search_query.R

#!/usr/bin/Rscript
library(optparse)

source("./network_generator_lib.R")

args <- commandArgs(trailingOnly = TRUE)
# args <- parser_arguments(args = c('--organism', 'Mus_musculus', '--cell_type', 'Embryonic_stem_cells', '--search', '1_173143867'))
# args <- parser_arguments(args = c('--organism', 'Mus_musculus', '--cell_type', 'Embryonic_stem_cells', '--search', '6:52155590-52158317'))
# args <- parser_arguments(args = c('--organism', 'Mus_musculus', '--cell_type', 'Embryonic_stem_cells', '--search', 'asdfasdfa'))
# args <- parser_arguments(args = c('--organism', 'Mus_musculus', '--cell_type', 'Embryonic_stem_cells', '--search', 'Hoxa1'))

args <- parser_arguments(args)
# Load Rdata
load(file.path("data", args$organism, args$cell_type, "search_cache.Rdata"))

suppressPackageStartupMessages(library(stringr))
suppressPackageStartupMessages(library(tibble))
suppressPackageStartupMessages(library(igraph))

if (str_detect(args$search, "(([12]?[0-9])|([XYxy])):\\d+(-\\d+)?$")) {
  # Only load GenomicRanges if the string searched is a range
  suppressPackageStartupMessages(library(GenomicRanges))
}

# Search the required subnetwork
required_subnet <- search_subnetwork(args$search, args$expand, args$nearest, net, curated_PCHiC_vertex, ensembl2name)

# Cytospace doesn't process networks with only one node
if (is.null(required_subnet) || length(V(required_subnet)) == 1) {
  cat("{}")
} else {
  library(rjson)
  # Convert the required subnetwork to Cytoscape Json format
  required_subnet_json <- generate_cytoscape_json(required_subnet)
  cat(required_subnet_json)
}