README

NAME
    perlcyc - A Perl interface for Pathway Tools software for UNIX-based
    systems.

SYNOPSIS
    perlcyc is a Perl interface for Pathway Tools software. Pathway Tools
    software needs to run a special socket server program for this module to
    work (see below).

    "use perlcyc;"

    "my $cyc = perlcyc -> new("ARA");" "my @pathways = $cyc ->
    all_pathways();"

PATHWAY TOOLS REQUIREMENTS
    To use the Perl module, you also need the socket_server.lisp program. In
    Pathway Tools version 8.0 or later, the server program can be started
    with the command line option "-api". On earlier versions, the server
    daemon needs to be loaded manually, as follows: start Pathway-Tools with
    the -lisp option, at the prompt, type: (load
    "/path/to/socket_server.lisp"), then start the socket_server by typing
    (start_external_access_daemon :verbose? t). The server is now ready to
    accept connections and queries.

DESCRIPTION
    perlcyc.pm is a Perl module for accessing internal Pathway-Tools
    functions. For the description of what the individual functions do,
    please refer to the Pathway Tools documentation at
    http://bioinformatics.ai.sri.com/ptools .

    In general, the Lisp function name has to be converted to something
    compatible with Perl: Dashes have to be replaced by underlines, and
    question marks with underline p (_p).

    Note that the optional parameters of all functions are not supported in
    perlcyc, except for all_pathways() which can use the optional arguments
    :all T to get the base pathways only (no super-pathways).

   Limitations
    Perlcyc does not run on Windows, because perlcyc creates a file system
    socket that is not supported in Windows. It should run in Solaris,
    Linux, MacOSX and other UNIX-like operating systems.

    Perlcyc does not implement the GFP objects in Perl; it just sends
    snippets of code to Pathway-Tools through the file socket connection.
    Because of this, only one such connection can be openend at any given
    time.

    Given that the objects are not implemented in Perl, only object
    references are supported.

   Available functions:
      Object functions:

       new
       Parameters: The knowledge base name. Required!

      GFP functions: 
      More information on these functions can be found at:
      http://www.ai.sri.com/~gfp/spec/paper/node63.html
        
   get_slot_values
       get_slot_value 
       get_class_all_instances 
       instance_all_instance_of_p
       member_slot_value_p 
       fequal 
       current_kb  
       put_slot_values
       put_slot_value
       add_slot_value
       replace_slot_value
       remove_slot_value
       coercible_to_frame_p
       class_all_type_of_p
       get_instance_direct_types
       get_instance_all_types
       get_frame_slots
       put_instance_types
       save_kb
       revert_kb
       
  Pathway-tools functions:
      More information on these functions can be found at:
      http://bioinformatics.ai.sri.com/ptools/ptools-fns.html

       select_organism 
       all_pathways   
       all_orgs
       all_rxns
       genes_of_reaction
       substrates_of_reaction
       enzymes_of_reaction
       reaction_reactants_and_products
       get_predecessors
       get_successors
       genes_of_pathway
       enzymes_of_pathway
       compounds_of_pathway
       substrates_of_pathway
       transcription_factor_p
       all_cofactors
       all_modulators
       monomers_of_protein
       components_of_protein
       genes_of_protein 
       reactions_of_enzyme
       enzyme_p 
       transport_p
       containers_of 
       modified_forms 
       modified_containers
       top_containers 
       reactions_of_protein
       regulon_of_protein 
       transcription_units_of_protein
       regulator_proteins_of_transcription_unit
       enzymes_of_gene 
       all_products_of_gene
       reactions_of_gene 
       pathways_of_gene 
       chromosome_of_gene
       transcription_unit_of_gene 
       transcription_unit_promoter 
       transcription_unit_genes 
       transcription_unit_binding_sites 
       transcription_unit_transcription_factors
       transcription_unit_terminators 
       all_transported_chemicals 
       reactions_of_compound 
       full_enzyme_name 
       enzyme_activity_name 
       find_indexed_frame
       create-instance
       create-class
       create-frame

       pwys-of-organism-in-meta
       enzymes-of-organism-in-meta
       lower-taxa-or-species-p org-frame
       get-class-all-subs

      added 5/2008 per Suzanne's request:
       genes-regulating-gene
       genes-regulated-by-gene
       terminators-affecting-gene
       transcription-unit-mrna-binding-sites
       transcription-unit-activators
       transcription-unit-inhibitors
       containing-tus
       direct-activators
       direct-inhibitors



      not supported:
       get_frames_matching_value (why not?)

      Internal functions:
       
   parselisp
       send_query
       retrieve_results
       wrap_query
       call_func
       debug 
       debug_on
       debug_off 

      Deprecated functions
       parse_lisp_list

EXAMPLES
    Change product type for all genes that are in a pathway to 'Enzyme'

     use perlcyc;

     my $cyc = perlcyc -> new ("ARA");
     my @pathways = $cyc -> all_pathways();

     foreach my $p (@pathways) {
       my @genes = $cyc -> genes_of_pathway($p);
       foreach my $g (@genes) {
         $cyc -> put_slot_value ($g, "Product-Types", "Enzyme");
       }
     }

    Load a file containing two columns with accession and a comment into the
    comment field of the corresponding accession:

     use perlcyc;
     use strict;
     
 my $file = shift;

     my $added=0;
     my $recs =0;

     open (F, "<$file") || die "Can't open file\n";

     print STDERR "Connecting to AraCyc...\n";
     my $cyc = perlcyc -> new("ARA");

     print STDERR "Getting Gene Information...\n";
     my @genes = $cyc -> get_class_all_instances("|Genes|");

     my %genes;

     print STDERR "Getting common names...\n";
     foreach my $g (@genes) {
       my $cname = $cyc -> get_slot_value($g, "common-name"); 
       $genes{$cname}=$g; 
     } 

     print STDERR "Processing file...\n";
     while (<F>) { 
       my ($locus, $location, @rest) = split /\t/;
       $recs++;
       if (exists $genes{$locus}) { 
           my $product = $cyc -> get_slot_value($genes{$locus}, "product");
             if ($product) {
             $cyc -> add_slot_value($product, "comment", "\"\nTargetP location: $location\n\"");
              #print STDERR "Added to description of frame $product\n";
             $added++;
           }
         }
     }

     close (F);

     print STDERR "Done. Added $added descriptions. Total lines in file: $recs. \n";

    Add a locus link to the TAIR locus page for each gene in the database

     use strict;
     use perlcyc;

     my $added =0;
     my $genesprocessed=0;

     print "Connecting to AraCyc...\n";
     my $cyc = perlcyc -> new ("ARA");

     print "Getting Gene Information...\n";
     my @genes = $cyc -> get_class_all_instances ("|Genes|");

     print "Adding TAIR links...\n";
     foreach my $g (@genes) {
       $genesprocessed++;
       my $common_name = $cyc -> get_slot_value($g, "common-name");
       if ($common_name && ($common_name ne "NIL")) {
         $cyc -> put_slot_value ($g, "dblinks", "(TAIR \"$common_name\")"); 
         $added++;
       }
       if ((!$genesprocessed ==0) && ($genesprocessed % 1000 == 0)) { print "$genesprocessed ";}
     }

     print "Done. Processed $genesprocessed genes and added $added links. Thanks!\n";
     $cyc -> close();

TROUBLESHOOTING
    If your program terminates with the following error message: "connect:
    No such file or directory at perlcyc.pm line 166." then the
    lisp_server.lisp module in Pathway Tools is not running. Refer to
    http://aracyc.stanford.edu for more information on how to run the server
    program.

    Please send bug reports and comments to lam87@cornell.edu

LICENSE
    According to the MIT License,
    http://www.opensource.org/licenses/mit-license.php

    Copyright (c) 2002 by Lukas Mueller, The Arabidopsis Information
    Resource (TAIR) and the Carnegie Institution of Washington.

    Permission is hereby granted, free of charge, to any person obtaining a
    copy of this software and associated documentation files (the
    "Software"), to deal in the Software without restriction, including
    without limitation the rights to use, copy, modify, merge, publish,
    distribute, sublicense, and/or sell copies of the Software, and to
    permit persons to whom the Software is furnished to do so, subject to
    the following conditions:

    The above copyright notice and this permission notice shall be included
    in all copies or substantial portions of the Software.

    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
    OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
    IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
    CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
    TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
    SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

AUTHOR
    Lukas Mueller <lam87@cornell.edu>

ACKNOWLEDGMENTS
    Many thanks to Suzanne Paley, Danny Yoo and Thomas Yan.