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# modelorg2text.R
# FBA and friends with R.
#
# Copyright (C) 2010-2014 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
# Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
# All right reserved.
# Email: geliudie@uni-duesseldorf.de
#
# This file is part of sybil.
#
# Sybil is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Sybil is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with sybil. If not, see <http://www.gnu.org/licenses/>.
################################################
# Function: modelorg2text
#
#
#
modelorg2text <- function(model, prefix, suffix, extMetFlag = "b",
fielddelim = "\t", genedelim = "/",
makeClosedNetwork = FALSE,
fpath = SYBIL_SETTINGS("PATH_TO_MODEL"),
...) {
if (!is(model, "modelorg")) {
stop("needs an object of class modelorg!")
}
# filenames
if (missing(prefix)) {
prefix <- gsub("\\s+", "_", mod_id(model))
}
if (missing(suffix)) {
suffix <- switch(fielddelim,
"\t" = { "tsv" },
";" = { "csv" },
"," = { "csv" },
"|" = { "dsv" },
{ "dsv" }
)
}
fname <- paste(prefix, suffix, sep = ".")
# path to output file
textfile <- file.path(fpath, fname)
#--------------------------------------------------------------------------#
# some functions
#--------------------------------------------------------------------------#
prepareRuleStrings <- function(rule, bp, no) {
}
#--------------------------------------------------------------------------#
# reactions list
#--------------------------------------------------------------------------#
rstr <- .createReactionString(model, makeClosedNetwork)
# rule abbreviation equation lowbnd uppbnd obj_coef
gprFRule <- gsub("&&?|and", "AND", gpr(model), perl = TRUE)
gprFRule <- gsub("\\|\\|?|or", "OR", gprFRule, perl = TRUE)
gpr_list <- strsplit(gprFRule, "", fixed = TRUE)
check_bp <- mapply(.check_brackets, gpr_list, SIMPLIFY = TRUE)
if ( sum(check_bp) != length(check_bp) ) {
warning(paste("Wrong gpr rules detected, setting to \"\". ",
"Check rule(s) no. ",
paste((1:react_num(model))[!check_bp], collapse = ", "),
".", sep = ""))
gpr_list[!check_bp] <- ""
}
gpr_bp <- mapply(.bracket_pairs, gpr_list, SIMPLIFY = FALSE)
gpr_str <- mapply(prepareRuleStrings,
gprFRule, gpr_bp, c(1:react_num(model)),
SIMPLIFY = FALSE)
# write.table(x = data.frame(
# equation = rstr$equat,
# lowbnd = lowbnd(model),
# uppbnd = uppbnd(model),
# obj_coef = obj_coef(model),
# ),
# row.names = FALSE, file = tsvfileR, sep = fielddelim, ...)
#--------------------------------------------------------------------------#
# end
#--------------------------------------------------------------------------#
return(TRUE)
}
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