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benchmark_parallelisations_compute_tr_all_overlap.R
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#####################################################################################
### Housekeeping
#####################################################################################
# Before executing this file, do: setwd("path/to/your/git/on/swissrepeat/results")
setwd("/home/matteo/polybox/MSc_ACLS/swissrepeat/results")
source("local_config.R")
setwd(paste0(local_base_path,"/results"))
rm(list = ls(all = TRUE))
gc()
source("helpers.R")
# Load library for benchmarking
devtools::install_github("eddelbuettel/rbenchmark")
library(rbenchmark)
#####################################################################################
### Data Loading
#####################################################################################
tr_path = "results/tr_annotations/tr_annotations.csv"
tr_all = load_tr_annotations(tr_path)
sp_path = "data/swissprot_annotations.tsv"
sp_all = load_swissprot(sp_path, tr_all)
# Add meta_data from sp_all to tr_all. -> Do a left join.
tr_all_sp = merge(x = tr_all, y = sp_all, by = "ID", all.x = TRUE)
# Add disorder information from modiDB
discoor_path = "results/disorder_annotations/mobidb_coordinates.csv"
discoor_all = load_disorder_annotations(discoor_path)
discoor_all$disorder_region_length = (discoor_all$end - discoor_all$start) + 1
discoor_all$center = floor(discoor_all$start + (discoor_all$disorder_region_length/2))
discoor_all_sp = merge(x = discoor_all, y = sp_all, by = "ID", all.x = TRUE)
# Remove eventual regions with incorrect coordinates
discoor_all_sp = discoor_all_sp[(discoor_all_sp$center<discoor_all_sp$Length),]
#Aggregate disordered regions by protein, calculate disorder residues count in a protein
sp_protein= ddply(discoor_all, .(ID), summarize,
disorder_count=(sum(disorder_region_length)))
sp_protein = merge(x = sp_protein, y = sp_all, by = "ID", all.x = TRUE)
#####################################################################################
### Define different approaches w/ and w/o parallel enviroments
#####################################################################################
no_par_for <- function(tr_all, sp_all, discoor_all){
# add to each TR a unique identification number: TR_id
tr_all <- tr_all %>%
mutate(TR_id = row_number())
# add to each TR the position in the protein where the TR sequence ends: end
tr_all <- tr_all %>%
mutate(end = begin+total_repeat_length)
# initallize for each TR the overlap columns
tr_all <- tr_all %>%
mutate(tail_overlap = 0,
head_overlap = 0,
DisinTR_overlap = 0,
TRinDis_overlap = 0,
total_overlap = 0)
# add to each disorder region a unique identification number: DIS_id
discoor_all <- discoor_all %>%
mutate(DIS_id = row_number())
for (IDprot in sp_all$ID[1:30]){ # for each protein in swissprot. Subset sp_all$ID[1:1000] takes about 10min
if (IDprot %in% tr_all$ID){ # check if the protein has a TR
for (IDdis in discoor_all$DIS_id[which(discoor_all$ID == IDprot)]){ # extract all disorder regions from this protein
for (IDtr in tr_all$TR_id[which(tr_all$ID == IDprot)]){ # loop through all TRs of this protein
if (tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{# check for each TR region if it has a tail-overlap with a disorder region
tr_all$tail_overlap[which(tr_all$TR_id == IDtr)] = tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]
}
if (discoor_all$end[which(discoor_all$DIS_id == IDdis)] > tr_all$begin[which(tr_all$TR_id == IDtr)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] < tr_all$end[which(tr_all$TR_id == IDtr)] &
discoor_all$start[which(discoor_all$DIS_id == IDdis)] <= tr_all$begin[which(tr_all$TR_id == IDtr)])
{ # or if it has a head-overlap with a disorder region
tr_all$head_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$end[which(discoor_all$DIS_id == IDdis)] - tr_all$begin[which(tr_all$TR_id == IDtr)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] <= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] <= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region lies in the TR-region
tr_all$DisinTR_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$disorder_region_length[which(discoor_all$DIS_id == IDdis)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] >= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region is bigger than the whole TR region. i.e. the whole TR region lies in a disorder region.
tr_all$TRinDis_overlap[which(tr_all$TR_id == IDtr)] = tr_all$total_repeat_length[which(tr_all$TR_id == IDtr)]
}
}
}
}
}
}
no_par_foreach_outer <- function(tr_all, sp_all, discoor_all){
# add to each TR a unique identification number: TR_id
tr_all <- tr_all %>%
mutate(TR_id = row_number())
# add to each TR the position in the protein where the TR sequence ends: end
tr_all <- tr_all %>%
mutate(end = begin+total_repeat_length)
# initallize for each TR the overlap columns
tr_all <- tr_all %>%
mutate(tail_overlap = 0,
head_overlap = 0,
DisinTR_overlap = 0,
TRinDis_overlap = 0,
total_overlap = 0)
# add to each disorder region a unique identification number: DIS_id
discoor_all <- discoor_all %>%
mutate(DIS_id = row_number())
### with foreach on the most outer loop (no paralell)
foreach(i=1:length(sp_all$ID[1:30]), .combine = 'rbind') %do% { # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
IDprot <- sp_all$ID[i]
if (IDprot %in% tr_all$ID){ # check if the protein has a TR
for (IDdis in discoor_all$DIS_id[which(discoor_all$ID == IDprot)]){ # extract all disorder regions from this protein
for (IDtr in tr_all$TR_id[which(tr_all$ID == IDprot)]){ # loop through all TRs of this protein
if (tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{# check for each TR region if it has a tail-overlap with a disorder region
tr_all$tail_overlap[which(tr_all$TR_id == IDtr)] = tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]
}
if (discoor_all$end[which(discoor_all$DIS_id == IDdis)] > tr_all$begin[which(tr_all$TR_id == IDtr)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] < tr_all$end[which(tr_all$TR_id == IDtr)] &
discoor_all$start[which(discoor_all$DIS_id == IDdis)] <= tr_all$begin[which(tr_all$TR_id == IDtr)])
{ # or if it has a head-overlap with a disorder region
tr_all$head_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$end[which(discoor_all$DIS_id == IDdis)] - tr_all$begin[which(tr_all$TR_id == IDtr)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] <= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] <= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region lies in the TR-region
tr_all$DisinTR_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$disorder_region_length[which(discoor_all$DIS_id == IDdis)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] >= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region is bigger than the whole TR region. i.e. the whole TR region lies in a disorder region.
tr_all$TRinDis_overlap[which(tr_all$TR_id == IDtr)] = tr_all$total_repeat_length[which(tr_all$TR_id == IDtr)]
}
}
}
}
}
}
no_par_foreach_outer_iterobj <- function(tr_all, sp_all, discoor_all){
# add to each TR a unique identification number: TR_id
tr_all <- tr_all %>%
mutate(TR_id = row_number())
# add to each TR the position in the protein where the TR sequence ends: end
tr_all <- tr_all %>%
mutate(end = begin+total_repeat_length)
# initallize for each TR the overlap columns
tr_all <- tr_all %>%
mutate(tail_overlap = 0,
head_overlap = 0,
DisinTR_overlap = 0,
TRinDis_overlap = 0,
total_overlap = 0)
# add to each disorder region a unique identification number: DIS_id
discoor_all <- discoor_all %>%
mutate(DIS_id = row_number())
### with foreach on the most outer loop and an iterator object (no paralell)
foreach(IDprot=iter(sp_all$ID[1:30]), .combine = 'rbind') %do% { # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
if (IDprot %in% tr_all$ID){ # check if the protein has a TR
for (IDdis in discoor_all$DIS_id[which(discoor_all$ID == IDprot)]){ # extract all disorder regions from this protein
for (IDtr in tr_all$TR_id[which(tr_all$ID == IDprot)]){ # loop through all TRs of this protein
if (tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{# check for each TR region if it has a tail-overlap with a disorder region
tr_all$tail_overlap[which(tr_all$TR_id == IDtr)] = tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]
}
if (discoor_all$end[which(discoor_all$DIS_id == IDdis)] > tr_all$begin[which(tr_all$TR_id == IDtr)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] < tr_all$end[which(tr_all$TR_id == IDtr)] &
discoor_all$start[which(discoor_all$DIS_id == IDdis)] <= tr_all$begin[which(tr_all$TR_id == IDtr)])
{ # or if it has a head-overlap with a disorder region
tr_all$head_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$end[which(discoor_all$DIS_id == IDdis)] - tr_all$begin[which(tr_all$TR_id == IDtr)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] <= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] <= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region lies in the TR-region
tr_all$DisinTR_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$disorder_region_length[which(discoor_all$DIS_id == IDdis)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] >= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region is bigger than the whole TR region. i.e. the whole TR region lies in a disorder region.
tr_all$TRinDis_overlap[which(tr_all$TR_id == IDtr)] = tr_all$total_repeat_length[which(tr_all$TR_id == IDtr)]
}
}
}
}
}
}
no_par_foreach_outer_iterobj_when <- function(tr_all, sp_all, discoor_all){
# add to each TR a unique identification number: TR_id
tr_all <- tr_all %>%
mutate(TR_id = row_number())
# add to each TR the position in the protein where the TR sequence ends: end
tr_all <- tr_all %>%
mutate(end = begin+total_repeat_length)
# initallize for each TR the overlap columns
tr_all <- tr_all %>%
mutate(tail_overlap = 0,
head_overlap = 0,
DisinTR_overlap = 0,
TRinDis_overlap = 0,
total_overlap = 0)
# add to each disorder region a unique identification number: DIS_id
discoor_all <- discoor_all %>%
mutate(DIS_id = row_number())
### with foreach on the most outer loop, iterator object, when statement (no paralell)
foreach(IDprot=iter(sp_all$ID[1:30]), .combine = 'rbind') %:%
when(IDprot %in% tr_all$ID) %do% { # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
for (IDdis in discoor_all$DIS_id[which(discoor_all$ID == IDprot)]){ # extract all disorder regions from this protein
for (IDtr in tr_all$TR_id[which(tr_all$ID == IDprot)]){ # loop through all TRs of this protein
if (tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{# check for each TR region if it has a tail-overlap with a disorder region
tr_all$tail_overlap[which(tr_all$TR_id == IDtr)] = tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]
}
if (discoor_all$end[which(discoor_all$DIS_id == IDdis)] > tr_all$begin[which(tr_all$TR_id == IDtr)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] < tr_all$end[which(tr_all$TR_id == IDtr)] &
discoor_all$start[which(discoor_all$DIS_id == IDdis)] <= tr_all$begin[which(tr_all$TR_id == IDtr)])
{ # or if it has a head-overlap with a disorder region
tr_all$head_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$end[which(discoor_all$DIS_id == IDdis)] - tr_all$begin[which(tr_all$TR_id == IDtr)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] <= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] <= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region lies in the TR-region
tr_all$DisinTR_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$disorder_region_length[which(discoor_all$DIS_id == IDdis)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] >= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region is bigger than the whole TR region. i.e. the whole TR region lies in a disorder region.
tr_all$TRinDis_overlap[which(tr_all$TR_id == IDtr)] = tr_all$total_repeat_length[which(tr_all$TR_id == IDtr)]
}
}
}
}
}
no_par_foreach_2outer_iterobj_when <- function(tr_all, sp_all, discoor_all){
# add to each TR a unique identification number: TR_id
tr_all <- tr_all %>%
mutate(TR_id = row_number())
# add to each TR the position in the protein where the TR sequence ends: end
tr_all <- tr_all %>%
mutate(end = begin+total_repeat_length)
# initallize for each TR the overlap columns
tr_all <- tr_all %>%
mutate(tail_overlap = 0,
head_overlap = 0,
DisinTR_overlap = 0,
TRinDis_overlap = 0,
total_overlap = 0)
# add to each disorder region a unique identification number: DIS_id
discoor_all <- discoor_all %>%
mutate(DIS_id = row_number())
### with foreach on the 2 outer loops, iterator object, when statement (no paralell)
foreach(IDprot=iter(sp_all$ID[1:30]), .combine = 'rbind') %:%
when(IDprot %in% tr_all$ID) %do% { # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
foreach(IDdis=iter(discoor_all$DIS_id[which(discoor_all$ID == IDprot)]), .combine = 'rbind') %do% { # extract all disorder regions from this protein
for (IDtr in tr_all$TR_id[which(tr_all$ID == IDprot)]){ # loop through all TRs of this protein
if (tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{# check for each TR region if it has a tail-overlap with a disorder region
tr_all$tail_overlap[which(tr_all$TR_id == IDtr)] = tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]
}
if (discoor_all$end[which(discoor_all$DIS_id == IDdis)] > tr_all$begin[which(tr_all$TR_id == IDtr)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] < tr_all$end[which(tr_all$TR_id == IDtr)] &
discoor_all$start[which(discoor_all$DIS_id == IDdis)] <= tr_all$begin[which(tr_all$TR_id == IDtr)])
{ # or if it has a head-overlap with a disorder region
tr_all$head_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$end[which(discoor_all$DIS_id == IDdis)] - tr_all$begin[which(tr_all$TR_id == IDtr)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] <= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] <= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region lies in the TR-region
tr_all$DisinTR_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$disorder_region_length[which(discoor_all$DIS_id == IDdis)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] >= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region is bigger than the whole TR region. i.e. the whole TR region lies in a disorder region.
tr_all$TRinDis_overlap[which(tr_all$TR_id == IDtr)] = tr_all$total_repeat_length[which(tr_all$TR_id == IDtr)]
}
}
}
}
}
no_par_foreach_3outer_iterobj_when <- function(tr_all, sp_all, discoor_all){
# add to each TR a unique identification number: TR_id
tr_all <- tr_all %>%
mutate(TR_id = row_number())
# add to each TR the position in the protein where the TR sequence ends: end
tr_all <- tr_all %>%
mutate(end = begin+total_repeat_length)
# initallize for each TR the overlap columns
tr_all <- tr_all %>%
mutate(tail_overlap = 0,
head_overlap = 0,
DisinTR_overlap = 0,
TRinDis_overlap = 0,
total_overlap = 0)
# add to each disorder region a unique identification number: DIS_id
discoor_all <- discoor_all %>%
mutate(DIS_id = row_number())
### with foreach on the 3 outer loops, iterator object, when statement (no paralell)
foreach(IDprot=iter(sp_all$ID[1:30]), .combine = 'rbind') %:%
when(IDprot %in% tr_all$ID) %:% # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
foreach(IDdis=iter(discoor_all$DIS_id[which(discoor_all$ID == IDprot)]), .combine = 'rbind') %:% # extract all disorder regions from this protein
foreach(IDtr=iter(tr_all$TR_id[which(tr_all$ID == IDprot)]), .combine = 'rbind') %do% { # loop through all TRs of this protein
if (tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{# check for each TR region if it has a tail-overlap with a disorder region
tr_all$tail_overlap[which(tr_all$TR_id == IDtr)] = tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]
}
if (discoor_all$end[which(discoor_all$DIS_id == IDdis)] > tr_all$begin[which(tr_all$TR_id == IDtr)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] < tr_all$end[which(tr_all$TR_id == IDtr)] &
discoor_all$start[which(discoor_all$DIS_id == IDdis)] <= tr_all$begin[which(tr_all$TR_id == IDtr)])
{ # or if it has a head-overlap with a disorder region
tr_all$head_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$end[which(discoor_all$DIS_id == IDdis)] - tr_all$begin[which(tr_all$TR_id == IDtr)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] <= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] <= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region lies in the TR-region
tr_all$DisinTR_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$disorder_region_length[which(discoor_all$DIS_id == IDdis)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] >= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region is bigger than the whole TR region. i.e. the whole TR region lies in a disorder region.
tr_all$TRinDis_overlap[which(tr_all$TR_id == IDtr)] = tr_all$total_repeat_length[which(tr_all$TR_id == IDtr)]
}
}
}
par_foreach_outer <- function(tr_all, sp_all, discoor_all, numcores){
# add to each TR a unique identification number: TR_id
tr_all <- tr_all %>%
mutate(TR_id = row_number())
# add to each TR the position in the protein where the TR sequence ends: end
tr_all <- tr_all %>%
mutate(end = begin+total_repeat_length)
# initallize for each TR the overlap columns
tr_all <- tr_all %>%
mutate(tail_overlap = 0,
head_overlap = 0,
DisinTR_overlap = 0,
TRinDis_overlap = 0,
total_overlap = 0)
# add to each disorder region a unique identification number: DIS_id
discoor_all <- discoor_all %>%
mutate(DIS_id = row_number())
# register cluster
cl <- makeCluster(numcores)
registerDoParallel(cl)
### with foreach on the most outer loop (paralell)
foreach(i=1:length(sp_all$ID[1:30]), .combine = 'rbind') %dopar% { # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
IDprot <- sp_all$ID[i]
if (IDprot %in% tr_all$ID){ # check if the protein has a TR
for (IDdis in discoor_all$DIS_id[which(discoor_all$ID == IDprot)]){ # extract all disorder regions from this protein
for (IDtr in tr_all$TR_id[which(tr_all$ID == IDprot)]){ # loop through all TRs of this protein
if (tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{# check for each TR region if it has a tail-overlap with a disorder region
tr_all$tail_overlap[which(tr_all$TR_id == IDtr)] = tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]
}
if (discoor_all$end[which(discoor_all$DIS_id == IDdis)] > tr_all$begin[which(tr_all$TR_id == IDtr)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] < tr_all$end[which(tr_all$TR_id == IDtr)] &
discoor_all$start[which(discoor_all$DIS_id == IDdis)] <= tr_all$begin[which(tr_all$TR_id == IDtr)])
{ # or if it has a head-overlap with a disorder region
tr_all$head_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$end[which(discoor_all$DIS_id == IDdis)] - tr_all$begin[which(tr_all$TR_id == IDtr)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] <= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] <= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region lies in the TR-region
tr_all$DisinTR_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$disorder_region_length[which(discoor_all$DIS_id == IDdis)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] >= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region is bigger than the whole TR region. i.e. the whole TR region lies in a disorder region.
tr_all$TRinDis_overlap[which(tr_all$TR_id == IDtr)] = tr_all$total_repeat_length[which(tr_all$TR_id == IDtr)]
}
}
}
}
}
stopCluster(cl)
}
par_foreach_outer_iterobj <- function(tr_all, sp_all, discoor_all, numcores){
# add to each TR a unique identification number: TR_id
tr_all <- tr_all %>%
mutate(TR_id = row_number())
# add to each TR the position in the protein where the TR sequence ends: end
tr_all <- tr_all %>%
mutate(end = begin+total_repeat_length)
# initallize for each TR the overlap columns
tr_all <- tr_all %>%
mutate(tail_overlap = 0,
head_overlap = 0,
DisinTR_overlap = 0,
TRinDis_overlap = 0,
total_overlap = 0)
# add to each disorder region a unique identification number: DIS_id
discoor_all <- discoor_all %>%
mutate(DIS_id = row_number())
# register cluster
cl <- makeCluster(numcores)
registerDoParallel(cl)
### with foreach on the most outer loop and an iterator object (no paralell)
foreach(IDprot=iter(sp_all$ID[1:30]), .combine = 'rbind') %dopar% { # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
if (IDprot %in% tr_all$ID){ # check if the protein has a TR
for (IDdis in discoor_all$DIS_id[which(discoor_all$ID == IDprot)]){ # extract all disorder regions from this protein
for (IDtr in tr_all$TR_id[which(tr_all$ID == IDprot)]){ # loop through all TRs of this protein
if (tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{# check for each TR region if it has a tail-overlap with a disorder region
tr_all$tail_overlap[which(tr_all$TR_id == IDtr)] = tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]
}
if (discoor_all$end[which(discoor_all$DIS_id == IDdis)] > tr_all$begin[which(tr_all$TR_id == IDtr)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] < tr_all$end[which(tr_all$TR_id == IDtr)] &
discoor_all$start[which(discoor_all$DIS_id == IDdis)] <= tr_all$begin[which(tr_all$TR_id == IDtr)])
{ # or if it has a head-overlap with a disorder region
tr_all$head_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$end[which(discoor_all$DIS_id == IDdis)] - tr_all$begin[which(tr_all$TR_id == IDtr)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] <= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] <= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region lies in the TR-region
tr_all$DisinTR_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$disorder_region_length[which(discoor_all$DIS_id == IDdis)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] >= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region is bigger than the whole TR region. i.e. the whole TR region lies in a disorder region.
tr_all$TRinDis_overlap[which(tr_all$TR_id == IDtr)] = tr_all$total_repeat_length[which(tr_all$TR_id == IDtr)]
}
}
}
}
}
stopCluster(cl)
}
par_foreach_outer_iterobj_when <- function(tr_all, sp_all, discoor_all, numcores){
# add to each TR a unique identification number: TR_id
tr_all <- tr_all %>%
mutate(TR_id = row_number())
# add to each TR the position in the protein where the TR sequence ends: end
tr_all <- tr_all %>%
mutate(end = begin+total_repeat_length)
# initallize for each TR the overlap columns
tr_all <- tr_all %>%
mutate(tail_overlap = 0,
head_overlap = 0,
DisinTR_overlap = 0,
TRinDis_overlap = 0,
total_overlap = 0)
# add to each disorder region a unique identification number: DIS_id
discoor_all <- discoor_all %>%
mutate(DIS_id = row_number())
# register cluster
cl <- makeCluster(numcores, type = "FORK")
registerDoParallel(cl)
### with foreach on the first outer loop, iterator object, when statement (forking instead of parallell)
foreach(IDprot=iter(sp_all$ID[1:300]), .combine = 'rbind', .inorder=TRUE) %:%
when(IDprot %in% tr_all$ID) %dopar% # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
for (IDdis in discoor_all$DIS_id[which(discoor_all$ID == IDprot)]){ # extract all disorder regions from this protein
for (IDtr in tr_all$TR_id[which(tr_all$ID == IDprot)]){ # loop through all TRs of this protein
if (tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{# check for each TR region if it has a tail-overlap with a disorder region
tr_all$tail_overlap[which(tr_all$TR_id == IDtr)] = tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]
}
if (discoor_all$end[which(discoor_all$DIS_id == IDdis)] > tr_all$begin[which(tr_all$TR_id == IDtr)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] < tr_all$end[which(tr_all$TR_id == IDtr)] &
discoor_all$start[which(discoor_all$DIS_id == IDdis)] <= tr_all$begin[which(tr_all$TR_id == IDtr)])
{ # or if it has a head-overlap with a disorder region
tr_all$head_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$end[which(discoor_all$DIS_id == IDdis)] - tr_all$begin[which(tr_all$TR_id == IDtr)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] <= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] <= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region lies in the TR-region
tr_all$DisinTR_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$disorder_region_length[which(discoor_all$DIS_id == IDdis)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] >= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region is bigger than the whole TR region. i.e. the whole TR region lies in a disorder region.
tr_all$TRinDis_overlap[which(tr_all$TR_id == IDtr)] = tr_all$total_repeat_length[which(tr_all$TR_id == IDtr)]
}
}
}
stopCluster(cl)
}
par_foreach_2outer_iterobj_when <- function(tr_all, sp_all, discoor_all, numcores){
# # add to each TR a unique identification number: TR_id
# tr_all <- tr_all %>%
# mutate(TR_id = row_number())
#
# # add to each TR the position in the protein where the TR sequence ends: end
# tr_all <- tr_all %>%
# mutate(end = begin+total_repeat_length)
#
# # initallize for each TR the overlap columns
# tr_all <- tr_all %>%
# mutate(tail_overlap = 0,
# head_overlap = 0,
# DisinTR_overlap = 0,
# TRinDis_overlap = 0,
# total_overlap = 0)
#
# # add to each disorder region a unique identification number: DIS_id
# discoor_all <- discoor_all %>%
# mutate(DIS_id = row_number())
#
# # register cluster
# cl <- makeCluster(numcores, type = "FORK")
# registerDoParallel(cl)
#
# ### with foreach on the 2 outer loops, iterator object, when statement (no paralell)
# foreach(IDprot=iter(sp_all$ID[1:30]), .combine = 'rbind') %:%
# when(IDprot %in% tr_all$ID) %:% { # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
# foreach(IDdis=iter(discoor_all$DIS_id[which(discoor_all$ID == IDprot)]), .combine = 'rbind') %dopar% { # extract all disorder regions from this protein
# for (IDtr in tr_all$TR_id[which(tr_all$ID == IDprot)]){ # loop through all TRs of this protein
# # NOTE: IDprott is not found.
# if (tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
# {# check for each TR region if it has a tail-overlap with a disorder region
# tr_all$tail_overlap[which(tr_all$TR_id == IDtr)] = tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]
# }
# if (discoor_all$end[which(discoor_all$DIS_id == IDdis)] > tr_all$begin[which(tr_all$TR_id == IDtr)] &
# discoor_all$end[which(discoor_all$DIS_id == IDdis)] < tr_all$end[which(tr_all$TR_id == IDtr)] &
# discoor_all$start[which(discoor_all$DIS_id == IDdis)] <= tr_all$begin[which(tr_all$TR_id == IDtr)])
# { # or if it has a head-overlap with a disorder region
# tr_all$head_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$end[which(discoor_all$DIS_id == IDdis)] - tr_all$begin[which(tr_all$TR_id == IDtr)]
# }
# if (tr_all$begin[which(tr_all$TR_id == IDtr)] <= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# discoor_all$end[which(discoor_all$DIS_id == IDdis)] <= tr_all$end[which(tr_all$TR_id == IDtr)])
# { # or if the whole disorder region lies in the TR-region
# tr_all$DisinTR_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$disorder_region_length[which(discoor_all$DIS_id == IDdis)]
# }
# if (tr_all$begin[which(tr_all$TR_id == IDtr)] >= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
# { # or if the whole disorder region is bigger than the whole TR region. i.e. the whole TR region lies in a disorder region.
# tr_all$TRinDis_overlap[which(tr_all$TR_id == IDtr)] = tr_all$total_repeat_length[which(tr_all$TR_id == IDtr)]
# }
# }
# }
# }
# stopCluster(cl)
}
par_foreach_3outer_iterobj_when <- function(tr_all, sp_all, discoor_all, numcores){
# add to each TR a unique identification number: TR_id
tr_all <- tr_all %>%
mutate(TR_id = row_number())
# add to each TR the position in the protein where the TR sequence ends: end
tr_all <- tr_all %>%
mutate(end = begin+total_repeat_length)
# initallize for each TR the overlap columns
tr_all <- tr_all %>%
mutate(tail_overlap = 0,
head_overlap = 0,
DisinTR_overlap = 0,
TRinDis_overlap = 0,
total_overlap = 0)
# add to each disorder region a unique identification number: DIS_id
discoor_all <- discoor_all %>%
mutate(DIS_id = row_number())
# register cluster
cl <- makeCluster(numcores)
registerDoParallel(cl)
### with foreach on the 3 outer loops, iterator object, when statement (no paralell)
foreach(IDprot=iter(sp_all$ID[1:30]), .combine = 'rbind') %:%
when(IDprot %in% tr_all$ID) %:% # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
foreach(IDdis=iter(discoor_all$DIS_id[which(discoor_all$ID == IDprot)]), .combine = 'rbind') %:% # extract all disorder regions from this protein
foreach(IDtr=iter(tr_all$TR_id[which(tr_all$ID == IDprot)]), .combine = 'rbind') %dopar% { # loop through all TRs of this protein
if (tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{# check for each TR region if it has a tail-overlap with a disorder region
tr_all$tail_overlap[which(tr_all$TR_id == IDtr)] = tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]
}
if (discoor_all$end[which(discoor_all$DIS_id == IDdis)] > tr_all$begin[which(tr_all$TR_id == IDtr)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] < tr_all$end[which(tr_all$TR_id == IDtr)] &
discoor_all$start[which(discoor_all$DIS_id == IDdis)] <= tr_all$begin[which(tr_all$TR_id == IDtr)])
{ # or if it has a head-overlap with a disorder region
tr_all$head_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$end[which(discoor_all$DIS_id == IDdis)] - tr_all$begin[which(tr_all$TR_id == IDtr)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] <= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] <= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region lies in the TR-region
tr_all$DisinTR_overlap[which(tr_all$TR_id == IDtr)] = discoor_all$disorder_region_length[which(discoor_all$DIS_id == IDdis)]
}
if (tr_all$begin[which(tr_all$TR_id == IDtr)] >= discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)])
{ # or if the whole disorder region is bigger than the whole TR region. i.e. the whole TR region lies in a disorder region.
tr_all$TRinDis_overlap[which(tr_all$TR_id == IDtr)] = tr_all$total_repeat_length[which(tr_all$TR_id == IDtr)]
}
}
stopCluster(cl)
}
#####################################################################################
### Benchmark results
#####################################################################################
print(paste("-------------------------------------------------------------------------------------------------------"))
print("Start evaluating time for different calculation approaches.")
print("The most outer data-frame is subsetted to 30 entries. Take care when interpolating the results to the whole dataset!")
start_time <- Sys.time()
bm <- benchmark("w/o par" = no_par_for(tr_all, sp_all, discoor_all),
"w/o par; foreach on 1. loop" = no_par_foreach_outer(tr_all, sp_all, discoor_all),
"w/o par; foreach on 1. loop; iterator object" = no_par_foreach_outer_iterobj(tr_all, sp_all, discoor_all),
"w/o par; foreach on 1. loop; iterator object; when statement" = no_par_foreach_outer_iterobj_when(tr_all, sp_all, discoor_all),
# "w/o par; foreach on 1.&2. loop; iterator object" = no_par_foreach_2outer_iterobj_when(tr_all, sp_all, discoor_all),
# "w/o par; foreach on 1.,2.&3. loop; iterator object" = no_par_foreach_3outer_iterobj_when(tr_all, sp_all, discoor_all),
"w/ par; foreach on 1. loop" = par_foreach_outer(tr_all, sp_all, discoor_all, numcores),
"w/ par; foreach on 1. loop; iterator object" = par_foreach_outer_iterobj(tr_all, sp_all, discoor_all, numcores),
"w/ par; foreach on 1. loop; iterator object; when statement" = par_foreach_outer_iterobj_when(tr_all, sp_all, discoor_all, numcores),
# "w/ par; foreach on 1.&2. loop; iterator object" = par_foreach_2outer_iterobj_when(tr_all, sp_all, discoor_all, numcores),
# "w/ par; foreach on 1.,2.&3. loop; iterator object" = par_foreach_3outer_iterobj_when(tr_all, sp_all, discoor_all, numcores),
replications = 1)
bm[base::order(rownames(bm), decreasing = FALSE),]
end_time <- Sys.time()
print(paste("End of benchmark. Time used for benchmarking: ", end_time-start_time))
print(paste("-------------------------------------------------------------------------------------------------------"))
# http://r.789695.n4.nabble.com/Meaning-of-proc-time-td2303263.html#a2306691
#####################################################################################
### More parallel approaches: However with difficulties.
#####################################################################################
# ### with foreach on the 3 outer loops, iterator object, multiple when statements (no paralell)
# NOTE: Multiple when statements in sequence are not evaluated correctly.
# foreach(IDprot=iter(sp_all$ID[1:30]), .combine = 'rbind') %:%
# when(IDprot %in% tr_all$ID) %:% # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
# foreach(IDdis=iter(discoor_all$DIS_id[which(discoor_all$ID == IDprot)]), .combine = 'rbind') %:% # extract all disorder regions from this protein
# foreach(IDtr=iter(tr_all$TR_id[which(tr_all$ID == IDprot)]), .combine = 'rbind') %:% # loop through all TRs of this protein
# when(tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)]) %do%
# {# check for each TR region if it has a tail-overlap with a disorder region
#
# ## This chunck is for debugging:
# print(paste("TR-id", IDtr,
# # "prot-id", IDprot,
# # "discoor-id", IDdis,
# # "discoor-protid", discoor_all$DIS_id[which(discoor_all$ID == IDprot)],
# "TR-start", tr_all$begin[which(tr_all$TR_id == IDtr)],
# "TR-end", tr_all$end[which(tr_all$TR_id == IDtr)],
# "discorr-start", discoor_all$start[which(discoor_all$DIS_id == IDdis)],
# "discorr-end", discoor_all$end[which(discoor_all$DIS_id == IDdis)],
# "tail_overlap", tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]))
# }
#
# ### with foreach on the 3 outer loops, iterator object, when statement (paralell)
# NOTE: Multiple when statements in sequence are not evaluated correctly.
# # register cluster
# cl <- makeCluster(numcores)
# registerDoParallel(cl)
#
# system.time(
# foreach(IDprot=iter(sp_all$ID[1:300]), .combine = 'rbind') %:%
# when(IDprot %in% tr_all$ID) %:% # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
# foreach(IDdis=iter(discoor_all$DIS_id[which(discoor_all$ID == IDprot)]), .combine = 'rbind') %:% # extract all disorder regions from this protein
# foreach(IDtr=iter(tr_all$TR_id[which(tr_all$ID == IDprot)]), .combine = 'rbind') %:% # loop through all TRs of this protein
# when(tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)]) %dopar%
# {# check for each TR region if it has a tail-overlap with a disorder region
#
# ## This chunck is for debugging:
# print(paste("TR-id", IDtr,
# # "prot-id", IDprot,
# # "discoor-id", IDdis,
# # "discoor-protid", discoor_all$DIS_id[which(discoor_all$ID == IDprot)],
# "TR-start", tr_all$begin[which(tr_all$TR_id == IDtr)],
# "TR-end", tr_all$end[which(tr_all$TR_id == IDtr)],
# "discorr-start", discoor_all$start[which(discoor_all$DIS_id == IDdis)],
# "discorr-end", discoor_all$end[which(discoor_all$DIS_id == IDdis)],
# "tail_overlap", tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]))
# }
# )
#
# stopCluster(cl)
### with foreach on the 3 outer loops, iterator object, when statement (paralell with NWS backend for chunking)
### NOTE: NWS not available for current R version. Using instead MPI
# # register cluster
# cl <- makeCluster(numcores)
# registerDoParallel(cl)
#
# system.time(
# foreach(IDprot=iter(sp_all$ID[1:300]), .combine = 'rbind') %:%
# when(IDprot %in% tr_all$ID) %:% # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
# foreach(IDdis=iter(discoor_all$DIS_id[which(discoor_all$ID == IDprot)]), .combine = 'rbind') %:% # extract all disorder regions from this protein
# foreach(IDtr=iter(tr_all$TR_id[which(tr_all$ID == IDprot)]), .combine = 'rbind', .options.nws=list(chunkSize=2)) %:% # loop through all TRs of this protein
# when(tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)]) %dopar%
# {# check for each TR region if it has a tail-overlap with a disorder region
#
# ## This chunck is for debugging:
# print(paste("TR-id", IDtr,
# # "prot-id", IDprot,
# # "discoor-id", IDdis,
# # "discoor-protid", discoor_all$DIS_id[which(discoor_all$ID == IDprot)],
# "TR-start", tr_all$begin[which(tr_all$TR_id == IDtr)],
# "TR-end", tr_all$end[which(tr_all$TR_id == IDtr)],
# "discorr-start", discoor_all$start[which(discoor_all$DIS_id == IDdis)],
# "discorr-end", discoor_all$end[which(discoor_all$DIS_id == IDdis)],
# "tail_overlap", tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]))
# }
# )
#
# stopCluster(cl)
### with foreach on the 3 outer loops, iterator object, when statement (paralell MPI backend for chunking)
### NOTE: R session crashes when closing the cluster
# # register cluster
# require(doMPI)
# cl <- startMPIcluster()
# registerDoMPI(cl)
# opt <- list(chunkSize=10)
#
#
# system.time(
# foreach(IDprot=iter(sp_all$ID[1:300]), .combine = 'rbind', .options.mpi=opt) %:%
# when(IDprot %in% tr_all$ID) %:% # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
# foreach(IDdis=iter(discoor_all$DIS_id[which(discoor_all$ID == IDprot)]), .combine = 'rbind') %:% # extract all disorder regions from this protein
# foreach(IDtr=iter(tr_all$TR_id[which(tr_all$ID == IDprot)]), .combine = 'rbind') %:% # loop through all TRs of this protein
# when(tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)]) %dopar%
# {# check for each TR region if it has a tail-overlap with a disorder region
#
# ## This chunck is for debugging:
# print(paste("TR-id", IDtr,
# # "prot-id", IDprot,
# # "discoor-id", IDdis,
# # "discoor-protid", discoor_all$DIS_id[which(discoor_all$ID == IDprot)],
# "TR-start", tr_all$begin[which(tr_all$TR_id == IDtr)],
# "TR-end", tr_all$end[which(tr_all$TR_id == IDtr)],
# "discorr-start", discoor_all$start[which(discoor_all$DIS_id == IDdis)],
# "discorr-end", discoor_all$end[which(discoor_all$DIS_id == IDdis)],
# "tail_overlap", tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]))
# }
# )
#
# closeCluster(cl)
#
# ### TODO with foreach on the 3 outer loops, iterator object, when statement (paralell, manual chunking)
# # register cluster
# cl <- makeCluster(numcores)
# registerDoParallel(cl)
#
# # split sp_all into equally sized chunks
# # foreach chunck of sp_all_chunk
# system.time(
# foreach(IDprot=iter(sp_all$ID[1:300]), .combine = 'rbind') %:%
# when(IDprot %in% tr_all$ID) %:% # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
# foreach(IDdis=iter(discoor_all$DIS_id[which(discoor_all$ID == IDprot)]), .combine = 'rbind') %:% # extract all disorder regions from this protein
# foreach(IDtr=iter(tr_all$TR_id[which(tr_all$ID == IDprot)]), .combine = 'rbind') %:% # loop through all TRs of this protein
# when(tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)]) %dopar%
# {# check for each TR region if it has a tail-overlap with a disorder region
#
# ## This chunck is for debugging:
# print(paste("TR-id", IDtr,
# # "prot-id", IDprot,
# # "discoor-id", IDdis,
# # "discoor-protid", discoor_all$DIS_id[which(discoor_all$ID == IDprot)],
# "TR-start", tr_all$begin[which(tr_all$TR_id == IDtr)],
# "TR-end", tr_all$end[which(tr_all$TR_id == IDtr)],
# "discorr-start", discoor_all$start[which(discoor_all$DIS_id == IDdis)],
# "discorr-end", discoor_all$end[which(discoor_all$DIS_id == IDdis)],
# "tail_overlap", tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]))
# }
# )
#
# stopCluster(cl)
#
# ### with foreach on the 3 outer loops, iterator object, when statement (forking instead of parallell)
# # register cluster
# cl <- makeCluster(numcores, type = "FORK")
# registerDoParallel(cl)
#
# system.time(
# foreach(IDprot=iter(sp_all$ID[1:300]), .combine = 'rbind', .inorder=TRUE) %:%
# when(IDprot %in% tr_all$ID) %:% # for each protein in swissprot. subset sp_all$ID[1:30] good for debugging, finds two results and takes about few seconds. Subset sp_all$ID[1:1000] takes about 10min
# foreach(IDdis=iter(discoor_all$DIS_id[which(discoor_all$ID == IDprot)]), .combine = 'rbind', .inorder=TRUE) %:% # extract all disorder regions from this protein
# foreach(IDtr=iter(tr_all$TR_id[which(tr_all$ID == IDprot)]), .combine = 'rbind', .inorder=TRUE) %:% # loop through all TRs of this protein
# when(tr_all$end[which(tr_all$TR_id == IDtr)] > discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# tr_all$begin[which(tr_all$TR_id == IDtr)] < discoor_all$start[which(discoor_all$DIS_id == IDdis)] &
# discoor_all$end[which(discoor_all$DIS_id == IDdis)] >= tr_all$end[which(tr_all$TR_id == IDtr)]) %dopar%
# {# check for each TR region if it has a tail-overlap with a disorder region
#
# ## This chunck is for debugging:
# print(paste("TR-id", IDtr,
# # "prot-id", IDprot,
# # "discoor-id", IDdis,
# # "discoor-protid", discoor_all$DIS_id[which(discoor_all$ID == IDprot)],
# "TR-start", tr_all$begin[which(tr_all$TR_id == IDtr)],
# "TR-end", tr_all$end[which(tr_all$TR_id == IDtr)],
# "discorr-start", discoor_all$start[which(discoor_all$DIS_id == IDdis)],
# "discorr-end", discoor_all$end[which(discoor_all$DIS_id == IDdis)],
# "tail_overlap", tr_all$end[which(tr_all$TR_id == IDtr)] - discoor_all$start[which(discoor_all$DIS_id == IDdis)]))
# }
#
# )
#
# stopCluster(cl)