PerlCyc.pm
| Description |
PerlCyc is a Perl interface for Pathway Tools software. It allows internal Pathay Tools Lisp functions to be accessed through Perl.
For a description of what the individual functions do, please refer to the Pathway Tools documentation at http://bioinformat- ics.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).
For a description of what the individual functions do, please refer to the Pathway Tools documentation at http://bioinformat- ics.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).
| Installation |
Installation is standard as for any Perl module. If you downloaded the
compressed tar file, uncompress and untar the file with the following
commands:
gzip < perlcyc.tar.gz | tar xvf -
This will create a directory called perlcyc in your current directory.
To install the program, type
make
make install
The program should now be available in all your Perl programs. "make
install" may require root access or access through sudo. For the latter
case, type
sudo make install
You will be prompted for your password.
| Limitations |
Perlcyc does not implement the GFP objects in Perl, rather it just
sends snippets of code to Pathway-Tools through a socket connection.
Only one such connection can be openend at any given time. Because the
objects are not implemented in Perl, only object references are supported.
| Supported 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
| 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.
| Download |
Download [FTP]
| Documentation |
perlcyc is a Perl interface for Pathway Tools software.
"use perlcyc;"
"my $cyc = perlcyc -> new("ARA");" "my @pathways = $cyc -> all_path-
ways();"
VERSION
Version 1.21 (May 2008).
VERSION HISTORY
Version History
0.1 March, 2002
[Lukas Mueller] initial version
0.3 April 22, 2002
[Danny Yoo] Added better list parsing
0.9 [Lukas Mueller]
Added more functions
1.0 August 28, 2002 [Lukas Mueller]
Added pod documentation and eliminated some bugs.
1.1 June 6, 2003
[Thomas Yan] Fixed some minor bugs.
1.2 December 7, 2006 [Lukas Mueller]
Added three functions: create-frame, create-class, and cre-
ate-instance.
1.21 May 7, 2008 [Lukas Mueller]
Added three functions that are new in PT v. 12:
pwys-of-organism-in-meta
enzymes-of-organism-in-meta
lower-taxa-or-species-p org-frame
other new functions:
get-class-all-subs
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
| 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 CXGN::Page=HASH(0x558bffaf0730) (@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
";
$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.open-source.org/licenses/mit-license.php
Copyright (c) 2002-2008 by Lukas Mueller, TAIR, BTI
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Soft-
ware"), 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 MER-
CHANTABILITY, 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 SOFT-
WARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
ACKNOWLEDGEMENTS
Many thanks to Suzanne Paley, Danny Yoo and Thomas Yan.
Working
