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run_CHMMAIRRa_db_subsampling.jl
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#!/bin/bash
################################################
#
# Run IgBLAST and CHMMAIRRa commands to generate data for the subsampling test in figure 4
#
################################################
# run 20 different seeds per database size
# D01 D04 EUR, D07 SAS, D14 EAS, D11 AFR
# ran with IgDiscover22 v1.0.4
using Pkg
Pkg.activate(".")
Pkg.develop(path = "../CHMMAIRRa.jl")
using CHMMAIRRa, Glob, CSV, DataFrames, FASTX, Random, StatsBase, CodecZlib
include("./src/utils.jl")
threads = 16
seeds = [1, 2, 3]
chain2sizes = Dict("IGH" => [30, 40],
"TRA" => [30, 40],
"TRB" => [40, 50],
"TRG" => [4, 6])
# set up paths to databases
IMGT_VQUEST_dir = "/home/mchernys/references/IMGT/V-QUEST/homo_sapiens/202430-2/"
human_gl_aux = "$(IMGT_VQUEST_dir)/human_gl.aux"
IMGT_dbs = Dict("IGH" => "$(IMGT_VQUEST_dir)/IG/F+P/H",
"TRA" => "$(IMGT_VQUEST_dir)/TR/F+P/A",
"TRB" => "$(IMGT_VQUEST_dir)/TR/F+P/B",
"TRG" => "$(IMGT_VQUEST_dir)/TR/F+P/G")
IMGT_F_dbs = Dict("IGH" => "$(IMGT_VQUEST_dir)/IG/F/H",
"TRA" => "$(IMGT_VQUEST_dir)/TR/F/A",
"TRB" => "$(IMGT_VQUEST_dir)/TR/F/B",
"TRG" => "$(IMGT_VQUEST_dir)/TR/F/G")
KITDB_dir = "/home/mchernys/references/KITDB"
KI_TCR_dbs = Dict("TRA" => "$(KITDB_dir)/TRA",
"TRB" => "$(KITDB_dir)/TRB",
"TRG" => "$(KITDB_dir)/TRG")
OGRDB_dir = "/home/mchernys/references/OGRDB/human/IGH/9/"
# set up paths to IgDiscover runs
igdiscover_dir = "/home/mchernys/ben/chimera_detection/data/igdiscover22/"
igdiscover_run_dirs = Dict("IGH" => ["$(igdiscover_dir)IML3694/runs/IgG/IML3694_acute",
"$(igdiscover_dir)IML3694/runs/IgG/IML3694_convalescent",
"$(igdiscover_dir)IML3694/runs/IgG/IML3694_post-vax",
"$(igdiscover_dir)IML3694/runs/IgM/IML3694_25cycle",
"$(igdiscover_dir)IML3695/runs/IgG/IML3695_acute",
"$(igdiscover_dir)IML3695/runs/IgG/IML3695_convalescent",
"$(igdiscover_dir)IML3695/runs/IgG/IML3695_post-vax",
"$(igdiscover_dir)IML3695/runs/IgM/IML3695_25cycle"],
"TRA" => ["$(igdiscover_dir)GKH_TCR/TRA/D01",
"$(igdiscover_dir)GKH_TCR/TRA/D04",
"$(igdiscover_dir)GKH_TCR/TRA/D07",
"$(igdiscover_dir)GKH_TCR/TRA/D14",
"$(igdiscover_dir)GKH_TCR/TRA/D11"],
"TRB" => ["$(igdiscover_dir)GKH_TCR/TRB/D01",
"$(igdiscover_dir)GKH_TCR/TRB/D04",
"$(igdiscover_dir)GKH_TCR/TRB/D07",
"$(igdiscover_dir)GKH_TCR/TRB/D14",
"$(igdiscover_dir)GKH_TCR/TRB/D11"],
"TRG" => ["$(igdiscover_dir)GKH_TCR/TRG/D01",
"$(igdiscover_dir)GKH_TCR/TRG/D04",
"$(igdiscover_dir)GKH_TCR/TRG/D07",
"$(igdiscover_dir)GKH_TCR/TRG/D14",
"$(igdiscover_dir)GKH_TCR/TRG/D11"])
# set up CHMMAIRRa args
args = Dict{String, Any}("align-database" => true,
"detailed" => true,
"count-chimeric-segments" => true)
function create_subsampled_db(igdiscover_dir::String, db_dir::String, db_size::Int, seed::Int)
cd(igdiscover_dir)
refnames, refseqs = read_fasta("final/database/V.fasta")
Random.seed!(seed)
inds = sample(collect(1:length(refseqs)), db_size, replace=false)
if ! isdir(db_dir)
mkdir(db_dir)
end
write_fasta(joinpath(db_dir, "V.fasta"), refseqs[inds], seq_names = refnames[inds])
cp("final/database/D.fasta", joinpath(db_dir, "D.fasta"), force = true)
cp("final/database/J.fasta", joinpath(db_dir, "J.fasta"), force = true)
cp("database/human_gl.aux", joinpath(db_dir, "human_gl.aux"), force = true)
return db_dir
end
for chain in ["IGH", "TRA", "TRB", "TRG"]
@info "Processing $(chain)"
args["receptor"] = chain == "IGH" ? "IG" : "TCR"
# PG subsets
for igdiscover_run_dir in igdiscover_run_dirs[chain]
cd(igdiscover_run_dir)
for size in chain2sizes[chain]
for seed in seeds
@info "Processing $(igdiscover_run_dir) PG.$(size)Vs.$(seed)seed"
PG_subset_dir = "$(size)Vs-$(seed)seed-database"
create_subsampled_db(igdiscover_run_dir, PG_subset_dir, size, seed)
run(`conda run -n igdiscover igdiscover igblastwrap --sequence-type $(sequence_type) --aux $(human_gl_aux)--threads $(threads) $(PG_subset_dir) reads/sequences_50000subsample.fasta.gz | pigz -c > final/$(size)Vs-$(seed)seed-airr.tsv.gz`)
run(`conda run -n igdiscover igdiscover augment --read-cdr3 $(PG_subset_dir) final/$(size)Vs-$(seed)seed-airr.tsv.gz | pigz -c > final/$(size)Vs-$(seed)seed-assigned.tsv.gz`)
run(`conda run -n igdiscover igdiscover filter final/$(size)Vs-$(seed)seed-assigned.tsv.gz | pigz -c > final/$(size)Vs-$(seed)seed-filtered.tsv.gz`)
args["V_fasta"] = "$(PG_subset_dir)/V.fasta"
args["assignments"] = "final/$(size)Vs-$(seed)seed-filtered.tsv.gz"
args["out"] = "final/CHMMAIRRa_out.PG.$(size)Vs.$(seed)seed.tsv.gz"
args["chimeric-alignments"] = "final/CHMMAIRRa_out.PG.$(size)Vs.$(seed)seed.fasta"
CHMMAIRRa.detect_chimeras_from_files(args["V_fasta"], args["assignments"], args["out"],
receptor = args["receptor"],
align_database = args["align-database"],
detailed = args["detailed"],
count_chimeric_segments = args["count-chimeric-segments"],
chimeric_alignments = args["chimeric-alignments"])
end
end
# PG
@info "Processing $(igdiscover_run_dir) PG"
run(`conda run -n igdiscover igdiscover igblastwrap --sequence-type $(sequence_type) --aux $(human_gl_aux) --threads $(threads) final/database/ reads/sequences_50000subsample.fasta.gz | pigz -c > final/PG-airr.tsv.gz;`)
run(`conda run -n igdiscover igdiscover augment --read-cdr3 final/database/ final/PG-airr.tsv.gz | pigz -c > final/PG-assigned.tsv.gz;`)
run(`conda run -n igdiscover igdiscover filter final/PG-assigned.tsv.gz | pigz -c > final/PG-filtered.tsv.gz;`)
args["V_fasta"] = "final/database/V.fasta"
args["assignments"] = "final/PG-filtered.tsv.gz"
args["out"] = "final/CHMMAIRRa_out.PG.tsv.gz"
args["chimeric-alignments"] = "final/CHMMAIRRa_out.PG.fasta"
CHMMAIRRa.detect_chimeras_from_files(args["V_fasta"], args["assignments"], args["out"],
receptor = args["receptor"],
align_database = args["align-database"],
detailed = args["detailed"],
count_chimeric_segments = args["count-chimeric-segments"],
chimeric_alignments = args["chimeric-alignments"])
## IMGT db comparison
@info "Processing $(igdiscover_run_dir) IMGT db"
run(`conda run -n igdiscover igdiscover igblastwrap --sequence-type $(sequence_type) --aux $(human_gl_aux) --threads $(threads) $(IMGT_dbs[chain]) reads/sequences_50000subsample.fasta.gz | pigz -c > final/IMGT-V-QUEST-F+P-airr.tsv.gz;`)
run(`conda run -n igdiscover igdiscover augment --read-cdr3 $(IMGT_dbs[chain]) final/IMGT-V-QUEST-F+P-airr.tsv.gz | pigz -c > final/IMGT-V-QUEST-F+P-assigned.tsv.gz;`)
run(`conda run -n igdiscover igdiscover filter final/IMGT-V-QUEST-F+P-assigned.tsv.gz | pigz -c > final/IMGT-V-QUEST-F+P-filtered.tsv.gz;`)
args["V_fasta"] = "$(IMGT_dbs[chain])/V.fasta"
args["assignments"] = "final/IMGT-V-QUEST-F+P-filtered.tsv.gz"
args["out"] = "final/CHMMAIRRa_out.IMGT-V-QUEST-F+P.tsv.gz"
args["chimeric-alignments"] = "final/CHMMAIRRa_out.IMGT-V-QUEST-F+P.fasta"
CHMMAIRRa.detect_chimeras_from_files(args["V_fasta"], args["assignments"], args["out"],
receptor = args["receptor"],
align_database = args["align-database"],
detailed = args["detailed"],
count_chimeric_segments = args["count-chimeric-segments"],
chimeric_alignments = args["chimeric-alignments"])
# IMGT F db comparison
@info "Processing $(igdiscover_run_dir) IMGT F db"
run(`conda run -n igdiscover igdiscover igblastwrap --sequence-type $(sequence_type) --aux $(human_gl_aux) --threads $(threads) $(IMGT_F_dbs[chain]) reads/sequences_50000subsample.fasta.gz | pigz -c > final/IMGT-V-QUEST-F-airr.tsv.gz;`)
run(`conda run -n igdiscover igdiscover augment --read-cdr3 $(IMGT_F_dbs[chain]) final/IMGT-V-QUEST-F-airr.tsv.gz | pigz -c > final/IMGT-V-QUEST-F-assigned.tsv.gz;`)
run(`conda run -n igdiscover igdiscover filter final/IMGT-V-QUEST-F-assigned.tsv.gz | pigz -c > final/IMGT-V-QUEST-F-filtered.tsv.gz;`)
args["V_fasta"] = "$(IMGT_dbs[chain])/V.fasta"
args["assignments"] = "final/IMGT-V-QUEST-F-filtered.tsv.gz"
args["out"] = "final/CHMMAIRRa_out.IMGT-V-QUEST-F.tsv.gz"
args["chimeric-alignments"] = "final/CHMMAIRRa_out.IMGT-V-QUEST-F.fasta"
CHMMAIRRa.detect_chimeras_from_files(args["V_fasta"], args["assignments"], args["out"],
receptor = args["receptor"],
align_database = args["align-database"],
detailed = args["detailed"],
count_chimeric_segments = args["count-chimeric-segments"],
chimeric_alignments = args["chimeric-alignments"])
if chain == "IGH"
@info "Processing $(igdiscover_run_dir) OGRDB"
run_igblastwrap_from_files(OGRDB_dir, "reads/sequences_50000subsample.fasta.gz", "final/OGRDB-airr.tsv.gz", sequence_type = "Ig", human_gl_aux = human_gl_aux, threads = threads)
run_augment_from_files(OGRDB_dir, "final/OGRDB-airr.tsv.gz", "final/OGRDB-assigned.tsv.gz")
run_filter_from_files("final/OGRDB-assigned.tsv.gz", "final/OGRDB-filtered.tsv.gz")
args["V_fasta"] = "$(OGRDB_dir)/V.fasta"
args["assignments"] = "final/OGRDB-filtered.tsv.gz"
args["out"] = "final/CHMMAIRRa_out.OGRDB.tsv.gz"
args["chimeric-alignments"] = "final/CHMMAIRRa_out.OGRDB.fasta"
CHMMAIRRa.detect_chimeras_from_files(args["V_fasta"], args["assignments"], args["out"],
receptor = args["receptor"],
align_database = args["align-database"],
detailed = args["detailed"],
count_chimeric_segments = args["count-chimeric-segments"],
chimeric_alignments = args["chimeric-alignments"])
end
if chain != "IGH"
# for KITDB
@info "Processing $(igdiscover_run_dir) KITDB"
run(`conda run -n igdiscover igdiscover igblastwrap --sequence-type $(sequence_type) --aux $(human_gl_aux) --threads $(threads) $(KI_TCR_dbs[chain]) reads/sequences_50000subsample.fasta.gz | pigz -c > final/KITDB-airr.tsv.gz;`)
run(`conda run -n igdiscover igdiscover augment --read-cdr3 $(KI_TCR_dbs[chain]) final/KITDB-airr.tsv.gz | pigz -c > final/KITDB-assigned.tsv.gz;`)
run(`conda run -n igdiscover igdiscover filter final/KITDB-assigned.tsv.gz | pigz -c > final/KITDB-filtered.tsv.gz;`)
args["V_fasta"] = "$(KI_TCR_dbs[chain])/V.fasta"
args["assignments"] = "final/KITDB-filtered.tsv.gz"
args["out"] = "final/CHMMAIRRa_out.KITDB.tsv.gz"
args["chimeric-alignments"] = "final/CHMMAIRRa_out.KITDB.fasta"
CHMMAIRRa.detect_chimeras_from_files(args["V_fasta"], args["assignments"], args["out"],
receptor = args["receptor"],
align_database = args["align-database"],
detailed = args["detailed"],
count_chimeric_segments = args["count-chimeric-segments"],
chimeric_alignments = args["chimeric-alignments"])
end
end
end
# set up paths to databases
IMGT_VQUEST_dir = "/home/mchernys/references/IMGT/V-QUEST/homo_sapiens/202430-2/"
IMGT_dbs = Dict("IGH" => "$(IMGT_VQUEST_dir)/IG/F+P/H",
"TRA" => "$(IMGT_VQUEST_dir)/TR/F+P/A",
"TRB" => "$(IMGT_VQUEST_dir)/TR/F+P/B",
"TRG" => "$(IMGT_VQUEST_dir)/TR/F+P/G")
IMGT_F_dbs = Dict("IGH" => "$(IMGT_VQUEST_dir)/IG/F/H",
"TRA" => "$(IMGT_VQUEST_dir)/TR/F/A",
"TRB" => "$(IMGT_VQUEST_dir)/TR/F/B",
"TRG" => "$(IMGT_VQUEST_dir)/TR/F/G")
# set up paths to IgDiscover runs
igdiscover_dir = "/home/mchernys/ben/chimera_detection/data/igdiscover22/"
# set up CHMMAIRRa args
args = Dict{String, Any}("align-database" => true,
"detailed" => true,
"count-chimeric-segments" => true)
# get recombfreqplot for D04 for supplementary figure 1
cd("$(igdiscover_dir)GKH_TCR/TRG/D04")
# IMGT
chain = "TRG"
args["V_fasta"] = "$(IMGT_dbs[chain])/V.fasta"
args["assignments"] = "final/IMGT-V-QUEST-F-filtered.tsv.gz"
args["out"] = "final/CHMMAIRRa_out.IMGT-V-QUEST-F.tsv.gz"
args["chimeric-alignments"] = "final/CHMMAIRRa_out.IMGT-V-QUEST-F.fasta"
CHMMAIRRa.detect_chimeras_from_files(args["V_fasta"], args["assignments"], args["out"],
receptor = "TCR",
align_database = args["align-database"],
detailed = args["detailed"],
count_chimeric_segments = args["count-chimeric-segments"],
chimeric_alignments = args["chimeric-alignments"],
recombfreqplot = "final/TRG_D04.recombfreqplot.IMGT-VQUEST-F.svg")
# PG
args["V_fasta"] = "final/database/V.fasta"
args["assignments"] = "final/PG-filtered.tsv.gz"
args["out"] = "final/CHMMAIRRa_out.PG.tsv.gz"
args["chimeric-alignments"] = "final/CHMMAIRRa_out.PG.fasta"
CHMMAIRRa.detect_chimeras_from_files(args["V_fasta"], args["assignments"], args["out"],
receptor = "TCR",
align_database = args["align-database"],
detailed = args["detailed"],
count_chimeric_segments = args["count-chimeric-segments"],
chimeric_alignments = args["chimeric-alignments"],
recombfreqplot = "final/TRG_D04.recombfreqplot.PG.svg")