cgi-bin/downloads/perlcyc.pl

   1
   2 use strict;
   3 use CXGN::Page;
   4 use CXGN::Page::FormattingHelpers qw | info_section_html |;
   5 my $p = CXGN::Page->new();
   6
   7 $p->header("PerlCyc.pm", "PerlCyc.pm");
   8
   9 print info_section_html (title=>"Description", contents=> <<HTML );
  10
  11
  12 PerlCyc is a Perl interface for <a href="http://bioinformatics.ai.sri.com/ptools/">Pathway Tools software</a>. It allows internal Pathay Tools Lisp functions to be accessed through Perl. <br /><br />
  13
  14 For a description of what the individual functions do, please
  15        refer to the Pathway Tools documentation at http://bioinformat-
  16        ics.ai.sri.com/ptools .
  17 <br /><br />
  18        In general, the Lisp function name has to be converted to something
  19        compatible with Perl: Dashes have to be replaced by underlines, and
  20        question marks with underline p (_p).
  21 <br /><br />
  22        Note that the optional parameters of all functions
  23        are not supported in perlcyc, except for all_pathways() which can
  24        use the optional arguments :all T to get the base pathways only (no
  25        super-pathways).
  26
  27 HTML
  28
  29     print info_section_html (title=>"Installation", contents=> <<HTML );
  30
  31 Installation is standard as for any Perl module. If you downloaded the
  32        compressed tar file, uncompress and untar the file with the following
  33        commands:
  34 <pre>
  35         gzip < perlcyc.tar.gz | tar xvf -
  36 </pre>
  37        This will create a directory called perlcyc in your current directory.
  38        To install the program, type
  39 <pre>
  40         make
  41         make install
  42 </pre>
  43        The program should now be available in all your Perl programs. "make
  44        install" may require root access or access through sudo. For the latter
  45        case, type
  46 <pre>
  47         sudo make install
  48 </pre>
  49        You will be prompted for your password.
  50
  51 HTML
  52
  53     print info_section_html (title=>"Limitations", contents=><<HTML);
  54
  55 Perlcyc does not implement the GFP objects in Perl, rather it just
  56        sends snippets of code to Pathway-Tools through a socket connection.
  57        Only one such connection can be openend at any given time. Because the
  58        objects are not implemented in Perl, only object references are supported.
  59
  60 HTML
  61
  62     print info_section_html (title=>"Supported functions", contents=><<HTML);
  63
  64
  65 Object functions:
  66
  67 <pre>
  68        new
  69        Parameters: The knowledge base name. Required!
  70 </pre>
  71        GFP functions: More information on these functions can be found at:
  72        http://www.ai.sri.com/~gfp/spec/paper/node63.html
  73 <pre>
  74         get_slot_values
  75         get_slot_value
  76         get_class_all_instances
  77         instance_all_instance_of_p
  78         member_slot_value_p
  79         fequal
  80         current_kb
  81         put_slot_values
  82         put_slot_value
  83         add_slot_value
  84         replace_slot_value
  85         remove_slot_value
  86         coercible_to_frame_p
  87         class_all_type_of_p
  88         get_instance_direct_types
  89         get_instance_all_types
  90         get_frame_slots
  91         put_instance_types
  92         save_kb
  93         revert_kb
  94 </pre>
  95        Pathway-tools functions: More information on these functions can be
  96        found at: http://bioinformatics.ai.sri.com/ptools/ptools-fns.html
  97 <pre>
  98         select_organism
  99         all_pathways
 100         all_orgs
 101         all_rxns
 102         genes_of_reaction
 103         substrates_of_reaction
 104         enzymes_of_reaction
 105         reaction_reactants_and_products
 106         get_predecessors
 107         get_successors
 108         genes_of_pathway
 109         enzymes_of_pathway
 110         compounds_of_pathway
 111         substrates_of_pathway
 112         transcription_factor_p
 113         all_cofactors
 114         all_modulators
 115         monomers_of_protein
 116         components_of_protein
 117         genes_of_protein
 118         reactions_of_enzyme
 119         enzyme_p
 120         transport_p
 121         containers_of
 122         modified_forms
 123         modified_containers
 124         top_containers
 125         reactions_of_protein
 126         regulon_of_protein
 127         transcription_units_of_protein
 128         regulator_proteins_of_transcription_unit
 129         enzymes_of_gene
 130         all_products_of_gene
 131         reactions_of_gene
 132         pathways_of_gene
 133         chromosome_of_gene
 134         transcription_unit_of_gene
 135         transcription_unit_promoter
 136         transcription_unit_genes
 137         transcription_unit_binding_sites
 138         transcription_unit_transcription_factors
 139         transcription_unit_terminators
 140         all_transported_chemicals
 141         reactions_of_compound
 142         full_enzyme_name
 143         enzyme_activity_name
 144         find_indexed_frame
 145         create-instance
 146         create-class
 147         create-frame
 148
 149         pwys-of-organism-in-meta
 150         enzymes-of-organism-in-meta
 151         lower-taxa-or-species-p org-frame
 152         get-class-all-subs
 153 </pre>
 154        added 5/2008 per Suzanne\'s request:
 155 <pre>
 156         genes-regulating-gene
 157         genes-regulated-by-gene
 158         terminators-affecting-gene
 159         transcription-unit-mrna-binding-sites
 160         transcription-unit-activators
 161         transcription-unit-inhibitors
 162         containing-tus
 163         direct-activators
 164         direct-inhibitors
 165 </pre>
 166        not supported:
 167 <pre>
 168         get_frames_matching_value (why not?)
 169 </pre>
 170        Internal functions:
 171 <pre>
 172         parselisp
 173         send_query
 174         retrieve_results
 175         wrap_query
 176         call_func
 177         debug
 178         debug_on
 179         debug_off
 180 </pre>
 181        Deprecated functions
 182 <pre>
 183         parse_lisp_list
 184 </pre>
 185
 186 HTML
 187
 188     print info_section_html(title=>"Requirements", contents=> <<HTML );
 189
 190        To use the Perl module, you also need the socket_server.lisp program.
 191        In Pathway Tools version 8.0 or later, the server program can be
 192        started with the command line option "-api". On earlier versions, the
 193        server daemon needs to be loaded manually, as follows: start Pathway-
 194        Tools with the -lisp option, at the prompt, type: (load
 195        "/path/to/socket_server.lisp"), then start the socket_server by typing
 196        (start_external_access_daemon :verbose? t). The server is now ready to
 197        accept connections and queries.
 198
 199 HTML
 200
 201 print    info_section_html (title=>"Download", contents=> <<HTML );
 202
 203 Download [<a href="ftp://ftp.sgn.cornell.edu/programs/perlcyc/">FTP</a>]
 204
 205 HTML
 206
 207     print info_section_html(title=>"Documentation", contents=> <<HTML );
 208
 209 <pre>
 210        perlcyc is a Perl interface for Pathway Tools software.
 211
 212        "use perlcyc;"
 213
 214        "my \$cyc = perlcyc -> new("ARA");" "my \@pathways = \$cyc -> all_path-
 215        ways();"
 216
 217 VERSION
 218        Version 1.21 (May 2008).
 219
 220 VERSION HISTORY
 221
 222        Version History
 223
 224        0.1  March, 2002
 225             [Lukas Mueller] initial version
 226
 227        0.3  April 22, 2002
 228             [Danny Yoo] Added better list parsing
 229
 230        0.9  [Lukas Mueller]
 231             Added more functions
 232
 233        1.0  August 28, 2002 [Lukas Mueller]
 234             Added pod documentation and eliminated some bugs.
 235
 236        1.1  June 6, 2003
 237             [Thomas Yan] Fixed some minor bugs.
 238
 239        1.2  December 7, 2006 [Lukas Mueller]
 240             Added three functions: create-frame, create-class, and cre-
 241             ate-instance.
 242
 243        1.21 May 7, 2008 [Lukas Mueller]
 244             Added three functions that are new in PT v. 12:
 245              pwys-of-organism-in-meta
 246              enzymes-of-organism-in-meta
 247              lower-taxa-or-species-p org-frame
 248
 249              other new functions:
 250              get-class-all-subs
 251
 252              genes-regulating-gene
 253              genes-regulated-by-gene
 254              terminators-affecting-gene
 255              transcription-unit-mrna-binding-sites
 256              transcription-unit-activators
 257              transcription-unit-inhibitors
 258              containing-tus
 259              direct-activators
 260              direct-inhibitors
 261
 262
 263
 264 </pre>
 265
 266 HTML
 267
 268     print info_section_html (title=>"Examples", contents=> <<HTML );
 269
 270        Change product type for all genes that are in a pathway to "Enzyme"
 271
 272 <pre>
 273         use perlcyc;
 274
 275         my \$cyc = perlcyc -> new ("ARA");
 276         my \@pathways = \$cyc -> all_pathways();
 277
 278         foreach my $p (\@pathways) {
 279           my \@genes = \$cyc -> genes_of_pathway(\$p);
 280           foreach my \$g (\@genes) {
 281             \$cyc -> put_slot_value (\$g, "Product-Types", "Enzyme");
 282           }
 283         }
 284 </pre>
 285        Load a file containing two columns with accession and a comment into
 286        the comment field of the corresponding accession:
 287 <pre>
 288         use perlcyc;
 289         use strict;
 290
 291         my \$file = shift;
 292
 293         my \$added=0;
 294         my \$recs =0;
 295
 296         open (F, "<\$file") || die "Can't open file\\n";
 297
 298         print STDERR "Connecting to AraCyc...\\n";
 299         my \$cyc = perlcyc -> new("ARA");
 300
 301         print STDERR "Getting Gene Information...\\n";
 302         my \@genes = \$cyc -> get_class_all_instances("|Genes|");
 303
 304         my %genes;
 305
 306         print STDERR "Getting common names...\\n";
 307         foreach my \$g (\@genes) {
 308           my \$cname = \$cyc -> get_slot_value(\$g, "common-name");
 309           \$genes{\$cname}=\$g;
 310         }
 311
 312         print STDERR "Processing file...\\n";
 313         while (&lt;F&gt;) {
 314           my (\$locus, \$location, \@rest) = split /\\t/;
 315           \$recs++;
 316           if (exists \$genes{\$locus}) {
 317               my \$product = \$cyc -> get_slot_value(\$genes{\$locus}, "product");
 318                 if (\$product) {
 319                 \$cyc -> add_slot_value(\$product, "comment", "\"\\nTargetP location: \$location\\n\"");
 320                  #print STDERR "Added to description of frame \$product\n";
 321                 \$added++;
 322               }
 323             }
 324         }
 325
 326         close (F);
 327
 328         print STDERR "Done. Added \$added descriptions. Total lines in file: \$recs. \\n";
 329 </pre>
 330        Add a locus link to the TAIR locus page for each gene in the database
 331 <pre>
 332         use strict;
 333         use perlcyc;
 334
 335         my \$added =0;
 336         my \$genesprocessed=0;
 337
 338         print "Connecting to AraCyc...\\n";
 339         my \$cyc = perlcyc -> new ("ARA");
 340
 341         print "Getting Gene Information...\\n";
 342         my \@genes = \$cyc -> get_class_all_instances ("|Genes|");
 343
 344         print "Adding TAIR links...\\n";
 345         foreach my \$g (\@genes) {
 346           \$genesprocessed++;
 347           my \$common_name = \$cyc -> get_slot_value(\$g, "common-name");
 348           if (\$common_name &amp;&amp; (\$common_name ne "NIL")) {
 349             \$cyc -> put_slot_value (\$g, "dblinks", "(TAIR \"\$common_name\")");
 350             \$added++;
 351           }
 352           if ((!\$genesprocessed ==0) &amp;&amp; (\$genesprocessed % 1000 == 0)) { print "\$genesprocessed ";}
 353         }
 354
 355         print "Done. Processed \$genesprocessed genes and added \$added links. Thanks!\\n";
 356         \$cyc -> close();
 357 </pre>
 358
 359 HTML
 360
 361     print info_section_html(title=>"Troubleshooting", contents=> <<HTML );
 362
 363        If your program terminates with the following error message: "connect:
 364        No such file or directory at perlcyc.pm line 166."  then the
 365        lisp_server.lisp module in Pathway Tools is not running.  Refer to
 366        http://aracyc.stanford.edu for more information on how to run the
 367        server program.
 368
 369        Please send bug reports and comments to LAM87\@cornell.edu
 370
 371 HTML
 372
 373     print info_section_html(title=>"License", contents=> <<HTML );
 374
 375 <pre>
 376        According to the MIT License:<br />
 377        http://www.open-source.org/licenses/mit-license.php
 378        <br /><br />
 379        Copyright (c) 2002-2008 by Lukas Mueller, TAIR, BTI
 380        <br /><br />
 381        Permission is hereby granted, free of charge, to any person obtaining a
 382        copy of this software and associated documentation files (the "Soft-
 383        ware"), to deal in the Software without restriction, including without
 384        limitation the rights to use, copy, modify, merge, publish, distribute,
 385        sublicense, and/or sell copies of the Software, and to permit persons
 386        to whom the Software is furnished to do so, subject to the following
 387        conditions:
 388        <br /><br />
 389        The above copyright notice and this permission notice shall be included
 390        in all copies or substantial portions of the Software.
 391        <br /><br />
 392        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 393        OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MER-
 394        CHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
 395        NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
 396        CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
 397        TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFT-
 398        WARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 399        <br /><br />
 400
 401 ACKNOWLEDGEMENTS
 402        Many thanks to Suzanne Paley, Danny Yoo and Thomas Yan.
 403
 404
 405 </pre>
 406
 407 HTML
 408
 409
 410     $p->footer();