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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.
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