LBMC » NucleoMiner

  if (nrow(regions) == 0) {return(regions)}

# remove_aligned_wp = function(# Remove wp nucs from common nucs list.

# ### It is based on common wp nucs index on nucs and region.

# strain_maps, ##<< Nuc maps.

# roi_index, ##<< The region of interest index.

# tmp_common_nucs, ##<< the list of wp nucs.

# strain##<< The strain to consider.

# ){

#   fuzzy_nucs = strain_maps[[strain]]

#   fuzzy_nucs = fuzzy_nucs[fuzzy_nucs$roi_index == roi_index,]

#   fuzzy_nucs = fuzzy_nucs[order(fuzzy_nucs$index_nuc),]

#   if (length(fuzzy_nucs[,1]) == 0) {return(fuzzy_nucs)}

#   if (sum(fuzzy_nucs$index_nuc == min(fuzzy_nucs$index_nuc):max(fuzzy_nucs$index_nuc)) != max(fuzzy_nucs$index_nuc)) {"Warning in index!"}

#   anti_index_1 = tmp_common_nucs[[paste("index_nuc", strain, sep="_")]]

#   fuzzy_nucs = fuzzy_nucs[-anti_index_1,]

#   return(fuzzy_nucs)

# }

# get_fuzzy = function(# Compute the fuzzy nucs.

# ### This function aggregate non common wp nucs for each strain and substract common wp nucs. It does not take care about the size of the resulting fuzzy regions. It will be take into account in the count read part og the pipeline.

# combi, ##<< The strain combination to consider.

# roi, ##<< The region of interest.

# roi_index, ##<< The region of interest index.

# strain_maps, ##<< Nuc maps.

# common_nuc_results, ##<< Common wp nuc maps

# config=NULL ##<< GLOBAL config variable

# ) {

#   print(roi_index)

#   PLOT = FALSE

#   tmp_common_nucs = common_nuc_results[[paste(combi[1], combi[2], sep="_")]]

#   tmp_common_nucs = tmp_common_nucs[tmp_common_nucs$roi_index == roi_index, ]

# 

#   print(paste("Dealing with fuzzy from", combi[1]))

#   tmp_fuzzy_nucs_1 = remove_aligned_wp(strain_maps, roi_index, tmp_common_nucs, combi[1])

#   tmp_fuzzy_nucs_1 = crop_fuzzy(tmp_fuzzy_nucs_1, roi, combi[1], config)

#   if (length(tmp_fuzzy_nucs_1[,1]) == 0) {return(NULL)}

#   agg_fuzzy_1 = union_regions(tmp_fuzzy_nucs_1)

#   if (PLOT) for (i in 1:length(agg_fuzzy_1[,1])) {

#     lines(c(agg_fuzzy_1[i,]$lower_bound, agg_fuzzy_1[i,]$upper_bound), c(+3.1,+3.1), col=2)

#   }

# 

#   print(paste("Dealing with fuzzy from ", combi[2]))

#   tmp_fuzzy_nucs_2 = remove_aligned_wp(strain_maps, roi_index, tmp_common_nucs, combi[2])

#   if (length(tmp_fuzzy_nucs_2[,1]) == 0) {return(NULL)}

#   agg_fuzzy_2 = union_regions(tmp_fuzzy_nucs_2)

#   agg_fuzzy_2 = crop_fuzzy(agg_fuzzy_2, roi, combi[2], config)

#   tr_agg_fuzzy_2 = translate_regions(agg_fuzzy_2, combi, roi_index, roi=roi, config=config)

#   tr_agg_fuzzy_2 = crop_fuzzy(tr_agg_fuzzy_2, roi, combi[2], config)

#   # tr_agg_fuzzy_2 = union_regions(tr_agg_fuzzy_2)

#   if (PLOT) for (i in 1:length(tr_agg_fuzzy_2[,1])) {

#     lines(c(tr_agg_fuzzy_2[i,]$lower_bound, tr_agg_fuzzy_2[i,]$upper_bound), c(+3.3,+3.3), col=2)

#   }

# 

#   print("Dealing with fuzzy from both...")

#   all_fuzzy = union_regions(rbind(agg_fuzzy_1, tr_agg_fuzzy_2))

#   if (PLOT) for (i in 1:length(all_fuzzy[,1])) {

#     lines(c(all_fuzzy[i,]$lower_bound, all_fuzzy[i,]$upper_bound), c(+3.2, +3.2), col=1)

#   }

# 

#   print(paste("Dealing with wp from", combi[1]))

#   wp_nucs_1 = extract_wp(strain_maps, roi_index, combi[1], tmp_common_nucs)

#   if (PLOT) for (i in 1:length(wp_nucs_1[,1])) {

#     lines(c(wp_nucs_1[i,]$lower_bound, wp_nucs_1[i,]$upper_bound), c(+3.5,+3.5), col=3)

#   }

# 

#   print(paste("Dealing with wp from", combi[2]))

#   wp_nucs_2 = extract_wp(strain_maps, roi_index, combi[2], tmp_common_nucs)

#   tr_wp_nucs_2 = translate_regions(wp_nucs_2, combi, roi_index, roi=roi, config=config)

#   if (PLOT) for (i in 1:length(tr_wp_nucs_2[,1])) {

#     lines(c(tr_wp_nucs_2[i,]$lower_bound, tr_wp_nucs_2[i,]$upper_bound), c(+3.7,+3.7), col=3)

#   }

# 

#   print("Dealing with wp from both...")

#   all_wp = union_regions(rbind(wp_nucs_1[,1:4], tr_wp_nucs_2))

#   if (PLOT) for (i in 1:length(all_wp[,1])) {

#     lines(c(all_wp[i,]$lower_bound, all_wp[i,]$upper_bound), c(+3.6, +3.6), col=1)

#   }

# 

#   print("Dealing with fuzzy and wp...")

#   non_inter_fuzzy = substract_region(all_fuzzy, all_wp)

#   if (is.null(non_inter_fuzzy)) { return(NULL) }

# 

#   non_inter_fuzzy$len = non_inter_fuzzy$upper_bound - non_inter_fuzzy$lower_bound

#   # non_inter_fuzzy = non_inter_fuzzy[non_inter_fuzzy$len >= min_fuzz_width,]

#   if (PLOT) for (i in 1:length(non_inter_fuzzy[,1])) {

#     lines(c(non_inter_fuzzy[i,]$lower_bound, non_inter_fuzzy[i,]$upper_bound), c(+3.9, +3.9), col=1)

#   }

# 

#   non_inter_fuzzy$index_nuc = 1:length(non_inter_fuzzy[,1])

#   return (non_inter_fuzzy)

# }