />
 455 <table summary="" cellpadding="10" width="100%"><tr><td valign="top" bgcolor="#EEEEEE" width="320">
 456
 457 HTML
 458     print <<HTML1
 459
 460 <br />
 461 Enter a list of identifiers or upload a file containing one identifer separated by whitespace (returns, spaces or tabs):<br />
 462
 463
 464 <table summary="" width="100%" cellpadding="0"><tr><td>
 465 <textarea name="ids" rows="5" cols="50"></textarea>
 466 </td>
 467 <td>
 468 <i>Example:</i>
 469 <pre style="border: 1px solid grey; width: 20em; height: 5em">
 470 SGN-U268057
 471 SGN-U562661
 472 SGN-U196026
 473 </pre>
 474 </td></tr></table>
 475 <br />
 476 <br />
 477
 478 And/or upload list file: <br /><input type="file" name="file" />
 479 <br />
 480 <br />
 481
 482 </td></tr></table>
 483
 484 HTML1
 485
 486       ;
 487
 488     if ( $debug eq "1" ) {
 489         print
 490 qq|<input type="checkbox" checked="checked" name="debug" /> print debug statements<br /><br />\n|;
 491     }
 492
 493     print <<HTML2
 494
 495         <input type=hidden name="idType" value="unigene_convert" />
 496         <input type="reset" />&nbsp;&nbsp;
 497 <input type="submit" value="Convert" /><br />
 498 </form>
 499
 500 HTML2
 501
 502       ;
 503 }
 504
 505 #deprecated
 506 sub output_type {
 507     print <<OUTPUT_TYPE;
 508
 509         Output type:<br />
 510         <input type="radio" name="outputType" value="html" checked="checked" /> HTML<br />
 511         <input type="radio" name="outputType" value="text" /> text<br />
 512         &nbsp; &nbsp; &nbsp;<input type="checkbox" name="fasta" /> Fasta<br />
 513         <br />
 514
 515 OUTPUT_TYPE
 516
 517 }
 518
 519 #method used by clone_name and microarray searches to display checkboxes
 520 sub output_list {
 521     print <<OUTPUT_LIST;
 522
 523         <b>Please select the information you would like for each identifier:</b><br />
 524         <input type="checkbox" name="clone_name" checked="checked" /> clone name<br />
 525         <input type="checkbox" name="SGN_C" checked="checked" /> clone id (SGN-C)<br />
 526         <input type="checkbox" name="SGN_T" checked="checked" /> sequence read id (SGN-T)<br />
 527         <input type="checkbox" name="SGN_E" checked="checked" /> est id (SGN-E)<br />
 528         <input type="checkbox" name="build_nr" checked="checked" /> unigene build nr<br />
 529         <input type="checkbox" name="SGN_U" checked="checked" /> unigene id (SGN-U)<br />
 530         <input type="checkbox" name="chipname" checked="checked" /> chipname<br />
 531         <input type="checkbox" name="SGN_S" checked="checked" /> microarray spot id (SGN-S)<br />
 532         <input type="checkbox" name="TUS" checked="checked" /> TUS number (used to order clones)<br />
 533         <input type="checkbox" name="manual_annotation" /> manual annotation<br />
 534         <input type="checkbox" name="automatic_annotation" /> automatic (BLAST) annotation<br />
 535         <input type="checkbox" name="sequence" onclick="check_fasta_option()" /> sequence<br />
 536         &nbsp;&nbsp;&nbsp;<input type="radio" name="seq_type" value="est_seq" checked="checked" /> EST sequence<br />
 537         &nbsp;&nbsp;&nbsp;<input type="radio" name="seq_type" value="unigene_seq" /> Unigene sequence<br />
 538
 539 OUTPUT_LIST
 540
 541 }
 542
 543 =head2 bac_search
 544
 545   Desc: sub bac_search
 546   Args: n/a
 547   Ret : BAC tab format
 548
 549   Defines the format of the BAC tab using html & perl. Speicfies
 550   information fields available for searching BACs. Prints the debug
 551   checkbox when debug parameter is set to one.
 552
 553 =cut
 554
 555 # new bac_search
 556 sub bac_search {
 557
 558     # displays the bac search input form
 559     #
 560     my ( $page, $db, $debug ) = @_;
 561
 562     my $content = "";
 563
 564     print <<HTML;
 565
 566 <form name="bulkform" action="download.pl" method="post" enctype="multipart/form-data">
 567
 568 <br />
 569 <table summary="" cellpadding="10" width="100%"><tr><td valign="top" bgcolor="#EEEEEE" width="320">
 570
 571
 572 <br />
 573 Enter a list of identifiers or upload a file containing identifers separated by whitespace (returns, spaces or tabs):<br />
 574 <table summary="" width="100%"><tr><td>
 575 <textarea name="ids" rows="5" cols="20"></textarea>
 576 </td>
 577 <td>
 578 <i>Example:</i>
 579 <pre style="border: 1px solid gray; width: 10em; height: 5em">
 580 LE_HBa0033F11
 581 SL_MboI0001A07
 582 SL_EcoRI0022A07
 583
 584 </pre>
 585 </td></tr></table>
 586 <br />
 587 <br />
 588 And/or upload list file: <br /><input type="file" name="file" />
 589 <br />
 590 <br />
 591
 592 </td><td valign="top" bgcolor="#EEEEEE" width="320">\n
 593 <b>Download BAC information:</b> <br />
 594 <div style="margin: 1em; white-space: nowrap">
 595   <input type="checkbox" name="arizona_clone_name" checked="checked"  /> Arizona-style clone name (LE_HBa0001A01) <br />
 596   <input type="checkbox" name="cornell_clone_name" checked="checked"  /> Old Cornell-style clone name (P001A01)<br />
 597   <input type="checkbox" name="chr_clone_name" checked="checked"  /> Clone name with chromosome (C01HBa0001A01)<br />
 598   <input type="checkbox" name="clone_type" checked="checked" /> clone type <br />
 599   <input type="checkbox" name="org_name" checked="checked" /> organism name <br />
 600   <input type="checkbox" name="accession_name" checked="checked" /> accession name <br />
 601   <input type="checkbox" name="library_name" checked="checked" /> library name <br />
 602   <input type="checkbox" name="estimated_length" checked="checked" /> estimated length <br />
 603   <input type="checkbox" name="genbank_accession" checked="checked" /> genbank accession<br />
 604 <!--    <input type="checkbox" name="overgo_matches" checked="checked" DISABLED /> overgo matches<br /> -->
 605 </div>
 606
 607 </td></tr></table>
 608 HTML
 609
 610     if ( $debug eq "1" ) {
 611         print
 612 qq|<input type="checkbox" checked="checked" name="debug" /> print debug statements<br /><br />\n|;
 613     }
 614
 615     print <<HTML;
 616
 617         <input type="hidden" name="idType" value="bac" />
 618         <input type="reset" />&nbsp;&nbsp;
 619         <input type="submit" value="Submit"><br />
 620    </form>
 621
 622 HTML
 623
 624 }
 625
 626 =head2 bac_end_search
 627
 628   Desc: sub bac_end_search
 629   Args: n/a
 630   Ret : BAC end tab format
 631
 632   Defines the format of the BAC end=head2 bac_end_search tab using html & perl.
 633   Specifies information fields available for searching BAC ends. Prints the debug
 634   checkbox when debug parameter is set to one.
 635
 636 =cut
 637
 638 # new bac_end
 639 sub bac_end_search {
 640
 641     # displays the bac search input form
 642     #
 643     my ( $page, $db, $debug ) = @_;
 644
 645     my $content = "";
 646
 647     print <<HTML;
 648
 649 <form name="bulkform" action="download.pl" method="post" enctype="multipart/form-data">
 650
 651 <br />
 652 <table summary="" cellpadding="10" width="100%"><tr><td valign="top" bgcolor="#EEEEEE" width="370">
 653
 654
 655 <br />
 656 Enter a list of identifiers or upload a file containing identifers separated by whitespace (returns, spaces or tabs):<br />
 657 <table summary="" width="100%"><tr><td>
 658 <textarea name="ids" rows="5" cols="25"></textarea>
 659 </td>
 660 <td>
 661 <i>Example:</i>
 662 <pre style="border: 1px solid gray; width: 15em; height: 5em">
 663 LE_HBa0011C24_SP6_121022
 664 SL_MboI0033A13_SP6_294865
 665 SL_EcoRI0022A07_T7_229350
 666
 667 </pre>
 668 </td></tr></table>
 669 <br />
 670 <br />
 671 And/or upload list file: <br /><input type="file" name="file" />
 672 <br />
 673 <br />
 674
 675 </td><td valign="top" bgcolor="#EEEEEE" width="280">\n
 676
 677 <b>Download BAC end information:</b><br />
 678 <div style="margin-left: 1em; white-space: nowrap">
 679   <input type="checkbox" name="bac_id" checked= "checked" /> bac end identifier <br />
 680   <input type="checkbox" name="clone_type" checked="checked" /> clone type <br />
 681   <input type="checkbox" name="org_name" checked="checked" /> organism name <br />
 682   <input type="checkbox" name="accession_name" checked="checked" /> accession name <br />
 683   <input type="checkbox" name="library_name" checked="checked" /> library name <br />
 684   <input type="checkbox" name="estimated_length" checked="checked" /> estimated length <br />
 685   <input type="checkbox" name="genbank_accession" checked="checked" /> genbank accession<br />
 686   <!--  <input type="checkbox" name="overgo_matches" checked="checked" DISABLED /> overgo matches <br /> -->  <br />
 687   <b>Choose format and type:</b><br />
 688   <input type="checkbox" name="bac_end_sequence" checked="checked" /> bac end sequence <br />
 689   <input type="checkbox" name="qual_value_seq" checked="checked" /> quality value <br />
 690   <div style="margin-left: 1em">
 691     <input type="radio" name="bac_seq_type" value="raw_seq" />raw sequence and/or quality<br />
 692     <input type="radio" name="bac_seq_type" value="trim_seq" checked="checked" />trimmed seq. and/or quality<br />
 693   </div>
 694 </div>
 695
 696
 697 </td></tr></table>
 698 HTML
 699
 700     if ( $debug eq "1" ) {
 701         print
 702 qq|<input type="checkbox" checked="checked" name="debug" /> print debug statements<br /><br />\n|;
 703     }
 704
 705     print <<HTML;
 706
 707         <input type="hidden" name="idType" value="bac_end" />
 708         <input type="reset" />&nbsp;&nbsp;
 709         <input type="submit" value="Submit"><br />
 710    </form>
 711
 712 HTML
 713
 714 }
 715
 716 =head2 ftp_site
 717
 718   Desc: sub ftp_site
 719   Args: n/a
 720   Ret : ftp tab format
 721
 722   Defines the format of the ftp tab using html & perl. Specifies
 723   links for downloading ftp information.
 724
 725 =cut
 726
 727 sub ftp_site {
 728     my $page = shift;
 729
 730     print <<HTML;
 731     <h3 style="margin-bottom: 0.3em">SGN FTP site</h3>
 732         <div style="margin: 0 1em 0 1em">Download complete datasets.</div><br />
 733
 734     <div style="margin: 0; padding: 1em; border: 1px solid #ccccff">
 735         <a class="folderlink" href="ftp://ftp.solgenomics.net">ftp top level</a>
 736
 737         <ul style="margin: 1em 0 0 0; list-style: none">
 738
 739 HTML
 740
 741     my %ftplinks = (
 742         'unigene_builds' =>
 743 'Sequence, quality, and membership information for all SGN unigene builds',
 744         'est_sequences' =>
 745           'Sequence and quality files for all SGN ESTs, organized by library',
 746         'maps_and_markers' =>
 747           'Marker sequences and marker position lists for all SGN maps',
 748         'physical_mapping' =>
 749 'Raw data files for Tomato HindIII BAC library FPC and overgo analyses',
 750         'blast_annotations' =>
 751 'Highest-ranked hits vs. Genbank NR and Arabidopsis for all SGN unigenes.',
 752         'manual_annotations' =>
 753           'Manual annotations for a number of SGN unigenes',
 754         'user_requests' =>
 755 'Custom-generated datasets for individual users (mail special requests to <a href="mailto:sgn-feedback@sgn.cornell.edu">sgn-feedback</a>)',
 756         'tomato_genome' =>
 757           'Tomato genomic data, including BAC end and full BAC sequences',
 758         'COSII' => 'COSII marker data'
 759     );
 760
 761     foreach my $dir ( sort keys %ftplinks ) {
 762         my $desc = $ftplinks{$dir};
 763         print <<HTML;
 764         <li><a class="folderlink" href="ftp://ftp.solgenomics.net/$dir"> $dir</a>
 765             <div class="folderdesc">$desc</div>
 766         </li>
 767 HTML
 768     }
 769
 770     print <<HTML;
 771         </ul>
 772     </div>
 773
 774         <br />
 775         <i>Note:</i> The SGN FTP site can also be accessed directly through <a href="ftp://ftp.solgenomics.net">ftp://ftp.solgenomics.net</a> using a browser or ftp program.
 776 HTML
 777
 778 }
 779
 780 =head1 BUGS
 781
 782   None known.
 783
 784 =head1 AUTHORS
 785
 786   Lukas Mueller, Caroline Nyenke, Alexander Naydich and Matthew Crumb
 787
 788 =head1 SEE ALSO
 789
 790   /bulk/download.pl
 791   /bulk/display.pl
 792
 793 =cut