testdata/run_tests.R
In airr-community/ogrdbstats: Analysis of Adaptive Immune Receptor Repertoire Germ Line Statistics
# Standalone script to run ogrdb against test data
library(ogrdbstats)
#argv = parse_args(p, c('IMGT_REF_GAPPED.fasta', 'Homosapiens', 'TWO01A_naive_genotyped.tsv', 'IGHV', '--inf_file', 'TWO01A_naive_novel_ungapped.fasta', '--hap_gene', 'IGHJ6', '--plot_unmutated'))
#setwd('D:\\Research\\ogrdbstats\\testdata\\VH_tigger')
#argv = parse_args(p, c('..\\..\\IMGT_REF_GAPPED.fasta', 'Homosapiens', 'filtered.tab', 'IGLV', '--inf_file', 'database/V.fasta'))
#setwd('D:\\Research\\from_martin_corcoran\\VL_second_analysis_2-14_combined\\final')
#argv = parse_args(p, c('IMGT_REF_GAPPED.fasta', 'Homosapiens', 'P8_I1_S1_airr.tsv', 'IGHV'))
#setwd('D:\\Research\\ogrdbstats\\testdata\\VH_airr_no_novel')
#argv = parse_args(p, c('IMGT_REF_GAPPED.fasta', 'Homosapiens', 'TW02A_OGRDB.tsv', 'IGHV', '--inf_file', 'TW02A_V_OGRDB.fasta', '--hap_gene', 'IGHJ6'))
#setwd('D:\\Research\\ogrdbstats\\testdata\\VH_partis')
#argv = parse_args(p, c('IMGT_REF_GAPPED.fasta', 'Homosapiens', 'Read_file.tab', 'IGKV', '--inf_file', 'Inferred_file.fasta', '--hap_gene', 'IGHJ6'))
#setwd('D:\\Research\\ogrdbstats\\testdata\\private\\PRJEB30386 - Kappa')
#argv = parse_args(p, c('human_gl_IGHmakedb_F+ORF+in-frame_P.fasta', 'Homosapiens', 'P1_I1_S1.tsv', 'IGHV', '--inf_file', 'P1_I1_S1_novel_gapped.fasta', '--hap_gene', 'IGHJ6'))
#setwd('D:\\Research\\ogrdbstats\\testdata\\private\\ogrdbstats_in_vdjbase')
#setwd('D:\\Research\\ogrdbstats\\testdata\\private\\hamster')
#argv = parse_args(p, c('hamster_IGH_VDJ.fasta', 'Hamster', 'igblast_001_db-pass.tsv', 'IGHV', '--all_novel'))
# setwd('D:\\Research\\ogrdbstats\\testdata\\trb')
# argv = parse_args(p, c('imgt_gapped.fasta', 'Homosapiens', 'SC9.tab', 'TRBV', '--inf_file', 'SC9_novel.fasta'))
# setwd('D:\\Research\\new_ham\\16. Leaders')
# argv = parse_args(p, c('ref/hamster_IGH_VDJ.fasta', 'hamster', 'leader_allele_matches.tsv', 'VH', '--inf_file', 'leader_aliases.fasta'))
# setwd('D:\\Research\\new_ham\\2. j_allele_search\\igblast')
# argv = parse_args(p, c('../ref/hamster_IGH_VDJ.fasta', 'hamster', 'igblast_009_x-clones.tsv', 'DH', '--all_novel'))
# setwd('D:\\Research\\ogrdbstats\\testdata\\trb2')
# argv = parse_args(p, c('personal_repo.fasta', 'Homosapiens', 'HIP00110_genotyped.tab', 'TRBV', '--inf_file', 'only_novel_repo.fasta'))
# setwd('D:\\Research\\ogrdbstats\\testdata\\private\\JK_changeo')
# argv = parse_args(p, c('IMGT-IGKJ-inc-novels.fasta', 'mouse', '129_igblast_db-pass.tsv', 'JK', '--all_novel'))
setwd('D:\\Research\\ogrdbstats\\testdata\\private\\ogrdbstats_in_vdjbase')
genotype_statistics_cmd(c('IMGTGENEDB-ReferenceSequences.fasta-nt-WithGaps-F+ORF+inframeP', 'Homosapiens', 'P1_I28_S1.tsv', 'IGHV', '--hap_gene', 'IGHJ6', '--plot_unmutated', '--inf_file', 'P1_I28_novels.fasta'))
#' Generate OGRDB reports using test data
genotype_statistics_test = function(testdir, full=F) {
Sys.setenv('R_MAX_VSIZE'=32000000000) # this setting may not be effective in Rstudio
setwd(testdir)
# VH - tigger (Example in Readme)
report('VH - tigger')
setwd('VH_tigger')
ref_filename = 'IMGT_REF_GAPPED.fasta'
species = 'Homosapiens'
inferred_filename = 'TWO01A_naive_novel_ungapped.fasta'
filename = 'TWO01A_naive_genotyped.tsv'
chain = 'VH'
hap_gene = 'IGHJ6'
segment = 'V'
chain_type = 'H'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
if(full) {
# VH - AIRR with no novel sequences
report('VH - AIRR no novel')
setwd('VH_airr_no_novel')
ref_filename = 'IMGT_REF_GAPPED.fasta'
species = 'Homosapiens'
inferred_filename = '-'
filename = 'P8_I1_S1_airr.tsv'
chain = 'IGHV'
hap_gene = 'IGHJ6'
segment = 'V'
chain_type = 'H'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
gc()
# VH - tigger with truncated sequences in IMGT alignment
report('VH - tigger with truncated sequences in IMGT alignment')
setwd('V_tigger_truncated')
ref_filename = 'IMGT_REF_GAPPED.fasta'
species = 'Homosapiens'
inferred_filename = 'TWO01A_naive_novel_ungapped.fasta'
filename = 'TWO01A_naive_genotyped.tsv'
chain = 'IGHV'
hap_gene = 'IGHJ6'
segment = 'V'
chain_type = 'H'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
gc()
# JH - tigger
report('JH - tigger')
setwd('JH_tigger')
ref_filename = 'IMGT_REF_GAPPED_J_CHANGES.fasta'
species = 'Homosapiens'
inferred_filename = 'TWO01A_naive_novel.fasta'
filename = 'TWO01A_naive.airr.tab'
chain = 'IGHJ'
hap_gene = 'IGHV2-5'
segment = 'J'
chain_type = 'H'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
gc()
# D - tigger
report('D - tigger')
setwd('D_tigger')
ref_filename = 'IMGT_REF_GAPPED_D_1_26_01_removed.fasta'
species = 'Homosapiens'
inferred_filename = 'TWO01A_naive_novel.fasta'
filename = 'TWO01A_naive.airr.tab'
chain = 'IGHD'
hap_gene = 'IGHJ6'
segment = 'D'
chain_type = 'H'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
gc()
# JH - igdiscover
report('JH - igdiscover')
setwd('JH_igdiscover')
ref_filename = 'IMGT_REF_GAPPED_fake_j.fasta'
species = 'Homosapiens'
inferred_filename = 'J.fasta'
filename = 'filtered.tab'
chain = 'IGHJ'
hap_gene = 'IGHV2-5'
segment = 'J'
chain_type = 'H'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
gc()
# JL - igdiscover
# just a fake based on JH
report('JL - igdiscover')
setwd('JL_igdiscover')
ref_filename = 'IMGT_REF_GAPPED_fake_j_fake_JK.fasta'
species = 'Homosapiens'
inferred_filename = 'J.fasta'
filename = 'filtered.tab'
chain = 'IGKJ'
hap_gene = 'IGHV2-5'
segment = 'J'
chain_type = 'L'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
gc()
# VH - partis
# This takes a lot of memory and does not run comfortably in RStudio
# report('VH - partis')
# setwd('VH_partis')
# ref_filename = 'IMGT_REF_GAPPED.fasta'
# species = 'Homosapiens'
# inferred_filename = 'TW02A_V_OGRDB.fasta'
# filename = 'TW02A_OGRDB.tsv'
# chain = 'VH'
# hap_gene = 'IGHJ6'
# segment = 'V'
# chain_type = 'H'
# generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
# setwd('..')
gc()
# JK - igDiscover
report('JK - igdiscover')
setwd('private/PRJEB30386 - Kappa')
ref_filename = 'IMGT_REF_GAPPED.fasta'
species = 'Homosapiens'
inferred_filename = 'Inferred_file.fasta'
filename = 'Read_file.tab'
chain = 'IGKJ'
hap_gene = 'IGHJ6'
segment = 'V'
chain_type = 'L'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
# VH - IgDiscover 1.51
# Recent versions of IgDiscover use IgBLAST output in filtered.tsv
# VH - IgDiscover 1.51
# Recent versions of IgDiscover use IgBLAST output in filtered.tsv
report('VK_igdiscover_151')
setwd('VK_igdiscover_151')
ref_filename = 'V_ref_gapped.fasta'
species = 'Homosapiens'
inferred_filename = 'V_head.fasta'
filename = 'filtered_head.tsv'
inferred_filename = 'V.fasta'
filename = 'filtered.tsv'
chain = 'IGKV'
hap_gene = 'IGKJ3'
segment = 'V'
chain_type = 'L'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
report('VL_igdiscover_151')
setwd('VL_igdiscover_151')
ref_filename = 'V_gapped.fasta'
species = 'Homosapiens'
#inferred_filename = 'V_head.fasta'
#filename = 'filtered_1_01.tsv'
inferred_filename = 'V.fasta'
filename = 'filtered.tsv'
chain = 'IGLV'
hap_gene = ''
segment = 'V'
chain_type = 'L'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
report('VL_mouse_igblast')
setwd('VL_mouse_igblast')
ref_filename = 'V_gapped.fasta'
species = 'Mouse'
filename = 'annotated_head.tsv'
#filename = 'annotated_full.tsv'
inferred_filename = '-'
chain = 'IGLV'
hap_gene = NA
segment = 'V'
chain_type = 'L'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, TRUE)
setwd('..')
}
}
airr-community/ogrdbstats documentation built on Feb. 17, 2025, 5:05 p.m.
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# Standalone script to run ogrdb against test data
library(ogrdbstats)
#argv = parse_args(p, c('IMGT_REF_GAPPED.fasta', 'Homosapiens', 'TWO01A_naive_genotyped.tsv', 'IGHV', '--inf_file', 'TWO01A_naive_novel_ungapped.fasta', '--hap_gene', 'IGHJ6', '--plot_unmutated'))
#setwd('D:\\Research\\ogrdbstats\\testdata\\VH_tigger')
#argv = parse_args(p, c('..\\..\\IMGT_REF_GAPPED.fasta', 'Homosapiens', 'filtered.tab', 'IGLV', '--inf_file', 'database/V.fasta'))
#setwd('D:\\Research\\from_martin_corcoran\\VL_second_analysis_2-14_combined\\final')
#argv = parse_args(p, c('IMGT_REF_GAPPED.fasta', 'Homosapiens', 'P8_I1_S1_airr.tsv', 'IGHV'))
#setwd('D:\\Research\\ogrdbstats\\testdata\\VH_airr_no_novel')
#argv = parse_args(p, c('IMGT_REF_GAPPED.fasta', 'Homosapiens', 'TW02A_OGRDB.tsv', 'IGHV', '--inf_file', 'TW02A_V_OGRDB.fasta', '--hap_gene', 'IGHJ6'))
#setwd('D:\\Research\\ogrdbstats\\testdata\\VH_partis')
#argv = parse_args(p, c('IMGT_REF_GAPPED.fasta', 'Homosapiens', 'Read_file.tab', 'IGKV', '--inf_file', 'Inferred_file.fasta', '--hap_gene', 'IGHJ6'))
#setwd('D:\\Research\\ogrdbstats\\testdata\\private\\PRJEB30386 - Kappa')
#argv = parse_args(p, c('human_gl_IGHmakedb_F+ORF+in-frame_P.fasta', 'Homosapiens', 'P1_I1_S1.tsv', 'IGHV', '--inf_file', 'P1_I1_S1_novel_gapped.fasta', '--hap_gene', 'IGHJ6'))
#setwd('D:\\Research\\ogrdbstats\\testdata\\private\\ogrdbstats_in_vdjbase')
#setwd('D:\\Research\\ogrdbstats\\testdata\\private\\hamster')
#argv = parse_args(p, c('hamster_IGH_VDJ.fasta', 'Hamster', 'igblast_001_db-pass.tsv', 'IGHV', '--all_novel'))
# setwd('D:\\Research\\ogrdbstats\\testdata\\trb')
# argv = parse_args(p, c('imgt_gapped.fasta', 'Homosapiens', 'SC9.tab', 'TRBV', '--inf_file', 'SC9_novel.fasta'))
# setwd('D:\\Research\\new_ham\\16. Leaders')
# argv = parse_args(p, c('ref/hamster_IGH_VDJ.fasta', 'hamster', 'leader_allele_matches.tsv', 'VH', '--inf_file', 'leader_aliases.fasta'))
# setwd('D:\\Research\\new_ham\\2. j_allele_search\\igblast')
# argv = parse_args(p, c('../ref/hamster_IGH_VDJ.fasta', 'hamster', 'igblast_009_x-clones.tsv', 'DH', '--all_novel'))
# setwd('D:\\Research\\ogrdbstats\\testdata\\trb2')
# argv = parse_args(p, c('personal_repo.fasta', 'Homosapiens', 'HIP00110_genotyped.tab', 'TRBV', '--inf_file', 'only_novel_repo.fasta'))
# setwd('D:\\Research\\ogrdbstats\\testdata\\private\\JK_changeo')
# argv = parse_args(p, c('IMGT-IGKJ-inc-novels.fasta', 'mouse', '129_igblast_db-pass.tsv', 'JK', '--all_novel'))
setwd('D:\\Research\\ogrdbstats\\testdata\\private\\ogrdbstats_in_vdjbase')
genotype_statistics_cmd(c('IMGTGENEDB-ReferenceSequences.fasta-nt-WithGaps-F+ORF+inframeP', 'Homosapiens', 'P1_I28_S1.tsv', 'IGHV', '--hap_gene', 'IGHJ6', '--plot_unmutated', '--inf_file', 'P1_I28_novels.fasta'))
#' Generate OGRDB reports using test data
genotype_statistics_test = function(testdir, full=F) {
Sys.setenv('R_MAX_VSIZE'=32000000000) # this setting may not be effective in Rstudio
setwd(testdir)
# VH - tigger (Example in Readme)
report('VH - tigger')
setwd('VH_tigger')
ref_filename = 'IMGT_REF_GAPPED.fasta'
species = 'Homosapiens'
inferred_filename = 'TWO01A_naive_novel_ungapped.fasta'
filename = 'TWO01A_naive_genotyped.tsv'
chain = 'VH'
hap_gene = 'IGHJ6'
segment = 'V'
chain_type = 'H'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
if(full) {
# VH - AIRR with no novel sequences
report('VH - AIRR no novel')
setwd('VH_airr_no_novel')
ref_filename = 'IMGT_REF_GAPPED.fasta'
species = 'Homosapiens'
inferred_filename = '-'
filename = 'P8_I1_S1_airr.tsv'
chain = 'IGHV'
hap_gene = 'IGHJ6'
segment = 'V'
chain_type = 'H'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
gc()
# VH - tigger with truncated sequences in IMGT alignment
report('VH - tigger with truncated sequences in IMGT alignment')
setwd('V_tigger_truncated')
ref_filename = 'IMGT_REF_GAPPED.fasta'
species = 'Homosapiens'
inferred_filename = 'TWO01A_naive_novel_ungapped.fasta'
filename = 'TWO01A_naive_genotyped.tsv'
chain = 'IGHV'
hap_gene = 'IGHJ6'
segment = 'V'
chain_type = 'H'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
gc()
# JH - tigger
report('JH - tigger')
setwd('JH_tigger')
ref_filename = 'IMGT_REF_GAPPED_J_CHANGES.fasta'
species = 'Homosapiens'
inferred_filename = 'TWO01A_naive_novel.fasta'
filename = 'TWO01A_naive.airr.tab'
chain = 'IGHJ'
hap_gene = 'IGHV2-5'
segment = 'J'
chain_type = 'H'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
gc()
# D - tigger
report('D - tigger')
setwd('D_tigger')
ref_filename = 'IMGT_REF_GAPPED_D_1_26_01_removed.fasta'
species = 'Homosapiens'
inferred_filename = 'TWO01A_naive_novel.fasta'
filename = 'TWO01A_naive.airr.tab'
chain = 'IGHD'
hap_gene = 'IGHJ6'
segment = 'D'
chain_type = 'H'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
gc()
# JH - igdiscover
report('JH - igdiscover')
setwd('JH_igdiscover')
ref_filename = 'IMGT_REF_GAPPED_fake_j.fasta'
species = 'Homosapiens'
inferred_filename = 'J.fasta'
filename = 'filtered.tab'
chain = 'IGHJ'
hap_gene = 'IGHV2-5'
segment = 'J'
chain_type = 'H'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
gc()
# JL - igdiscover
# just a fake based on JH
report('JL - igdiscover')
setwd('JL_igdiscover')
ref_filename = 'IMGT_REF_GAPPED_fake_j_fake_JK.fasta'
species = 'Homosapiens'
inferred_filename = 'J.fasta'
filename = 'filtered.tab'
chain = 'IGKJ'
hap_gene = 'IGHV2-5'
segment = 'J'
chain_type = 'L'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
gc()
# VH - partis
# This takes a lot of memory and does not run comfortably in RStudio
# report('VH - partis')
# setwd('VH_partis')
# ref_filename = 'IMGT_REF_GAPPED.fasta'
# species = 'Homosapiens'
# inferred_filename = 'TW02A_V_OGRDB.fasta'
# filename = 'TW02A_OGRDB.tsv'
# chain = 'VH'
# hap_gene = 'IGHJ6'
# segment = 'V'
# chain_type = 'H'
# generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
# setwd('..')
gc()
# JK - igDiscover
report('JK - igdiscover')
setwd('private/PRJEB30386 - Kappa')
ref_filename = 'IMGT_REF_GAPPED.fasta'
species = 'Homosapiens'
inferred_filename = 'Inferred_file.fasta'
filename = 'Read_file.tab'
chain = 'IGKJ'
hap_gene = 'IGHJ6'
segment = 'V'
chain_type = 'L'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
# VH - IgDiscover 1.51
# Recent versions of IgDiscover use IgBLAST output in filtered.tsv
# VH - IgDiscover 1.51
# Recent versions of IgDiscover use IgBLAST output in filtered.tsv
report('VK_igdiscover_151')
setwd('VK_igdiscover_151')
ref_filename = 'V_ref_gapped.fasta'
species = 'Homosapiens'
inferred_filename = 'V_head.fasta'
filename = 'filtered_head.tsv'
inferred_filename = 'V.fasta'
filename = 'filtered.tsv'
chain = 'IGKV'
hap_gene = 'IGKJ3'
segment = 'V'
chain_type = 'L'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
report('VL_igdiscover_151')
setwd('VL_igdiscover_151')
ref_filename = 'V_gapped.fasta'
species = 'Homosapiens'
#inferred_filename = 'V_head.fasta'
#filename = 'filtered_1_01.tsv'
inferred_filename = 'V.fasta'
filename = 'filtered.tsv'
chain = 'IGLV'
hap_gene = ''
segment = 'V'
chain_type = 'L'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, FALSE)
setwd('..')
report('VL_mouse_igblast')
setwd('VL_mouse_igblast')
ref_filename = 'V_gapped.fasta'
species = 'Mouse'
filename = 'annotated_head.tsv'
#filename = 'annotated_full.tsv'
inferred_filename = '-'
chain = 'IGLV'
hap_gene = NA
segment = 'V'
chain_type = 'L'
generate_ogrdb_report(ref_filename, inferred_filename, species, filename, chain, hap_gene, segment, chain_type, TRUE)
setwd('..')
}
}
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