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Commit message:
planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c |
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modified:
CHANGELOG.md gene_identification.py shm_csr.xml tests/test_shm_csr.py wrapper.sh |
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added:
__pycache__/igm_naive_mutations.cpython-39.pyc igm_naive_mutations.py nt_overview.r sequence_overview.py split_imgt_file.py tests/__pycache__/test_shm_csr.cpython-39-pytest-7.2.0.pyc |
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removed:
new_imgt.r sequence_overview.r test-output/IGA.pdf test-output/IGA.png test-output/IGA1_mean_n.txt test-output/IGA1_mean_value.txt test-output/IGA1_median_n.txt test-output/IGA1_median_value.txt test-output/IGA1_sum_n.txt test-output/IGA1_sum_value.txt test-output/IGA2_mean_n.txt test-output/IGA2_mean_value.txt test-output/IGA2_median_n.txt test-output/IGA2_median_value.txt test-output/IGA2_sum_n.txt test-output/IGA2_sum_value.txt test-output/IGA_mean_n.txt test-output/IGA_mean_value.txt test-output/IGA_median_n.txt test-output/IGA_median_value.txt test-output/IGA_pie.txt test-output/IGA_sum_n.txt test-output/IGA_sum_value.txt test-output/IGE_mean_n.txt test-output/IGE_mean_value.txt test-output/IGE_median_n.txt test-output/IGE_median_value.txt test-output/IGE_sum_n.txt test-output/IGE_sum_value.txt test-output/IGG.pdf test-output/IGG.png test-output/IGG1_mean_n.txt test-output/IGG1_mean_value.txt test-output/IGG1_median_n.txt test-output/IGG1_median_value.txt test-output/IGG1_sum_n.txt test-output/IGG1_sum_value.txt test-output/IGG2_mean_n.txt test-output/IGG2_mean_value.txt test-output/IGG2_median_n.txt test-output/IGG2_median_value.txt test-output/IGG2_sum_n.txt test-output/IGG2_sum_value.txt test-output/IGG3_mean_n.txt test-output/IGG3_mean_value.txt test-output/IGG3_median_n.txt test-output/IGG3_median_value.txt test-output/IGG3_sum_n.txt test-output/IGG3_sum_value.txt test-output/IGG4_mean_n.txt test-output/IGG4_mean_value.txt test-output/IGG4_median_n.txt test-output/IGG4_median_value.txt test-output/IGG4_sum_n.txt test-output/IGG4_sum_value.txt test-output/IGG_mean_n.txt test-output/IGG_mean_value.txt test-output/IGG_median_n.txt test-output/IGG_median_value.txt test-output/IGG_pie.txt test-output/IGG_sum_n.txt test-output/IGG_sum_value.txt test-output/IGM_mean_n.txt test-output/IGM_mean_value.txt test-output/IGM_median_n.txt test-output/IGM_median_value.txt test-output/IGM_sum_n.txt test-output/IGM_sum_value.txt test-output/aa_id_mutations.txt test-output/absent_aa_id.txt test-output/all_mean_n.txt test-output/all_mean_value.txt test-output/all_median_n.txt test-output/all_median_value.txt test-output/all_sum_n.txt test-output/all_sum_value.txt test-output/hotspot_analysis_mean.txt test-output/hotspot_analysis_median.txt test-output/hotspot_analysis_sum.txt test-output/motif_per_seq.txt test-output/mutation_by_id.txt test-output/shm_overview_tandem_row.txt test-output/tandem_frequency.txt test-output/tandems_by_id.txt test-output/unmatched.txt test-output/unmatched_mean_n.txt test-output/unmatched_mean_value.txt test-output/unmatched_median_n.txt test-output/unmatched_median_value.txt test-output/unmatched_sum_n.txt test-output/unmatched_sum_value.txt tests/.pytest_cache/.gitignore tests/.pytest_cache/CACHEDIR.TAG tests/.pytest_cache/README.md tests/.pytest_cache/v/cache/lastfailed tests/.pytest_cache/v/cache/nodeids tests/.pytest_cache/v/cache/stepwise tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc tests/__pycache__/test_shm_csr.cpython-37.pyc tests/__pycache__/test_shm_csr.cpython-39-pytest-6.2.5.pyc tests/data/intermediate_files/RGYW.txt tests/data/intermediate_files/merged.txt tests/data/intermediate_files/mutation_in_motifs.txt tests/data/intermediate_files/mutationdict.txt |
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| diff -r f387cc1580c6 -r cf8ad181628f CHANGELOG.md --- a/CHANGELOG.md Wed Feb 02 10:57:36 2022 +0000 +++ b/CHANGELOG.md Mon Dec 12 12:32:44 2022 +0000 |
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| @@ -1,3 +1,14 @@ +version 1.6.0 +------------- ++ Faster runtime due to faster gene identification, sequence overview creation + and IMGT TAR archive creation. ++ Two extra IMGT files are provided. One for IGM with less than 2% mutations + (naive) and one for IGM with more than 2% mutations (naive memory). ++ All IMGT files per sequence class are always provided regardless of how the + ``Fast`` option is set. Previously this had to be set to ``no``. ++ Fix a bug in sequence overview where links to unmatched sequences where not + working properly in the by_id.html file. + version 1.5.0 ------------- + Add an option to download all output files in a zip file. |
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| diff -r f387cc1580c6 -r cf8ad181628f __pycache__/igm_naive_mutations.cpython-39.pyc |
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| Binary file __pycache__/igm_naive_mutations.cpython-39.pyc has changed |
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| diff -r f387cc1580c6 -r cf8ad181628f gene_identification.py --- a/gene_identification.py Wed Feb 02 10:57:36 2022 +0000 +++ b/gene_identification.py Mon Dec 12 12:32:44 2022 +0000 |
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| b'@@ -1,134 +1,123 @@\n-import re\n-import argparse\n-import time\n-starttime= int(time.time() * 1000)\n-\n-parser = argparse.ArgumentParser()\n-parser.add_argument("--input", help="The 1_Summary file from an IMGT zip file")\n-parser.add_argument("--output", help="The annotated output file to be merged back with the summary file")\n+#!/usr/bin/env python3\n \n-args = parser.parse_args()\n-\n-infile = args.input\n-#infile = "test_VH-Ca_Cg_25nt/1_Summary_test_VH-Ca_Cg_25nt_241013.txt"\n-output = args.output\n-#outfile = "identified.txt"\n-\n-dic = dict()\n-total = 0\n+import argparse\n+import re\n+from typing import Dict, Iterator, List, Tuple\n \n \n-first = True\n-IDIndex = 0\n-seqIndex = 0\n+def generate_sequence_and_id_from_summary(summary_file: str\n+ ) -> Iterator[Tuple[str, str]]:\n+ with open(summary_file, "rt") as summary:\n+ header = next(summary)\n+ column_names = header.strip("\\n").split("\\t")\n+ id_column = column_names.index("Sequence ID")\n+ sequence_column = column_names.index("Sequence")\n+ for line in summary:\n+ values = line.strip("\\n").split("\\t")\n+ id = values[id_column]\n+ try:\n+ sequence = values[sequence_column]\n+ except IndexError: # weird rows without a sequence\n+ sequence = ""\n+ yield id, sequence\n \n-with open(infile, \'r\') as f: #read all sequences into a dictionary as key = ID, value = sequence\n- for line in f:\n- total += 1\n- linesplt = line.split("\\t")\n- if first:\n- print("linesplt", linesplt)\n- IDIndex = linesplt.index("Sequence ID")\n- seqIndex = linesplt.index("Sequence")\n- first = False\n- continue\n- \n- ID = linesplt[IDIndex]\n- if len(linesplt) < 28: #weird rows without a sequence\n- dic[ID] = ""\n- else:\n- dic[ID] = linesplt[seqIndex]\n- \n-print("Number of input sequences:", len(dic))\n \n-#old cm sequence: gggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattccc\n-#old cg sequence: ctccaccaagggcccatcggtcttccccctggcaccctcctccaagagcacctctgggggcacagcggccctgggctgcctggtcaaggactacttccccgaaccggtgacggtgtcgtggaactcaggcgccctgaccag\n-\n-#lambda/kappa reference sequence\n-searchstrings = {"ca": "catccccgaccagccccaaggtcttcccgctgagcctctgcagcacccagccagatgggaacgtggtcatcgcctgcctgg",\n- "cg": "ctccaccaagggcccatcggtcttccccctggcaccctcctccaagagcacctctgggggcacagcggcc",\n- "ce": "gcctccacacagagcccatccgtcttccccttgacccgctgctgcaaaaacattccctcc",\n+# old cm sequence: gggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattccc\n+# old cg sequence: ctccaccaagggcccatcggtcttccccctggcaccctcctccaagagcacctctg\n+# ggggcacagcggccctgggctgcctggtcaaggactacttccccgaaccggtgacggtgtcgtggaactcagg\n+# cgccctgaccag\n+SEARCHSTRINGS = {"ca": "catccccgaccagccccaaggtcttcccgctgagcctctgcagcacccagccag"\n+ "atgggaacgtggtcatcgcctgcctgg",\n+ "cg": "ctccaccaagggcccatcggtcttccccctggcaccctcctccaagagcacctc"\n+ "tgggggcacagcggcc",\n+ "ce": "gcctccacacagagcccatccgtcttccccttgacccgctgctgcaaaaacatt"\n+ "ccctcc",\n "cm": "gggagtgcatccgccccaacc"} #new (shorter) cm sequence\n \n-compiledregex = {"ca": [],\n- "cg": [],\n- "ce": [],\n- "cm": []}\n-\n-#lambda/kappa reference sequence variable nucleotides\n-ca1 = {38: \'t\', 39: \'g\', 48: \'a\', 49: \'g\', 51: \'c\', 68: \'a\', 73: \'c\'}\n-ca2 = {38: \'g\', 39: \'a\', 48: \'c\', 49: \'c\', 51: \'a\', 68: \'g\', 73: \'a\'}\n-cg1 = {0: \'c\', 33: \'a\', 38: \'c\', 44: \'a\', 54: \'t\', 56: \'g\', 58: \'g\', 66: \'g\', 132: \'c\'}\n-cg2 = {0: \'c\', 33: \'g\', 38: \'g\', 44: \'g\', 54: \'c\', 56: \'a\', 58: \'a\', 66: \'g\', 132: \'t\'}\n-cg3 = {0: \'t\', 33: \'g\', 38: \'g\', 44: \'g\', 54: \'t\', 56: \'g\', 58: \'g\', 66: \'g\', 132: \'c\'}\n-cg4 = {0: \'t\', 33: \'g\', 38: \'g\', 44: \'g\', 54: \'c\', 56: \'a\', 58: \'a\', 66: \'c\', 132: \'c\'}\n+#lambda/kappa referesearchstringsnce sequence variable nucle'..b' cghits >= cehits: #its a cg gene\n- cg1hits = currentIDHits["cg1"]\n- cg2hits = currentIDHits["cg2"]\n- cg3hits = currentIDHits["cg3"]\n- cg4hits = currentIDHits["cg4"]\n- if cg1hits >= cg2hits and cg1hits >= cg3hits and cg1hits >= cg4hits: #cg1 gene\n- o.write(ID + "\\tIGG1\\t" + str(round_int(cg1hits / varsInCG * 100)) + "\\t" + str(round_int(cghits / possiblecg * 100)) + "\\t" + start_location[ID + "_cg"] + "\\n")\n- elif cg2hits >= cg1hits and cg2hits >= cg3hits and cg2hits >= cg4hits: #cg2 gene\n- o.write(ID + "\\tIGG2\\t" + str(round_int(cg2hits / varsInCG * 100)) + "\\t" + str(round_int(cghits / possiblecg * 100)) + "\\t" + start_location[ID + "_cg"] + "\\n")\n- elif cg3hits >= cg1hits and cg3hits >= cg2hits and cg3hits >= cg4hits: #cg3 gene\n- o.write(ID + "\\tIGG3\\t" + str(round_int(cg3hits / varsInCG * 100)) + "\\t" + str(round_int(cghits / possiblecg * 100)) + "\\t" + start_location[ID + "_cg"] + "\\n")\n- else: #cg4 gene\n- o.write(ID + "\\tIGG4\\t" + str(round_int(cg4hits / varsInCG * 100)) + "\\t" + str(round_int(cghits / possiblecg * 100)) + "\\t" + start_location[ID + "_cg"] + "\\n")\n- else: #its a cm or ce gene\n- if cmhits >= cehits:\n- o.write(ID + "\\tIGM\\t100\\t" + str(round_int(cmhits / possiblecm * 100)) + "\\t" + start_location[ID + "_cm"] + "\\n")\n- else:\n- o.write(ID + "\\tIGE\\t100\\t" + str(round_int(cehits / possiblece * 100)) + "\\t" + start_location[ID + "_ce"] + "\\n")\n- seq_write_count += 1\n-\n-print("Time: %i" % (int(time.time() * 1000) - starttime))\n-\n-print("Number of sequences written to file:", seq_write_count)\n+def main():\n+ parser = argparse.ArgumentParser()\n+ parser.add_argument("--input",\n+ help="The 1_Summary file from an IMGT zip file")\n+ parser.add_argument("--output",\n+ help="The annotated output file to be merged back "\n+ "with the summary file")\n+ args = parser.parse_args()\n+ varsInCA = float(len(list(CA1_MUTATIONS.keys())) * 2)\n+ varsInCG = float(len(list(\n+ CG1_MUTATIONS.keys())) * 2) - 2 # -2 because the sliding window doesn\'t hit the first and last nt twice\n+ subclass_vars = {\n+ "IGA1": varsInCA, "IGA2": varsInCA,\n+ "IGG1": varsInCG, "IGG2": varsInCG, "IGG3": varsInCG, "IGG4": varsInCG,\n+ "IGE": 0,\n+ "IGM": 0,\n+ }\n+ compiledregex = create_compiled_regexes()\n+ possibleca = float(len(compiledregex["ca"]))\n+ possiblecg = float(len(compiledregex["cg"]))\n+ possiblecm = float(len(compiledregex["cm"]))\n+ possiblece = float(len(compiledregex["ce"]))\n+ class_chunks = {\n+ "IGA1": possibleca, "IGA2": possibleca,\n+ "IGE": possiblece,\n+ "IGG1": possiblecg, "IGG2": possiblecg, "IGG3": possiblecg,\n+ "IGG4": possiblecg,\n+ "IGM": possiblecm\n+ }\n+ with open(args.output, "wt") as output:\n+ output.write("Sequence ID\\tbest_match\\tnt_hit_percentage\\t"\n+ "chunk_hit_percentage\\tstart_locations\\n")\n+ for id, sequence in generate_sequence_and_id_from_summary(args.input):\n+ best_match, subclass_hits, class_hits, start_locations = \\\n+ match_sequence(sequence, compiledregex)\n+ variable_nucs = subclass_vars[best_match]\n+ if variable_nucs:\n+ subclass_percentage = round(subclass_hits * 100 /\n+ variable_nucs)\n+ else:\n+ subclass_percentage = 100\n+ class_percentage = round(class_hits * 100 / class_chunks[best_match])\n+ output.write(f"{id}\\t{best_match}\\t{subclass_percentage}\\t"\n+ f"{class_percentage}\\t{start_locations}\\n")\n \n \n-\n-\n-\n+if __name__ == "__main__":\n+ main()\n' |
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| diff -r f387cc1580c6 -r cf8ad181628f igm_naive_mutations.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/igm_naive_mutations.py Mon Dec 12 12:32:44 2022 +0000 |
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| @@ -0,0 +1,46 @@ +#!/usr/bin/env python3 + +""" +Find naive mutations (< 2% mutated) for IGM genes +""" + +import argparse +import contextlib + + +def find_naive_mutations(mutation_file, naive_file, naive_memory_file, + percentage_cutoff=0.02): + # A compound with statement throws a syntax error with the included python + # 3.7.1 in the container, so use an exit stack instead. + with contextlib.ExitStack() as stack: + mutations = stack.enter_context(open(mutation_file, "rt")) + naive = stack.enter_context(open(naive_file, "wt")) + naive_memory = stack.enter_context(open(naive_memory_file, "wt")) + header = next(mutations) + naive.write(header) + naive_memory.write(header) + for line in mutations: + sequence_id, best_match, mutation_no, region_length, _ = \ + line.strip('\n').split('\t') + if best_match != "IGM": + continue + mutation_no = int(mutation_no) + region_length = int(region_length) + if (mutation_no / region_length) < percentage_cutoff: + naive.write(line) + else: + naive_memory.write(line) + + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument("mutation_file", help="scatter.txt") + parser.add_argument("naive_file") + parser.add_argument("naive_memory_file") + args = parser.parse_args() + find_naive_mutations(args.mutation_file, args.naive_file, + args.naive_memory_file) + + +if __name__ == "__main__": + main() \ No newline at end of file |
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| diff -r f387cc1580c6 -r cf8ad181628f new_imgt.r --- a/new_imgt.r Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,40 +0,0 @@ -args <- commandArgs(trailingOnly = TRUE) - -imgt.dir = args[1] -merged.file = args[2] -gene = args[3] - -merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F, comment.char="", quote="") - -if(!("Sequence.ID" %in% names(merged))){ #change-o db - print("Change-O DB changing 'SEQUENCE_ID' to 'Sequence.ID'") - names(merged)[which(names[merged] == "SEQUENCE_ID")] = "Sequence.ID" -} - -if(gene != "-"){ - merged = merged[grepl(paste("^", gene, sep=""), merged$best_match),] -} - -if("best_match" %in% names(merged)){ - merged = merged[!grepl("unmatched", merged$best_match),] -} - -nrow_dat = 0 - -for(f in list.files(imgt.dir, pattern="*.txt$")){ - #print(paste("filtering", f)) - path = file.path(imgt.dir, f) - dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F, check.names=FALSE, comment.char="") - - dat = dat[dat[,"Sequence ID"] %in% merged$Sequence.ID,] - - nrow_dat = nrow(dat) - - if(nrow(dat) > 0 & grepl("^8_", f)){ #change the FR1 columns to 0 in the "8_..." file - dat[,grepl("^FR1", names(dat))] = 0 - } - - write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T, na="") -} - -print(paste("Creating new zip for ", gene, "with", nrow_dat, "sequences")) |
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| diff -r f387cc1580c6 -r cf8ad181628f nt_overview.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nt_overview.r Mon Dec 12 12:32:44 2022 +0000 |
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| @@ -0,0 +1,74 @@ +args <- commandArgs(trailingOnly = TRUE) + +merged.file = args[1] +outputdir = args[2] +gene.classes = unlist(strsplit(args[3], ",")) +hotspot.analysis.sum.file = args[4] +NToverview.file = paste(outputdir, "ntoverview.txt", sep="/") +empty.region.filter = args[5] + + +setwd(outputdir) + +merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="") +hotspot.analysis.sum = read.table(hotspot.analysis.sum.file, header=F, sep=",", fill=T, stringsAsFactors=F, quote="") + +#ACGT overview + +NToverview = merged + +if(empty.region.filter == "leader"){ + NToverview$seq = paste(NToverview$FR1.IMGT.seq, NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq) +} else if(empty.region.filter == "FR1"){ + NToverview$seq = paste(NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq) +} else if(empty.region.filter == "CDR1"){ + NToverview$seq = paste(NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq) +} else if(empty.region.filter == "FR2"){ + NToverview$seq = paste(NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq) +} + +NToverview$A = nchar(gsub("[^Aa]", "", NToverview$seq)) +NToverview$C = nchar(gsub("[^Cc]", "", NToverview$seq)) +NToverview$G = nchar(gsub("[^Gg]", "", NToverview$seq)) +NToverview$T = nchar(gsub("[^Tt]", "", NToverview$seq)) + +#Nsum = data.frame(Sequence.ID="-", best_match="Sum", seq="-", A = sum(NToverview$A), C = sum(NToverview$C), G = sum(NToverview$G), T = sum(NToverview$T)) + +#NToverview = rbind(NToverview, NTsum) + +NTresult = data.frame(nt=c("A", "C", "T", "G")) + +for(clazz in gene.classes){ + print(paste("class:", clazz)) + NToverview.sub = NToverview[grepl(paste("^", clazz, sep=""), NToverview$best_match),] + print(paste("nrow:", nrow(NToverview.sub))) + new.col.x = c(sum(NToverview.sub$A), sum(NToverview.sub$C), sum(NToverview.sub$T), sum(NToverview.sub$G)) + new.col.y = sum(new.col.x) + new.col.z = round(new.col.x / new.col.y * 100, 2) + + tmp = names(NTresult) + NTresult = cbind(NTresult, data.frame(new.col.x, new.col.y, new.col.z)) + names(NTresult) = c(tmp, paste(clazz, c("x", "y", "z"), sep="")) +} + +NToverview.tmp = NToverview[,c("Sequence.ID", "best_match", "seq", "A", "C", "G", "T")] + +names(NToverview.tmp) = c("Sequence.ID", "best_match", "Sequence of the analysed region", "A", "C", "G", "T") + +write.table(NToverview.tmp, NToverview.file, quote=F, sep="\t", row.names=F, col.names=T) + +NToverview = NToverview[!grepl("unmatched", NToverview$best_match),] + +new.col.x = c(sum(NToverview$A), sum(NToverview$C), sum(NToverview$T), sum(NToverview$G)) +new.col.y = sum(new.col.x) +new.col.z = round(new.col.x / new.col.y * 100, 2) + +tmp = names(NTresult) +NTresult = cbind(NTresult, data.frame(new.col.x, new.col.y, new.col.z)) +names(NTresult) = c(tmp, paste("all", c("x", "y", "z"), sep="")) + +names(hotspot.analysis.sum) = names(NTresult) + +hotspot.analysis.sum = rbind(hotspot.analysis.sum, NTresult) + +write.table(hotspot.analysis.sum, hotspot.analysis.sum.file, quote=F, sep=",", row.names=F, col.names=F, na="0") |
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| diff -r f387cc1580c6 -r cf8ad181628f sequence_overview.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sequence_overview.py Mon Dec 12 12:32:44 2022 +0000 |
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| b'@@ -0,0 +1,257 @@\n+#!/usr/bin/env/python3\n+\n+"""Create a HTML sequence overview"""\n+\n+import argparse\n+import os\n+import typing\n+from collections import defaultdict\n+from pathlib import Path\n+from typing import Dict, Iterable, List\n+\n+\n+class SequenceTableRow(typing.NamedTuple):\n+ sequence_id: str\n+ sequence: str\n+ best_match: str\n+ functionality: str\n+\n+\n+class SequenceStats:\n+ __slots__ = ("counts", "table_rows")\n+\n+ def __init__(self):\n+ self.counts: Dict[str, int] = {\n+ "IGA1": 0,\n+ "IGA2": 0,\n+ "IGE": 0,\n+ "IGG1": 0,\n+ "IGG2": 0,\n+ "IGG3": 0,\n+ "IGG4": 0,\n+ "IGM": 0,\n+ "unmatched": 0}\n+ self.table_rows: List[SequenceTableRow] = []\n+\n+\n+def get_sequence_stats(before_unique: str,\n+ sequence_columns: List[str]):\n+ sequence_statistics = defaultdict(SequenceStats)\n+ with open(before_unique, "rt") as table:\n+ header = next(table)\n+ header_columns = header.strip("\\n").split("\\t")\n+ for line in table:\n+ values = line.strip("\\n").split("\\t")\n+ row_dict = dict(zip(header_columns, values))\n+ sequence = " ".join(row_dict[column] for column in sequence_columns)\n+ best_match = row_dict["best_match"]\n+ original_match = best_match\n+ if best_match.startswith("unmatched"):\n+ best_match = "unmatched"\n+ sequence_statistics[sequence].counts[best_match] += 1\n+ functionality = row_dict["Functionality"]\n+ sequence_statistics[sequence].table_rows.append(\n+ SequenceTableRow(row_dict["Sequence.ID"], sequence,\n+ original_match, functionality))\n+ return sequence_statistics\n+\n+\n+def get_background_color(value: str):\n+ if value in ("TRUE", "T"):\n+ return "#eafaf1"\n+ elif value in ("FALSE", "F"):\n+ return "#f9ebea"\n+ try:\n+ flt = float(value)\n+ except ValueError:\n+ return "white"\n+ if flt > 0:\n+ return "#eaecee"\n+ return "white"\n+\n+\n+def td(val):\n+ return f"<td bgcolor=\'{get_background_color(val)}\'>{val}</td>"\n+\n+\n+def tr(val: Iterable[str]):\n+ return f"<tr>{\'\'.join(td(v) for v in val)}</tr>\\n"\n+\n+\n+def make_link(link, val):\n+ return f"<a href=\'{link}\'>{val}</a>"\n+\n+\n+def tbl(df: Iterable[Iterable[str]]):\n+ return f"<table border=\'1\'>{\'\'.join(tr(v) for v in df)}</table>\\n"\n+\n+\n+def to_bool_str(cond):\n+ return "TRUE" if cond else "FALSE"\n+\n+\n+def sequence_overview(before_unique: str,\n+ outdir: str,\n+ empty_region_filter: str):\n+ os.makedirs(outdir, exist_ok=True)\n+ sequence_columns = [\n+ "FR1.IMGT.seq", "CDR1.IMGT.seq", "FR2.IMGT.seq", "CDR2.IMGT.seq",\n+ "FR3.IMGT.seq", "CDR3.IMGT.seq"]\n+ if empty_region_filter == "leader":\n+ sequence_columns = sequence_columns\n+ elif empty_region_filter == "FR1":\n+ sequence_columns = sequence_columns[1:]\n+ elif empty_region_filter == "CDR1":\n+ sequence_columns = sequence_columns[2:]\n+ elif empty_region_filter == "FR2":\n+ sequence_columns = sequence_columns[3:]\n+ else:\n+ raise ValueError(f"Unknown region filter: {empty_region_filter}")\n+ main_html_file = os.path.join(outdir, "index.html")\n+ by_id_file = os.path.join(outdir, "by_id.html")\n+ with open(main_html_file, "wt") as main_html, open(by_id_file, "wt") as by_id:\n+ main_html.write("<center><img src=\'data:image/png;base64,"\n+ "iVBORw0KGgoAAAANSUhEUgAAAA8AAAAPCAYAAAA71pVKAAAAzElEQ"\n+ "VQoka2TwQ2CQBBFpwTshw4ImW8ogJMlUIMmhNCDxgasAi50oSXA8X"\n+ "lAjCG7aqKTzGX/vsnM31mzR0gk7tTudO5MEizpzvQ4ryUSe408J3X"\n+ "n+grE0p1rnpOamVmWsZG4rS+dzzAMsN8Hi9yyjI1JNGtxu4VxBJgL"\n+ "RLpoTKIPiW0LlwtUVRTubW2OBGUJu92cZRmdfbKQMAw8o+vi5v0fL"\n+ '..b'n sequence_stat.table_rows}\n+ functionality = ",".join(functionality_dict.keys())\n+ links: Dict[str, str] = {}\n+ for key, value in count_dict.items():\n+ name_key = "un" if key == "unmatched" else key\n+ html_file = f"{name_key}_{i}.html"\n+ links[key] = html_file\n+ if value > 0:\n+ rows = [row for row in sequence_stat.table_rows\n+ # Startswith to also get unmatched columns\n+ if row.best_match.startswith(key)]\n+ Path(outdir, html_file).write_text(tbl(rows))\n+ for row in rows:\n+ by_id.write(make_link(html_file, row.sequence_id) + "<br />\\n")\n+ iga_count = count_dict["IGA1"] + count_dict["IGA2"]\n+ igg_count = count_dict["IGG1"] + count_dict["IGG2"] + \\\n+ count_dict["IGG3"] + count_dict["IGG4"]\n+\n+ contained_classes = set(key for key, value\n+ in count_dict.items() if value > 0)\n+ if iga_count:\n+ contained_classes.add("IGA")\n+ if igg_count:\n+ contained_classes.add("IGG")\n+ main_row = [\n+ sequence, functionality,\n+ make_link(links["IGA1"], count_dict["IGA1"]),\n+ make_link(links["IGA2"], count_dict["IGA2"]),\n+ make_link(links["IGG1"], count_dict["IGG1"]),\n+ make_link(links["IGG2"], count_dict["IGG2"]),\n+ make_link(links["IGG3"], count_dict["IGG3"]),\n+ make_link(links["IGG4"], count_dict["IGG4"]),\n+ make_link(links["IGM"], count_dict["IGM"]),\n+ make_link(links["IGE"], count_dict["IGE"]),\n+ make_link(links["unmatched"], count_dict["unmatched"]),\n+ iga_count,\n+ igg_count,\n+ count_dict["IGM"],\n+ count_dict["IGE"],\n+ in_classes,\n+ to_bool_str({"IGA", "IGG"}.issubset(contained_classes)),\n+ to_bool_str({"IGA", "IGG", "IGM"}.issubset(contained_classes)),\n+ to_bool_str({"IGA", "IGG", "IGE"}.issubset(contained_classes)),\n+ to_bool_str({"IGA", "IGG", "IGM", "IGE"}.issubset(contained_classes)),\n+ to_bool_str({"IGA1", "IGA2"}.issubset(contained_classes)),\n+ to_bool_str({"IGG1", "IGG2"}.issubset(contained_classes)),\n+ to_bool_str({"IGG1", "IGG3"}.issubset(contained_classes)),\n+ to_bool_str({"IGG1", "IGG4"}.issubset(contained_classes)),\n+ to_bool_str({"IGG2", "IGG3"}.issubset(contained_classes)),\n+ to_bool_str({"IGG2", "IGG4"}.issubset(contained_classes)),\n+ to_bool_str({"IGG3", "IGG4"}.issubset(contained_classes)),\n+ to_bool_str({"IGG1", "IGG2", "IGG3"}.issubset(contained_classes)),\n+ to_bool_str({"IGG2", "IGG3", "IGG4"}.issubset(contained_classes)),\n+ to_bool_str({"IGG1", "IGG2", "IGG4"}.issubset(contained_classes)),\n+ to_bool_str({"IGG1", "IGG3", "IGG4"}.issubset(contained_classes)),\n+ to_bool_str({"IGG1", "IGG2", "IGG3", "IGG4"}.issubset(contained_classes)),\n+ ]\n+ main_html.write(tr(main_row))\n+ main_html.write("</table>")\n+\n+\n+def argument_parser() -> argparse.ArgumentParser:\n+ parser = argparse.ArgumentParser()\n+ parser.add_argument("--before-unique", help="File with the overview before unique filters")\n+ parser.add_argument("--outdir", help="Output directory")\n+ parser.add_argument("--empty-region-filter")\n+ return parser\n+\n+\n+def main():\n+ args = argument_parser().parse_args()\n+ sequence_overview(args.before_unique,\n+ args.outdir,\n+ args.empty_region_filter)\n+\n+\n+if __name__ == "__main__":\n+ main()\n\\ No newline at end of file\n' |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f sequence_overview.r --- a/sequence_overview.r Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,363 +0,0 @@\n-library(reshape2)\n-\n-args <- commandArgs(trailingOnly = TRUE)\n-\n-before.unique.file = args[1]\n-merged.file = args[2]\n-outputdir = args[3]\n-gene.classes = unlist(strsplit(args[4], ","))\n-hotspot.analysis.sum.file = args[5]\n-NToverview.file = paste(outputdir, "ntoverview.txt", sep="/")\n-NTsum.file = paste(outputdir, "ntsum.txt", sep="/")\n-main.html = "index.html"\n-empty.region.filter = args[6]\n-\n-\n-setwd(outputdir)\n-\n-before.unique = read.table(before.unique.file, header=T, sep="\\t", fill=T, stringsAsFactors=F, quote="")\n-merged = read.table(merged.file, header=T, sep="\\t", fill=T, stringsAsFactors=F, quote="")\n-hotspot.analysis.sum = read.table(hotspot.analysis.sum.file, header=F, sep=",", fill=T, stringsAsFactors=F, quote="")\n-\n-#before.unique = before.unique[!grepl("unmatched", before.unique$best_match),]\n-\n-if(empty.region.filter == "leader"){\n-\tbefore.unique$seq_conc = paste(before.unique$FR1.IMGT.seq, before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq)\n-} else if(empty.region.filter == "FR1"){\n-\tbefore.unique$seq_conc = paste(before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq)\n-} else if(empty.region.filter == "CDR1"){\n-\tbefore.unique$seq_conc = paste(before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq)\n-} else if(empty.region.filter == "FR2"){\n-\tbefore.unique$seq_conc = paste(before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq)\n-}\n-\n-IDs = before.unique[,c("Sequence.ID", "seq_conc", "best_match", "Functionality")]\n-IDs$best_match = as.character(IDs$best_match)\n-\n-dat = data.frame(table(before.unique$seq_conc))\n-\n-names(dat) = c("seq_conc", "Freq")\n-\n-dat$seq_conc = factor(dat$seq_conc)\n-\n-dat = dat[order(as.character(dat$seq_conc)),]\n-\n-#writing html from R...\n-get.bg.color = function(val){\n-\tif(val %in% c("TRUE", "FALSE", "T", "F")){ #if its a logical value, give the background a green/red color\n-\t\treturn(ifelse(val,"#eafaf1","#f9ebea"))\n-\t} else if (!is.na(as.numeric(val))) { #if its a numerical value, give it a grey tint if its >0\n-\t\treturn(ifelse(val > 0,"#eaecee","white"))\n-\t} else {\n-\t\treturn("white")\n-\t}\n-}\n-td = function(val) {\n- return(paste("<td bgcolor=\'", get.bg.color(val), "\'>", val, "</td>", sep=""))\n-}\n-tr = function(val) { \n-\treturn(paste(c("<tr>", sapply(val, td), "</tr>"), collapse="")) \n-}\n-\n-make.link = function(id, clss, val) { \n-\tpaste("<a href=\'", clss, "_", id, ".html\'>", val, "</a>", sep="") \n-}\n-tbl = function(df) {\n-\tres = "<table border=\'1\'>"\n-\tfor(i in 1:nrow(df)){ \n-\t\tres = paste(res, tr(df[i,]), sep="")\n-\t}\n-\tres = paste(res, "</table>")\n-}\n-\n-cat("<center><img src=\'data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAA8AAAAPCAYAAAA71pVKAAAAzElEQVQoka2TwQ2CQBBFpwTshw4ImW8ogJMlUIMmhNCDxgasAi50oSXA8XlAjCG7aqKTzGX/vsnM31mzR0gk7tTudO5MEizpzvQ4ryUSe408J3Xn+grE0p1rnpOamVmWsZG4rS+dzzAMsN8Hi9yyjI1JNGtxu4VxBJgLRLpoTKIPiW0LlwtUVRTubW2OBGUJu92cZRmdfbKQMAw8o+vi5v0fLorZ7Y9waGYJjsf38DJz0O1PsEQffOcv4Sa6YYfDDJ5Obzbsp93+5VfdATueO1fdLdI0AAAAAElFTkSuQmCC\'> Please note that this tab is based on all sequences before filter unique sequences and the remove duplicates based on filters are applied. In this table only sequences occuring more than once are included. </center>", file=main.html, append=F)\n-cat("<table border=\'1\' class=\'pure-table pure-table-striped\'>", file=main.html, append=T)\n-\n-if(empty.region.filter == "leader"){\n-\tcat("<caption>FR1+CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)\n-} else if(empty.region.filter == "FR1"){\n-\tcat("<caption>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)\n-} else if(empty.region.filter == "CDR1"){\n-\tcat("<caption>FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file='..b' & cg3.n > 0 & cg4.n > 0)\n-\t\n-\tin.cg.all = (cg1.n > 0 & cg2.n > 0 & cg3.n > 0 & cg4.n > 0)\n-\t\n-\t#rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, un.html)\n-\trw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, ce.html, un.html)\n-\trw = c(rw, ca.n, cg.n, cm.n, ce.n, in.classes, in.ca.cg, in.ca.cg.cm, in.ca.cg.ce, in.ca.cg.cm.ce, in.ca1.ca2, in.cg1.cg2, in.cg1.cg3, in.cg1.cg4, in.cg2.cg3, in.cg2.cg4, in.cg3.cg4, in.cg1.cg2.cg3, in.cg2.cg3.cg4, in.cg1.cg2.cg4, in.cg1.cg3.cg4, in.cg.all)\n-\t\n-\t\n-\n-\tcat(tr(rw), file=main.html, append=T)\n-\t\n-\t\n-\tfor(i in 1:nrow(allc)){ #generate html by id\n-\t\thtml = make.link(id, allc[i,"best_match"], allc[i,"Sequence.ID"])\n-\t\tcat(paste(html, "<br />"), file=sequence.id.page, append=T)\n-\t}\n-}\n-\n-cat("</table>", file=main.html, append=T)\n-\n-print(paste("Single sequences:", single.sequences))\n-print(paste("Sequences in multiple subclasses:", in.multiple))\n-print(paste("Multiple sequences in one subclass:", multiple.in.one))\n-print(paste("Matched with unmatched:", some.unmatched))\n-print(paste("Count that should match \'matched\' sequences:", matched))\n-\n-#ACGT overview\n-\n-#NToverview = merged[!grepl("^unmatched", merged$best_match),]\n-NToverview = merged\n-\n-if(empty.region.filter == "leader"){\n-\tNToverview$seq = paste(NToverview$FR1.IMGT.seq, NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)\n-} else if(empty.region.filter == "FR1"){\n-\tNToverview$seq = paste(NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)\n-} else if(empty.region.filter == "CDR1"){\n-\tNToverview$seq = paste(NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)\n-} else if(empty.region.filter == "FR2"){\n-\tNToverview$seq = paste(NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)\n-}\n-\n-NToverview$A = nchar(gsub("[^Aa]", "", NToverview$seq))\n-NToverview$C = nchar(gsub("[^Cc]", "", NToverview$seq))\n-NToverview$G = nchar(gsub("[^Gg]", "", NToverview$seq))\n-NToverview$T = nchar(gsub("[^Tt]", "", NToverview$seq))\n-\n-#Nsum = data.frame(Sequence.ID="-", best_match="Sum", seq="-", A = sum(NToverview$A), C = sum(NToverview$C), G = sum(NToverview$G), T = sum(NToverview$T))\n-\n-#NToverview = rbind(NToverview, NTsum)\n-\n-NTresult = data.frame(nt=c("A", "C", "T", "G"))\n-\n-for(clazz in gene.classes){\n-\tprint(paste("class:", clazz))\n-\tNToverview.sub = NToverview[grepl(paste("^", clazz, sep=""), NToverview$best_match),]\n-\tprint(paste("nrow:", nrow(NToverview.sub)))\n-\tnew.col.x = c(sum(NToverview.sub$A), sum(NToverview.sub$C), sum(NToverview.sub$T), sum(NToverview.sub$G))\n-\tnew.col.y = sum(new.col.x)\n-\tnew.col.z = round(new.col.x / new.col.y * 100, 2)\n-\t\n-\ttmp = names(NTresult)\n-\tNTresult = cbind(NTresult, data.frame(new.col.x, new.col.y, new.col.z))\n-\tnames(NTresult) = c(tmp, paste(clazz, c("x", "y", "z"), sep=""))\n-}\n-\n-NToverview.tmp = NToverview[,c("Sequence.ID", "best_match", "seq", "A", "C", "G", "T")]\n-\n-names(NToverview.tmp) = c("Sequence.ID", "best_match", "Sequence of the analysed region", "A", "C", "G", "T")\n-\n-write.table(NToverview.tmp, NToverview.file, quote=F, sep="\\t", row.names=F, col.names=T)\n-\n-NToverview = NToverview[!grepl("unmatched", NToverview$best_match),]\n-\n-new.col.x = c(sum(NToverview$A), sum(NToverview$C), sum(NToverview$T), sum(NToverview$G))\n-new.col.y = sum(new.col.x)\n-new.col.z = round(new.col.x / new.col.y * 100, 2)\n-\n-tmp = names(NTresult)\n-NTresult = cbind(NTresult, data.frame(new.col.x, new.col.y, new.col.z))\n-names(NTresult) = c(tmp, paste("all", c("x", "y", "z"), sep=""))\n-\n-names(hotspot.analysis.sum) = names(NTresult)\n-\n-hotspot.analysis.sum = rbind(hotspot.analysis.sum, NTresult)\n-\n-write.table(hotspot.analysis.sum, hotspot.analysis.sum.file, quote=F, sep=",", row.names=F, col.names=F, na="0")\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n' |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f shm_csr.xml --- a/shm_csr.xml Wed Feb 02 10:57:36 2022 +0000 +++ b/shm_csr.xml Mon Dec 12 12:32:44 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="shm_csr" name="SHM & CSR pipeline" version="1.5.0"> +<tool id="shm_csr" name="SHM & CSR pipeline" version="1.6.0"> <description></description> <requirements> <requirement type="package" version="3.7.1">python</requirement> @@ -89,7 +89,7 @@ <when value="yes"></when> <when value="no"></when> </conditional> - <param name="fast" type="select" label="Fast" help="Skips generating the new ZIP files and Change-O/Baseline" > + <param name="fast" type="select" label="Fast" help="Skips Change-O/Baseline" > <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f split_imgt_file.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/split_imgt_file.py Mon Dec 12 12:32:44 2022 +0000 |
| [ |
| @@ -0,0 +1,147 @@ +#!/usr/bin/env python3 + +""" +Script to split IMGT file into several archives for each of the genes + +Rather than creating each new archive individually this script will read +the input files only once and as such enormously shorten processing time. +""" + +import argparse +import io +import os +import tarfile +import tempfile +from typing import Iterator, List, Tuple + + +def merged_txt_to_match_dict(merged: str): + with open(merged, "rt") as f: + header = next(f).strip("\n") + column_names = header.split("\t") + # For the baseline result there is no best_match column + if "best_match" in column_names: + best_match_index = column_names.index("best_match") + else: + best_match_index = None + sequence_id_index = column_names.index("Sequence.ID") + match_dict = {} + for line in f: + values = line.strip().split("\t") + sequence_id = values[sequence_id_index] + if best_match_index is not None: + best_match = values[best_match_index] + if "unmatched" in best_match: + # For some reason the table has values such as: unmatched, IGA2 + continue + else: + best_match = "" + match_dict[sequence_id] = best_match + return match_dict + + +def imgt_to_tables(imgt_file: str) -> Iterator[Tuple[str, io.TextIOWrapper]]: + print(f"opening IMGT file: {imgt_file}") + with tarfile.open(imgt_file, "r") as archive: + while True: + member = archive.next() + if member is None: + return + if member.name in {"README.txt"}: + continue + if member.name.startswith("11_"): + continue + f = archive.extractfile(member) + f_text = io.TextIOWrapper(f) + yield member.name, f_text + f_text.close() + + +def split_imgt(imgt_file: str, merged_file: str, outdir: str, genes: List[str], + prefix: str): + """ + This function creates a separate tar file for each of the gene matches + based on the merged file. Unmatched genes are left out. + :param imgt_file: The original IMGT file + :param merged_file: The merged data file generated by SHM&CSR pipeline + :param outdir: The output directory. + :param genes: The genes to split out. Use '-' for all identified genes. + :return: + """ + match_dict = merged_txt_to_match_dict(merged_file) + gene_tarfiles = [] + os.makedirs(outdir, exist_ok=True) + for gene in genes: + new_filename = f"{prefix}_{gene}.txz" if gene else f"{prefix}.txz" + gene_tarfiles.append( + tarfile.open(os.path.join(outdir, new_filename), mode="w:xz") + ) + for name, table in imgt_to_tables(imgt_file): + # Read each table one by one and per line select in which output + # files it should go. + gene_files = [] + for gene in genes: + fp, fname = tempfile.mkstemp() + # The file pointer fp will be wrapped in a python file object + # so we can ensure there remain no open files. + f = open(fp, mode="wt") + gene_files.append((gene, f, fname)) + header = next(table) + header_number_of_tabs = header.count('\t') + column_names = header.strip("\n").split("\t") + fr1_columns = [index for index, column in enumerate(column_names) + if column.startswith("FR1")] + sequence_id_index = column_names.index("Sequence ID") + for _, gene_file, _ in gene_files: + gene_file.write(header) + for line in table: + # IMGT sometimes delivers half-empty rows. + row_number_of_tabs = line.count("\t") + missing_tabs = header_number_of_tabs - row_number_of_tabs + if missing_tabs: + line = line.strip("\n") + missing_tabs * "\t" + "\n" + values = line.strip("\n").split("\t") + sequence_id = values[sequence_id_index] + match = match_dict.get(sequence_id) + if match is None: + continue + if name.startswith("8_"): + # change the FR1 columns to 0 in the "8_..." file + for index in fr1_columns: + values[index] = "0" + line = "\t".join(values) + "\n" + for gene, gene_file, _ in gene_files: + if gene in match: + gene_file.write(line) + for gene_tarfile, (_, gene_file, fname) in zip(gene_tarfiles, gene_files): + gene_file.flush() + gene_tarfile.add(fname, name) + gene_file.close() + os.remove(fname) + for gene_tarfile in gene_tarfiles: + gene_tarfile.close() + + +def argument_parser() -> argparse.ArgumentParser: + parser = argparse.ArgumentParser() + parser.add_argument("imgt_file", help="The original IMGT FILE") + parser.add_argument("merged", help="merged.txt file") + parser.add_argument("--outdir", help="output directory") + parser.add_argument( + "genes", + nargs="+", + help="The genes to split out. Use '-' for all identified genes.") + parser.add_argument("--prefix", help="Prefix for the archives and " + "directories") + return parser + + +def main(): + args = argument_parser().parse_args() + genes = ["" if gene == "-" else gene for gene in args.genes] + split_imgt(args.imgt_file, args.merged, args.outdir, genes, + args.prefix) + + +if __name__ == "__main__": + main() |
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| @@ -1,5 +0,0 @@ -Gene Freq label -IGG1 274 IGG1 - 274 -IGG2 150 IGG2 - 150 -IGG3 26 IGG3 - 26 -IGG4 19 IGG4 - 19 |
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| @@ -1,1 +0,0 @@ -469 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/IGG_sum_value.txt --- a/test-output/IGG_sum_value.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -9036 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/IGM_mean_n.txt --- a/test-output/IGM_mean_n.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -1 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/IGM_mean_value.txt --- a/test-output/IGM_mean_value.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -0 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/IGM_median_n.txt --- a/test-output/IGM_median_n.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -1 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/IGM_median_value.txt --- a/test-output/IGM_median_value.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -0 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/IGM_sum_n.txt --- a/test-output/IGM_sum_n.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -1 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/IGM_sum_value.txt --- a/test-output/IGM_sum_value.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -0 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/aa_id_mutations.txt --- a/test-output/aa_id_mutations.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1577 +0,0 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2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01A09OY\tIGA2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t1\t0\t0\t1\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01A0C2Y\tIGG1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t1\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t1\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0'..b'\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\n-JY8QFUQ01DG2P7\tunmatched, IGA2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DG5KX\tunmatched, IGA2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DG6GC\tunmatched, IGA2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t2\t1\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DHXHT\tunmatched, IGG1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t1\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t1\t0\t2\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DI39D\tunmatched, IGA1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DIBNC\tunmatched, IGG1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DJFIZ\tunmatched, IGG1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t3\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t1\t2\t3\t3\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t2\t0\t0\t1\t2\t0\t0\t0\t2\t0\t0\t0\n-JY8QFUQ01DLDLD\tunmatched, IGA1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DMF0A\tunmatched, IGA1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t3\t0\t2\t2\t1\t2\t0\t0\t0\t0\t0\t2\t1\t0\t0\t0\t0\t0\t0\t0\t2\t2\t1\t2\t2\t0\t0\t0\t0\t3\t0\t2\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t1\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t1\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t1\t0\n-JY8QFUQ01DOVL5\tunmatched, IGA2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t1\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DPT8R\tunmatched, IGA2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DUD3U\tunmatched, IGA2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t3\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t2\t2\t0\t0\t0\t0\t1\t1\t0\t1\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DV4HU\tunmatched, IGG2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t2\t1\t0\t0\t0\t2\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DV8LF\tunmatched, IGA2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DVBU0\tunmatched, IGA2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t2\t0\t0\t0\t1\t2\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DXDOM\tunmatched, IGA2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t1\t2\t1\t1\t1\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t0\t0\t2\t1\t1\t1\t0\t0\t0\t1\t2\t2\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t1\t0\t0\t0\t0\n' |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/absent_aa_id.txt --- a/test-output/absent_aa_id.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1577 +0,0 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1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01A09OY\t8\t8\tIGA2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01A0C2Y\t8\t8\tIGG1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1'..b'1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DG2P7\t8\t7\tunmatched, IGA2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DG5KX\t8\t7\tunmatched, IGA2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DG6GC\t8\t8\tunmatched, IGA2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DHXHT\t10\t7\tunmatched, IGG1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DI39D\t8\t8\tunmatched, IGA1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DIBNC\t10\t7\tunmatched, IGG1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DJFIZ\t8\t8\tunmatched, IGG1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DLDLD\t8\t8\tunmatched, IGA1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DMF0A\t10\t7\tunmatched, IGA1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DOVL5\t8\t8\tunmatched, IGA2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DPT8R\t8\t7\tunmatched, IGA2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DUD3U\t8\t8\tunmatched, IGA2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DV4HU\t8\t8\tunmatched, IGG2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DV8LF\t8\t8\tunmatched, IGA2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DVBU0\t8\t7\tunmatched, IGA2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n-JY8QFUQ01DXDOM\t8\t7\tunmatched, IGA2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n' |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/all_mean_n.txt --- a/test-output/all_mean_n.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -1387 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/all_mean_value.txt --- a/test-output/all_mean_value.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -19.5 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/all_median_n.txt --- a/test-output/all_median_n.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -1387 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/all_median_value.txt --- a/test-output/all_median_value.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -18 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/all_sum_n.txt --- a/test-output/all_sum_n.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -1387 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/all_sum_value.txt --- a/test-output/all_sum_value.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -27013 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/hotspot_analysis_mean.txt --- a/test-output/hotspot_analysis_mean.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -RGYW (%),3,19.6,15.3,4,20.6,19.4,3,17.8,16.9,3,19.3,15.5,3,20.0,15.0,3,18.5,16.2,2,14.9,13.4,3,19.9,15.1,0,0,0,0,0,0,3,18.4,16.3,3,19.5,15.4 -WRCY (%),3,19.6,15.3,4,20.6,19.4,3,17.8,16.9,3,19.3,15.5,3,20.0,15.0,3,18.5,16.2,2,14.9,13.4,3,19.9,15.1,0,0,0,0,0,0,3,18.4,16.3,3,19.5,15.4 -WA (%),3,19.6,15.3,3,20.6,14.6,3,17.8,16.9,3,19.3,15.5,3,20.0,15.0,3,18.5,16.2,3,14.9,20.1,3,19.9,15.1,0,0,0,0,0,0,3,18.4,16.3,3,19.5,15.4 -TW (%),2,19.6,10.2,2,20.6,9.7,2,17.8,11.2,2,19.3,10.4,2,20.0,10.0,2,18.5,10.8,1,14.9,6.7,2,19.9,10.1,0,0,0,0,0,0,2,18.4,10.9,2,19.5,10.3 |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/hotspot_analysis_median.txt --- a/test-output/hotspot_analysis_median.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -RGYW (%),3,19.0,15.8,3,20.0,15.0,2,16.5,12.1,3,18.0,16.7,3,18.0,16.7,3,17.0,17.6,2,13.5,14.8,3,18.0,16.7,0,0,0,0,0,0,2,16.0,12.5,3,18.0,16.7 -WRCY (%),3,19.0,15.8,3,20.0,15.0,3,16.5,18.2,3,18.0,16.7,3,18.0,16.7,3,17.0,17.6,1,13.5,7.4,2,18.0,11.1,0,0,0,0,0,0,3,16.0,18.8,3,18.0,16.7 -WA (%),3,19.0,15.8,3,20.0,15.0,2,16.5,12.1,3,18.0,16.7,3,18.0,16.7,3,17.0,17.6,3,13.5,22.2,2,18.0,11.1,0,0,0,0,0,0,2,16.0,12.5,3,18.0,16.7 -TW (%),2,19.0,10.5,2,20.0,10.0,1,16.5,6.1,2,18.0,11.1,2,18.0,11.1,2,17.0,11.8,1,13.5,7.4,2,18.0,11.1,0,0,0,0,0,0,2,16.0,12.5,2,18.0,11.1 |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/hotspot_analysis_sum.txt --- a/test-output/hotspot_analysis_sum.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -RGYW (%),3163,17977.0,17.6,2186,12223.0,17.9,978,5754.0,17.0,1524,9036.0,16.9,910,5492.0,16.6,485,2777.0,17.5,63,388.0,16.2,65,379.0,17.2,0,0,0,0,0,0,602,3486.0,17.3,4686,27013.0,17.3 -WRCY (%),2984,17977.0,16.6,2060,12223.0,16.9,924,5754.0,16.1,1444,9036.0,16.0,888,5492.0,16.2,455,2777.0,16.4,52,388.0,13.4,50,379.0,13.2,0,0,0,0,0,0,614,3486.0,17.6,4428,27013.0,16.4 -WA (%),2610,17977.0,14.5,1715,12223.0,14.0,895,5754.0,15.6,1420,9036.0,15.7,859,5492.0,15.6,433,2777.0,15.6,67,388.0,17.3,61,379.0,16.1,0,0,0,0,0,0,540,3486.0,15.5,4030,27013.0,14.9 -TW (%),1561,17977.0,8.7,1044,12223.0,8.5,517,5754.0,9.0,818,9036.0,9.1,474,5492.0,8.6,265,2777.0,9.5,34,388.0,8.8,46,379.0,12.1,0,0,0,0,0,0,330,3486.0,9.5,2379,27013.0,8.8 |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/motif_per_seq.txt --- a/test-output/motif_per_seq.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1577 +0,0 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|
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/mutation_by_id.txt --- a/test-output/mutation_by_id.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1577 +0,0 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6\t10\t3\t3\t1'..b'\t6\t9\t5\t1\t4\t5\t0\t6\n-JY8QFUQ01BCZ6T\t18\t210\t9\t9\t7\t2\t3\t6\t0\t9\n-JY8QFUQ01BDHSG\t12\t213\t7\t5\t5\t2\t4\t4\t0\t4\n-JY8QFUQ01BF6IL\t10\t213\t7\t3\t3\t4\t2\t3\t0\t5\n-JY8QFUQ01BG2KZ\t17\t213\t10\t7\t3\t7\t0\t9\t2\t6\n-JY8QFUQ01BG9LH\t19\t213\t15\t4\t8\t7\t4\t7\t1\t7\n-JY8QFUQ01BGU0C\t20\t210\t11\t9\t8\t3\t3\t8\t0\t9\n-JY8QFUQ01BHYPA\t9\t213\t6\t3\t3\t3\t1\t4\t1\t3\n-JY8QFUQ01BJC1Y\t8\t213\t5\t3\t2\t3\t1\t2\t0\t5\n-JY8QFUQ01BKLR9\t20\t213\t8\t12\t6\t2\t5\t4\t5\t6\n-JY8QFUQ01BLF36\t38\t213\t21\t17\t10\t11\t6\t21\t3\t8\n-JY8QFUQ01BLJYE\t35\t213\t18\t17\t9\t9\t6\t19\t0\t10\n-JY8QFUQ01BLLRQ\t12\t213\t9\t3\t3\t6\t2\t3\t2\t5\n-JY8QFUQ01BM2SX\t26\t213\t19\t7\t10\t9\t6\t13\t1\t6\n-JY8QFUQ01BM631\t10\t213\t7\t3\t2\t5\t0\t6\t1\t3\n-JY8QFUQ01BMPYC\t19\t213\t12\t7\t9\t3\t4\t10\t0\t5\n-JY8QFUQ01BMULR\t13\t213\t10\t3\t7\t3\t3\t3\t1\t6\n-JY8QFUQ01BNJBB\t27\t210\t15\t12\t8\t7\t7\t12\t4\t4\n-JY8QFUQ01BNJGF\t28\t213\t18\t10\t13\t5\t6\t13\t2\t7\n-JY8QFUQ01BP3M1\t14\t213\t10\t4\t6\t4\t2\t5\t2\t5\n-JY8QFUQ01BPT8C\t16\t216\t8\t8\t3\t5\t3\t6\t0\t7\n-JY8QFUQ01BPXZS\t31\t216\t19\t12\t12\t7\t7\t14\t5\t5\n-JY8QFUQ01BR9V1\t8\t213\t4\t4\t2\t2\t1\t4\t1\t2\n-JY8QFUQ01BRGSI\t9\t213\t7\t2\t2\t5\t2\t3\t0\t4\n-JY8QFUQ01BRNFF\t17\t213\t12\t5\t9\t3\t6\t7\t2\t2\n-JY8QFUQ01BSGO4\t11\t213\t5\t6\t4\t1\t1\t4\t0\t6\n-JY8QFUQ01BT0O2\t19\t213\t12\t7\t8\t4\t4\t7\t1\t7\n-JY8QFUQ01BT4AX\t11\t213\t8\t3\t5\t3\t2\t5\t0\t4\n-JY8QFUQ01BT86M\t10\t213\t7\t3\t4\t3\t2\t3\t1\t4\n-JY8QFUQ01BTQAH\t26\t213\t12\t14\t7\t5\t3\t9\t1\t13\n-JY8QFUQ01BURMR\t36\t213\t21\t15\t7\t14\t5\t18\t3\t10\n-JY8QFUQ01BV9YG\t22\t213\t13\t9\t5\t8\t5\t6\t1\t10\n-JY8QFUQ01BW9QL\t9\t213\t6\t3\t5\t1\t1\t2\t1\t5\n-JY8QFUQ01BWI2D\t29\t213\t17\t12\t11\t6\t6\t13\t2\t8\n-JY8QFUQ01BXYLF\t15\t213\t9\t6\t7\t2\t3\t9\t0\t3\n-JY8QFUQ01BY231\t19\t216\t11\t8\t7\t4\t3\t11\t0\t5\n-JY8QFUQ01BYGN8\t20\t213\t13\t7\t8\t5\t5\t8\t2\t5\n-JY8QFUQ01C2NGE\t15\t210\t10\t5\t3\t7\t6\t4\t1\t4\n-JY8QFUQ01C2ROO\t7\t213\t3\t4\t2\t1\t2\t2\t1\t2\n-JY8QFUQ01C3QHH\t13\t213\t8\t5\t4\t4\t2\t6\t1\t4\n-JY8QFUQ01C4MHW\t11\t213\t5\t6\t4\t1\t3\t5\t0\t3\n-JY8QFUQ01C5Q2O\t16\t213\t5\t11\t2\t3\t3\t4\t0\t9\n-JY8QFUQ01C8QWZ\t11\t213\t4\t7\t3\t1\t0\t4\t1\t6\n-JY8QFUQ01C92F8\t13\t222\t9\t4\t5\t4\t2\t6\t0\t5\n-JY8QFUQ01C966Y\t10\t213\t4\t6\t1\t3\t2\t3\t0\t5\n-JY8QFUQ01C98A9\t11\t213\t8\t3\t6\t2\t3\t3\t1\t4\n-JY8QFUQ01CANL1\t20\t213\t13\t7\t7\t6\t4\t5\t0\t11\n-JY8QFUQ01CD8ZK\t30\t213\t20\t10\t8\t12\t8\t10\t1\t11\n-JY8QFUQ01CD9VK\t15\t213\t9\t6\t7\t2\t2\t4\t0\t9\n-JY8QFUQ01CDZ5R\t23\t212\t16\t7\t8\t8\t5\t12\t2\t4\n-JY8QFUQ01CE8P9\t18\t213\t13\t5\t8\t5\t6\t10\t1\t1\n-JY8QFUQ01CF06T\t12\t213\t8\t4\t5\t3\t4\t3\t1\t4\n-JY8QFUQ01CG8U2\t18\t210\t11\t7\t8\t3\t5\t5\t1\t7\n-JY8QFUQ01CGLTX\t15\t219\t9\t6\t7\t2\t1\t9\t1\t4\n-JY8QFUQ01CGQFF\t21\t213\t13\t8\t8\t5\t4\t7\t2\t8\n-JY8QFUQ01CHDDF\t23\t219\t11\t12\t8\t3\t4\t9\t1\t9\n-JY8QFUQ01CHKLB\t8\t213\t5\t3\t2\t3\t1\t4\t1\t2\n-JY8QFUQ01CHW93\t13\t213\t7\t6\t5\t2\t3\t4\t2\t4\n-JY8QFUQ01CII5W\t30\t210\t15\t15\t3\t12\t6\t11\t1\t12\n-JY8QFUQ01CINZT\t5\t213\t2\t3\t0\t2\t0\t1\t1\t3\n-JY8QFUQ01CJLXK\t22\t213\t12\t10\t9\t3\t6\t9\t0\t7\n-JY8QFUQ01CJT9B\t31\t213\t18\t13\t10\t8\t5\t16\t3\t7\n-JY8QFUQ01CK1VY\t28\t216\t19\t9\t12\t7\t7\t14\t2\t5\n-JY8QFUQ01CKN3U\t25\t213\t17\t8\t8\t9\t4\t9\t4\t8\n-JY8QFUQ01CLP4K\t14\t213\t7\t7\t5\t2\t5\t4\t0\t5\n-JY8QFUQ01CNCW4\t10\t213\t5\t5\t3\t2\t2\t2\t0\t6\n-JY8QFUQ01CO019\t16\t213\t10\t6\t5\t5\t5\t5\t0\t6\n-JY8QFUQ01CPVUP\t25\t213\t11\t14\t8\t3\t6\t10\t2\t7\n-JY8QFUQ01CPYJ0\t14\t213\t7\t7\t6\t1\t3\t5\t0\t6\n-JY8QFUQ01CQH14\t14\t213\t11\t3\t8\t3\t2\t5\t2\t5\n-JY8QFUQ01CST8T\t17\t213\t10\t7\t6\t4\t2\t4\t1\t10\n-JY8QFUQ01CU1XI\t17\t209\t8\t9\t5\t3\t6\t6\t0\t5\n-JY8QFUQ01CU5CB\t20\t213\t13\t7\t9\t4\t5\t7\t2\t6\n-JY8QFUQ01CUGFD\t30\t213\t13\t17\t8\t5\t6\t10\t2\t12\n-JY8QFUQ01CURPS\t32\t213\t20\t12\t16\t4\t7\t17\t3\t5\n-JY8QFUQ01CY2WW\t12\t213\t6\t6\t2\t4\t3\t5\t0\t4\n-JY8QFUQ01CY6MC\t16\t213\t9\t7\t6\t3\t2\t7\t0\t7\n-JY8QFUQ01CYWC2\t12\t213\t7\t5\t4\t3\t1\t3\t2\t6\n-JY8QFUQ01DA9FW\t13\t213\t9\t4\t6\t3\t3\t6\t2\t2\n-JY8QFUQ01DA9S4\t0\t216\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DC4QI\t21\t213\t12\t9\t7\t5\t5\t9\t2\t5\n-JY8QFUQ01DC8OC\t26\t210\t11\t15\t4\t7\t4\t13\t0\t9\n-JY8QFUQ01DCPGQ\t19\t213\t14\t5\t6\t8\t7\t6\t1\t5\n-JY8QFUQ01DEKWC\t17\t213\t6\t11\t5\t1\t2\t8\t1\t6\n-JY8QFUQ01DG2P7\t11\t211\t4\t7\t3\t1\t0\t4\t1\t6\n-JY8QFUQ01DG5KX\t21\t210\t11\t10\t8\t3\t6\t5\t4\t6\n-JY8QFUQ01DG6GC\t15\t213\t6\t9\t2\t4\t1\t6\t2\t6\n-JY8QFUQ01DHXHT\t20\t216\t10\t10\t4\t6\t2\t10\t2\t6\n-JY8QFUQ01DI39D\t8\t213\t4\t4\t3\t1\t2\t2\t0\t4\n-JY8QFUQ01DIBNC\t0\t216\t0\t0\t0\t0\t0\t0\t0\t0\n-JY8QFUQ01DJFIZ\t43\t213\t23\t20\t12\t11\t8\t15\t5\t15\n-JY8QFUQ01DLDLD\t7\t213\t4\t3\t2\t2\t1\t3\t0\t3\n-JY8QFUQ01DMF0A\t53\t216\t27\t26\t12\t15\t10\t22\t2\t19\n-JY8QFUQ01DOVL5\t15\t213\t10\t5\t6\t4\t1\t4\t2\t8\n-JY8QFUQ01DPT8R\t8\t212\t4\t4\t1\t3\t4\t2\t0\t2\n-JY8QFUQ01DUD3U\t29\t213\t18\t11\t12\t6\t7\t9\t2\t11\n-JY8QFUQ01DV4HU\t22\t213\t14\t8\t8\t6\t5\t10\t2\t5\n-JY8QFUQ01DV8LF\t6\t213\t1\t5\t0\t1\t2\t1\t0\t3\n-JY8QFUQ01DVBU0\t15\t212\t6\t9\t2\t4\t3\t4\t1\t7\n-JY8QFUQ01DXDOM\t36\t210\t22\t14\t12\t10\t7\t12\t0\t17\n' |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/shm_overview_tandem_row.txt --- a/test-output/shm_overview_tandem_row.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -Tandems/Expected (ratio),2438,1921.45,1.27,1680,1360.14,1.24,758,561.32,1.35,1212,959.09,1.26,769,603.44,1.27,357,273.25,1.31,43,38.75,1.11,43,43.64,0.99,0,0.0,0,0,0.0,0,482,349.88,1.38,3650,2880.54,1.27 |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/tandem_frequency.txt --- a/test-output/tandem_frequency.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -2 3292 -3 652 -4 143 -5 27 -6 11 -7 3 -8 2 -9 1 -10 1 |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/tandems_by_id.txt --- a/test-output/tandems_by_id.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1553 +0,0 @@\n-Sequence.ID\tnumber_of_mutations\tnumber_of_tandems\tregion_length\texpected_tandems\tlongest_tandem\ttandems\n-JY8QFUQ01A0005\t18\t1\t216\t1.42\t2\t[(147, 2)]\n-JY8QFUQ01A004N\t20\t3\t216\t1.76\t3\t[(106, 3), (164, 2), (275, 2)]\n-JY8QFUQ01A006G\t32\t4\t216\t4.59\t2\t[(106, 2), (205, 2), (220, 2), (251, 2)]\n-JY8QFUQ01A018V\t31\t5\t216\t4.31\t5\t[(104, 5), (119, 2), (237, 2), (254, 2), (301, 3)]\n-JY8QFUQ01A019O\t19\t2\t213\t1.61\t2\t[(104, 2), (254, 2)]\n-JY8QFUQ01A01KX\t29\t4\t213\t3.81\t3\t[(119, 2), (189, 3), (253, 3), (263, 3)]\n-JY8QFUQ01A0207\t16\t2\t213\t1.13\t2\t[(188, 2), (257, 2)]\n-JY8QFUQ01A02HL\t13\t0\t213\t0.73\t0\t[]\n-JY8QFUQ01A02KS\t14\t2\t213\t0.85\t2\t[(119, 2), (171, 2)]\n-JY8QFUQ01A02XZ\t10\t1\t213\t0.42\t2\t[(89, 2)]\n-JY8QFUQ01A03E3\t21\t3\t213\t1.97\t4\t[(172, 3), (189, 3), (196, 4)]\n-JY8QFUQ01A03N6\t39\t5\t213\t6.96\t2\t[(107, 2), (110, 2), (191, 2), (229, 2), (244, 2)]\n-JY8QFUQ01A0939\t15\t1\t222\t0.95\t2\t[(190, 2)]\n-JY8QFUQ01A09OY\t12\t0\t213\t0.62\t0\t[]\n-JY8QFUQ01A0C2Y\t18\t2\t213\t1.44\t2\t[(104, 2), (194, 2)]\n-JY8QFUQ01A0C33\t13\t0\t213\t0.73\t0\t[]\n-JY8QFUQ01A0C4X\t13\t2\t213\t0.73\t3\t[(103, 3), (107, 2)]\n-JY8QFUQ01A0D2K\t10\t0\t213\t0.42\t0\t[]\n-JY8QFUQ01A0D5E\t28\t5\t212\t3.57\t6\t[(87, 2), (172, 6), (190, 2), (258, 2), (301, 2)]\n-JY8QFUQ01A0DA8\t23\t2\t213\t2.38\t3\t[(103, 3), (301, 3)]\n-JY8QFUQ01A0DCS\t22\t3\t213\t2.17\t3\t[(85, 3), (107, 2), (192, 2)]\n-JY8QFUQ01A0EF3\t12\t1\t213\t0.62\t3\t[(106, 3)]\n-JY8QFUQ01A0ESJ\t17\t2\t213\t1.28\t2\t[(185, 2), (286, 2)]\n-JY8QFUQ01A0FII\t26\t1\t213\t3.05\t4\t[(171, 4)]\n-JY8QFUQ01A0FO5\t11\t2\t213\t0.52\t2\t[(196, 2), (300, 2)]\n-JY8QFUQ01A0GVR\t24\t3\t216\t2.56\t2\t[(106, 2), (171, 2), (275, 2)]\n-JY8QFUQ01A0GVY\t30\t3\t213\t4.08\t2\t[(187, 2), (192, 2), (255, 2)]\n-JY8QFUQ01A0IZI\t18\t4\t213\t1.44\t2\t[(86, 2), (164, 2), (187, 2), (190, 2)]\n-JY8QFUQ01A0LAJ\t29\t3\t219\t3.71\t3\t[(177, 2), (185, 3), (244, 2)]\n-JY8QFUQ01A0LBC\t31\t7\t213\t4.37\t4\t[(85, 2), (162, 2), (172, 2), (189, 2), (194, 4), (247, 2), (258, 2)]\n-JY8QFUQ01A0LEW\t9\t1\t213\t0.34\t2\t[(228, 2)]\n-JY8QFUQ01A0LZ5\t20\t4\t213\t1.78\t2\t[(108, 2), (163, 2), (173, 2), (184, 2)]\n-JY8QFUQ01A0N8H\t13\t0\t222\t0.70\t0\t[]\n-JY8QFUQ01A0OC8\t12\t0\t212\t0.62\t0\t[]\n-JY8QFUQ01A0OMH\t26\t2\t213\t3.05\t3\t[(103, 3), (150, 2)]\n-JY8QFUQ01A0OTP\t15\t0\t209\t1.00\t0\t[]\n-JY8QFUQ01A0RJS\t17\t2\t212\t1.28\t2\t[(104, 2), (194, 2)]\n-JY8QFUQ01A0S1H\t16\t1\t213\t1.13\t3\t[(105, 3)]\n-JY8QFUQ01A0TAV\t12\t1\t213\t0.62\t2\t[(162, 2)]\n-JY8QFUQ01A0TNI\t24\t1\t213\t2.59\t2\t[(192, 2)]\n-JY8QFUQ01A0UZS\t20\t2\t213\t1.78\t3\t[(118, 3), (190, 2)]\n-JY8QFUQ01A0VIE\t23\t3\t213\t2.38\t2\t[(106, 2), (209, 2), (254, 2)]\n-JY8QFUQ01A0WDV\t18\t3\t210\t1.46\t2\t[(119, 2), (165, 2), (172, 2)]\n-JY8QFUQ01A0WZB\t34\t4\t210\t5.34\t4\t[(165, 2), (174, 3), (191, 3), (300, 4)]\n-JY8QFUQ01A0X8W\t10\t0\t213\t0.42\t0\t[]\n-JY8QFUQ01A0XE3\t27\t4\t211\t3.33\t3\t[(119, 2), (189, 3), (253, 3), (263, 3)]\n-JY8QFUQ01A0Z64\t9\t0\t213\t0.34\t0\t[]\n-JY8QFUQ01A0ZW5\t27\t3\t216\t3.25\t3\t[(142, 2), (187, 3), (197, 2)]\n-JY8QFUQ01A0ZX6\t12\t0\t213\t0.62\t0\t[]\n-JY8QFUQ01A110D\t14\t0\t213\t0.85\t0\t[]\n-JY8QFUQ01A12BY\t14\t2\t213\t0.85\t4\t[(107, 2), (194, 4)]\n-JY8QFUQ01A12KV\t29\t5\t213\t3.81\t2\t[(86, 2), (104, 2), (118, 2), (159, 2), (276, 2)]\n-JY8QFUQ01A12V0\t28\t5\t213\t3.55\t3\t[(107, 2), (151, 3), (172, 2), (233, 2), (258, 2)]\n-JY8QFUQ01A14EE\t30\t5\t213\t4.08\t4\t[(104, 2), (164, 2), (173, 4), (188, 2), (196, 2)]\n-JY8QFUQ01A152R\t19\t2\t213\t1.61\t3\t[(107, 2), (172, 3)]\n-JY8QFUQ01A15L6\t31\t6\t215\t4.33\t3\t[(145, 3), (165, 2), (173, 3), (192, 3), (239, 2), (275, 2)]\n-JY8QFUQ01A15SR\t48\t8\t216\t10.44\t10\t[(79, 2), (82, 10), (100, 3), (110, 7), (118, 2), (135, 2), (155, 2), (275, 2)]\n-JY8QFUQ01A17D9\t17\t1\t213\t1.28\t2\t[(165, 2)]\n-JY8QFUQ01A17TV\t14\t0\t210\t0.87\t0\t[]\n-JY8QFUQ01A18L5\t12\t1\t213\t0.62\t2\t[(106, 2)]\n-JY8QFUQ01A1963\t12\t1\t212\t0.62\t2\t[(107, 2)]\n-JY8QFUQ01A1ALH\t22\t5\t216\t2.14\t2\t[(111, 2), (165, 2), (170, 2), (229, 2), (254, 2)]\n-JY8QFUQ01A1AYP\t14\t1\t213\t0.85\t2\t[(79, 2)]\n-JY8QFUQ01A1BK7\t14\t1\t213\t0.85\t3\t[(172, 3)]\n-JY8QFUQ01A1BT3\t24\t1\t210\t2.63\t2\t[(269, 2)]\n-JY8QFUQ01A1CLZ\t18\t1\t216\t1.42\t2\t[(103, 2)]\n-JY8QFUQ01A1CTT\t15\t4\t213\t0.99\t2\t[(86, 2), (104, 2), (107, 2), (184, 2)]\n-JY8QFUQ01A1DJR\t14\t1\t213\t0.85\t2\t[(197, 2)]\n-JY8QFUQ01A1DVA\t35\t4\t213\t5.59\t3\t[(86, 2), (163, 2), (175, 3), (187, 3)]\n-JY8'..b'Q01BV9YG\t22\t5\t213\t2.17\t4\t[(80, 2), (104, 2), (118, 2), (173, 2), (186, 4)]\n-JY8QFUQ01BW9QL\t9\t0\t213\t0.34\t0\t[]\n-JY8QFUQ01BWI2D\t29\t5\t213\t3.81\t4\t[(103, 2), (188, 3), (195, 2), (258, 4), (308, 2)]\n-JY8QFUQ01BXYLF\t15\t2\t213\t0.99\t3\t[(117, 3), (275, 2)]\n-JY8QFUQ01BY231\t19\t1\t216\t1.58\t2\t[(133, 2)]\n-JY8QFUQ01BYGN8\t20\t6\t213\t1.78\t2\t[(119, 2), (163, 2), (172, 2), (188, 2), (258, 2), (261, 2)]\n-JY8QFUQ01C2NGE\t15\t0\t210\t1.00\t0\t[]\n-JY8QFUQ01C2ROO\t7\t0\t213\t0.20\t0\t[]\n-JY8QFUQ01C3QHH\t13\t1\t213\t0.73\t2\t[(191, 2)]\n-JY8QFUQ01C4MHW\t11\t1\t213\t0.52\t2\t[(196, 2)]\n-JY8QFUQ01C5Q2O\t16\t5\t213\t1.13\t2\t[(173, 2), (176, 2), (190, 2), (196, 2), (248, 2)]\n-JY8QFUQ01C8QWZ\t11\t1\t213\t0.52\t2\t[(184, 2)]\n-JY8QFUQ01C92F8\t13\t0\t222\t0.70\t0\t[]\n-JY8QFUQ01C966Y\t10\t0\t213\t0.42\t0\t[]\n-JY8QFUQ01C98A9\t11\t0\t213\t0.52\t0\t[]\n-JY8QFUQ01CANL1\t20\t3\t213\t1.78\t3\t[(104, 3), (165, 2), (168, 2)]\n-JY8QFUQ01CD8ZK\t30\t5\t213\t4.08\t4\t[(104, 2), (164, 2), (173, 4), (188, 2), (196, 2)]\n-JY8QFUQ01CD9VK\t15\t4\t213\t0.99\t2\t[(86, 2), (104, 2), (107, 2), (184, 2)]\n-JY8QFUQ01CDZ5R\t23\t3\t212\t2.39\t2\t[(106, 2), (209, 2), (254, 2)]\n-JY8QFUQ01CE8P9\t18\t0\t213\t1.44\t0\t[]\n-JY8QFUQ01CF06T\t12\t0\t213\t0.62\t0\t[]\n-JY8QFUQ01CG8U2\t18\t3\t210\t1.46\t3\t[(106, 3), (110, 2), (162, 2)]\n-JY8QFUQ01CGLTX\t15\t2\t219\t0.96\t3\t[(178, 2), (227, 3)]\n-JY8QFUQ01CGQFF\t21\t3\t213\t1.97\t2\t[(86, 2), (119, 2), (193, 2)]\n-JY8QFUQ01CHDDF\t23\t4\t219\t2.31\t2\t[(110, 2), (174, 2), (221, 2), (287, 2)]\n-JY8QFUQ01CHKLB\t8\t0\t213\t0.26\t0\t[]\n-JY8QFUQ01CHW93\t13\t1\t213\t0.73\t2\t[(119, 2)]\n-JY8QFUQ01CII5W\t30\t5\t210\t4.14\t4\t[(106, 2), (118, 2), (193, 4), (258, 2), (285, 2)]\n-JY8QFUQ01CINZT\t5\t1\t213\t0.09\t2\t[(86, 2)]\n-JY8QFUQ01CJLXK\t22\t3\t213\t2.17\t3\t[(108, 2), (165, 2), (257, 3)]\n-JY8QFUQ01CJT9B\t31\t6\t213\t4.37\t3\t[(84, 3), (118, 2), (162, 3), (257, 2), (279, 2), (301, 2)]\n-JY8QFUQ01CK1VY\t28\t7\t216\t3.50\t3\t[(174, 3), (190, 2), (199, 2), (202, 2), (221, 2), (237, 3), (275, 2)]\n-JY8QFUQ01CKN3U\t25\t6\t213\t2.82\t3\t[(86, 2), (106, 3), (142, 2), (170, 2), (175, 2), (203, 2)]\n-JY8QFUQ01CLP4K\t14\t0\t213\t0.85\t0\t[]\n-JY8QFUQ01CNCW4\t10\t1\t213\t0.42\t2\t[(81, 2)]\n-JY8QFUQ01CO019\t16\t2\t213\t1.13\t2\t[(191, 2), (308, 2)]\n-JY8QFUQ01CPVUP\t25\t4\t213\t2.82\t2\t[(106, 2), (113, 2), (164, 2), (190, 2)]\n-JY8QFUQ01CPYJ0\t14\t2\t213\t0.85\t2\t[(106, 2), (164, 2)]\n-JY8QFUQ01CQH14\t14\t1\t213\t0.85\t2\t[(197, 2)]\n-JY8QFUQ01CST8T\t17\t3\t213\t1.28\t4\t[(172, 3), (188, 4), (197, 2)]\n-JY8QFUQ01CU1XI\t17\t2\t209\t1.30\t3\t[(155, 2), (190, 3)]\n-JY8QFUQ01CU5CB\t20\t3\t213\t1.78\t3\t[(172, 3), (229, 2), (300, 2)]\n-JY8QFUQ01CUGFD\t30\t4\t213\t4.08\t4\t[(118, 3), (166, 2), (170, 3), (188, 4)]\n-JY8QFUQ01CURPS\t32\t4\t213\t4.66\t4\t[(139, 3), (164, 2), (173, 2), (201, 4)]\n-JY8QFUQ01CY2WW\t12\t0\t213\t0.62\t0\t[]\n-JY8QFUQ01CY6MC\t16\t3\t213\t1.13\t3\t[(103, 2), (258, 2), (278, 3)]\n-JY8QFUQ01CYWC2\t12\t0\t213\t0.62\t0\t[]\n-JY8QFUQ01DA9FW\t13\t0\t213\t0.73\t0\t[]\n-JY8QFUQ01DC4QI\t21\t5\t213\t1.97\t4\t[(86, 2), (106, 2), (175, 2), (254, 2), (300, 4)]\n-JY8QFUQ01DC8OC\t26\t4\t210\t3.10\t3\t[(118, 2), (163, 3), (190, 2), (202, 2)]\n-JY8QFUQ01DCPGQ\t19\t3\t213\t1.61\t2\t[(106, 2), (191, 2), (244, 2)]\n-JY8QFUQ01DEKWC\t17\t3\t213\t1.28\t3\t[(86, 2), (118, 2), (162, 3)]\n-JY8QFUQ01DG2P7\t11\t1\t211\t0.52\t2\t[(184, 2)]\n-JY8QFUQ01DG5KX\t21\t4\t210\t2.00\t2\t[(106, 2), (172, 2), (261, 2), (279, 2)]\n-JY8QFUQ01DG6GC\t15\t2\t213\t0.99\t2\t[(191, 2), (196, 2)]\n-JY8QFUQ01DHXHT\t20\t3\t216\t1.76\t3\t[(106, 3), (164, 2), (275, 2)]\n-JY8QFUQ01DI39D\t8\t0\t213\t0.26\t0\t[]\n-JY8QFUQ01DJFIZ\t43\t10\t213\t8.48\t8\t[(103, 3), (107, 2), (110, 2), (164, 2), (174, 4), (191, 8), (258, 2), (264, 2), (277, 2), (290, 2)]\n-JY8QFUQ01DLDLD\t7\t1\t213\t0.20\t2\t[(190, 2)]\n-JY8QFUQ01DMF0A\t53\t12\t216\t12.76\t4\t[(103, 3), (113, 2), (117, 3), (162, 2), (165, 3), (172, 2), (175, 2), (189, 4), (207, 2), (213, 2), (274, 3), (301, 3)]\n-JY8QFUQ01DOVL5\t15\t3\t213\t0.99\t2\t[(109, 2), (113, 2), (286, 2)]\n-JY8QFUQ01DPT8R\t8\t1\t212\t0.26\t2\t[(196, 2)]\n-JY8QFUQ01DUD3U\t29\t4\t213\t3.81\t3\t[(108, 2), (112, 3), (163, 2), (173, 2)]\n-JY8QFUQ01DV4HU\t22\t2\t213\t2.17\t2\t[(103, 2), (119, 2)]\n-JY8QFUQ01DV8LF\t6\t0\t213\t0.14\t0\t[]\n-JY8QFUQ01DVBU0\t15\t4\t212\t0.99\t2\t[(176, 2), (190, 2), (196, 2), (248, 2)]\n-JY8QFUQ01DXDOM\t36\t4\t210\t6.00\t2\t[(86, 2), (190, 2), (194, 2), (213, 2)]\n' |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/unmatched.txt --- a/test-output/unmatched.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,190 +0,0 @@\n-Sequence.ID\tchunk_hit_percentage\tnt_hit_percentage\tstart_locations\tbest_match\n-JY8QFUQ01A0JN8\t89\t57\t[279, 280]\tunmatched, IGA2\n-JY8QFUQ01A0KG1\t95\t57\t[299, 301]\tunmatched, IGA2\n-JY8QFUQ01A0XAA\t89\t57\t[284]\tunmatched, IGA2\n-JY8QFUQ01A1201\t89\t57\t[294, 295]\tunmatched, IGA2\n-JY8QFUQ01A1J69\t89\t57\t[281, 282]\tunmatched, IGA2\n-JY8QFUQ01A2Y02\t89\t57\t[291]\tunmatched, IGA2\n-JY8QFUQ01A2ZKE\t88\t64\t[301, 302]\tunmatched, IGG2\n-JY8QFUQ01A36OR\t89\t57\t[278, 279]\tunmatched, IGA2\n-JY8QFUQ01A3PZ4\t89\t57\t[287, 288]\tunmatched, IGA2\n-JY8QFUQ01A3U1I\t63\t36\t[296, 293]\tunmatched, IGA2\n-JY8QFUQ01A4H9C\t79\t64\t[280]\tunmatched, IGA2\n-JY8QFUQ01A55QU\t88\t64\t[276]\tunmatched, IGG1\n-JY8QFUQ01A56OJ\t89\t57\t[272, 273]\tunmatched, IGA2\n-JY8QFUQ01A5K3B\t79\t57\t[290, 291, 288]\tunmatched, IGA2\n-JY8QFUQ01A6DSA\t89\t57\t[282, 283]\tunmatched, IGA2\n-JY8QFUQ01A6FSC\t88\t64\t[280]\tunmatched, IGG2\n-JY8QFUQ01A6GAE\t89\t57\t[292, 293]\tunmatched, IGA2\n-JY8QFUQ01A72DW\t75\t57\t[305, 304]\tunmatched, IGG1\n-JY8QFUQ01A75AZ\t89\t57\t[272, 273]\tunmatched, IGA2\n-JY8QFUQ01A7UAO\t62\t93\t[293]\tunmatched, IGG2\n-JY8QFUQ01A9CSP\t84\t50\t[314, 315]\tunmatched, IGA2\n-JY8QFUQ01A9KBS\t79\t57\t[298, 297, 296]\tunmatched, IGA2\n-JY8QFUQ01A9XMX\t89\t57\t[299, 301]\tunmatched, IGA1\n-JY8QFUQ01AAWJ6\t50\t64\t[261, 289]\tunmatched, IGG4\n-JY8QFUQ01AB8R5\t89\t57\t[278, 279]\tunmatched, IGA2\n-JY8QFUQ01ABJSU\t89\t57\t[278, 279]\tunmatched, IGA2\n-JY8QFUQ01ACF7S\t84\t57\t[286]\tunmatched, IGA2\n-JY8QFUQ01ACGK8\t74\t64\t[295, 296]\tunmatched, IGA1\n-JY8QFUQ01ACMHQ\t79\t64\t[309]\tunmatched, IGA1\n-JY8QFUQ01AD6VN\t89\t57\t[281, 282]\tunmatched, IGA2\n-JY8QFUQ01ADNPS\t89\t57\t[293, 294]\tunmatched, IGA2\n-JY8QFUQ01ADX4W\t89\t57\t[302, 303]\tunmatched, IGA2\n-JY8QFUQ01AEXEP\t89\t57\t[286, 287]\tunmatched, IGA2\n-JY8QFUQ01AFU74\t84\t57\t[289, 290]\tunmatched, IGA2\n-JY8QFUQ01AG0BX\t62\t79\t[282]\tunmatched, IGG2\n-JY8QFUQ01AGTXI\t89\t57\t[300, 301]\tunmatched, IGA2\n-JY8QFUQ01AHQN6\t89\t57\t[311, 312]\tunmatched, IGA2\n-JY8QFUQ01AIE5M\t75\t57\t[303]\tunmatched, IGG2\n-JY8QFUQ01AIYO5\t68\t86\t[293, 292]\tunmatched, IGA1\n-JY8QFUQ01AJFOA\t89\t57\t[278]\tunmatched, IGA2\n-JY8QFUQ01AJTH3\t100\t64\t[287, 288]\tunmatched, IGA2\n-JY8QFUQ01AMBVG\t58\t50\t[304]\tunmatched, IGA1\n-JY8QFUQ01AMG29\t0\t0\t[]\tunmatched, IGA1\n-JY8QFUQ01AMV93\t100\t64\t[279, 280]\tunmatched, IGA2\n-JY8QFUQ01ANFJ6\t89\t57\t[301]\tunmatched, IGA2\n-JY8QFUQ01ANN07\t62\t50\t[285, 277]\tunmatched, IGG4\n-JY8QFUQ01ANOBA\t75\t64\t[299, 298]\tunmatched, IGG4\n-JY8QFUQ01ANT01\t89\t57\t[283, 284]\tunmatched, IGA2\n-JY8QFUQ01ANU9C\t89\t57\t[276, 277]\tunmatched, IGA2\n-JY8QFUQ01AP4OP\t79\t64\t[302, 304]\tunmatched, IGA2\n-JY8QFUQ01APLX8\t89\t57\t[278, 279]\tunmatched, IGA2\n-JY8QFUQ01APOB5\t89\t57\t[290, 291]\tunmatched, IGA2\n-JY8QFUQ01APXHX\t88\t64\t[283]\tunmatched, IGG2\n-JY8QFUQ01AQ36T\t89\t57\t[282, 283]\tunmatched, IGA2\n-JY8QFUQ01AQ6RF\t79\t64\t[292]\tunmatched, IGA2\n-JY8QFUQ01AQQ9J\t89\t57\t[305, 306]\tunmatched, IGA2\n-JY8QFUQ01AR5SV\t69\t64\t[285, 287]\tunmatched, IGG1\n-JY8QFUQ01ARLVF\t63\t86\t[288]\tunmatched, IGA2\n-JY8QFUQ01ARS0N\t89\t57\t[279, 280]\tunmatched, IGA2\n-JY8QFUQ01AT43H\t84\t57\t[276, 278]\tunmatched, IGA2\n-JY8QFUQ01AT8N2\t79\t57\t[286, 281, 283]\tunmatched, IGA2\n-JY8QFUQ01ATKPT\t69\t79\t[307]\tunmatched, IGG1\n-JY8QFUQ01AU2BA\t88\t64\t[294]\tunmatched, IGG1\n-JY8QFUQ01AUBMD\t84\t50\t[269, 268]\tunmatched, IGA1\n-JY8QFUQ01AVBV0\t100\t57\t[307]\tunmatched, IGG1\n-JY8QFUQ01AVKTX\t89\t57\t[277, 278]\tunmatched, IGA1\n-JY8QFUQ01AW6B3\t62\t57\t[293, 295]\tunmatched, IGG2\n-JY8QFUQ01AWTQR\t89\t57\t[303]\tunmatched, IGA2\n-JY8QFUQ01AY4JM\t75\t57\t[276, 277]\tunmatched, IGG1\n-JY8QFUQ01B0222\t89\t57\t[300, 301]\tunmatched, IGA2\n-JY8QFUQ01B19RC\t75\t64\t[306, 307, 302]\tunmatched, IGG1\n-JY8QFUQ01B1HC5\t84\t57\t[280, 281]\tunmatched, IGA2\n-JY8QFUQ01B1QV9\t89\t57\t[308, 309]\tunmatched, IGA2\n-JY8QFUQ01B1S6W\t84\t64\t[295, 297]\tunmatched, IGA1\n-JY8QFUQ01B2ACS\t74\t43\t[284, 285]\tunmatched, IGA2\n-JY8QFUQ01B2E25\t84\t57\t[270]\tunmatched, IGA2\n-JY8QFUQ01B2GL4\t74\t43\t[288, 289]\tunmatched, IGA2\n-JY8QFUQ01B2XE6\t81\t64\t[301, 300]\tunmatched, IGG2\n-JY8QFUQ01B2XKD\t95\t64\t[279, 278]\tunmatched, IGA2\n-JY8QFUQ01B37IT\t100\t57\t[294]\tunmatched, IGG1\n-JY8QFUQ01B5KCJ\t89\t57\t[294, 295]\tunmatched, IGA2\n-JY8QFUQ01B5XDW\t79\t50\t[298, 2'..b'nmatched, IGA1\n-JY8QFUQ01BNJBB\t68\t29\t[293, 295]\tunmatched, IGA1\n-JY8QFUQ01BNJGF\t89\t57\t[275, 276]\tunmatched, IGA2\n-JY8QFUQ01BP3M1\t84\t64\t[279]\tunmatched, IGA2\n-JY8QFUQ01BPT8C\t89\t57\t[290, 291]\tunmatched, IGA2\n-JY8QFUQ01BPXZS\t89\t57\t[297, 298]\tunmatched, IGA2\n-JY8QFUQ01BR9V1\t74\t57\t[301, 300]\tunmatched, IGA2\n-JY8QFUQ01BRGSI\t84\t57\t[282, 283]\tunmatched, IGA2\n-JY8QFUQ01BRNFF\t79\t57\t[282, 281]\tunmatched, IGA1\n-JY8QFUQ01BSGO4\t26\t0\t[281]\tunmatched, IGA1\n-JY8QFUQ01BT0O2\t89\t57\t[278, 279]\tunmatched, IGA2\n-JY8QFUQ01BT4AX\t81\t64\t[292, 291]\tunmatched, IGG1\n-JY8QFUQ01BT86M\t89\t57\t[302]\tunmatched, IGA2\n-JY8QFUQ01BTQAH\t89\t57\t[294, 295]\tunmatched, IGA2\n-JY8QFUQ01BURMR\t84\t64\t[288, 289]\tunmatched, IGA1\n-JY8QFUQ01BV9YG\t62\t71\t[303, 301]\tunmatched, IGG1\n-JY8QFUQ01BW9QL\t100\t57\t[309]\tunmatched, IGG1\n-JY8QFUQ01BWI2D\t89\t57\t[284, 285]\tunmatched, IGA2\n-JY8QFUQ01BXYLF\t53\t43\t[285, 275]\tunmatched, IGA2\n-JY8QFUQ01BY231\t63\t71\t[308, 309, 307]\tunmatched, IGA1\n-JY8QFUQ01BYGN8\t74\t57\t[301, 302]\tunmatched, IGA2\n-JY8QFUQ01C2NGE\t81\t64\t[282, 281]\tunmatched, IGG1\n-JY8QFUQ01C2ROO\t74\t50\t[281, 283]\tunmatched, IGA2\n-JY8QFUQ01C3QHH\t89\t57\t[311, 312]\tunmatched, IGA2\n-JY8QFUQ01C4MHW\t79\t57\t[277, 278]\tunmatched, IGA2\n-JY8QFUQ01C5Q2O\t74\t57\t[285, 286]\tunmatched, IGA2\n-JY8QFUQ01C8QWZ\t79\t57\t[273, 274]\tunmatched, IGA2\n-JY8QFUQ01C92F8\t84\t57\t[299, 300]\tunmatched, 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IGA2\n' |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/unmatched_mean_n.txt --- a/test-output/unmatched_mean_n.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -189 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/unmatched_mean_value.txt --- a/test-output/unmatched_mean_value.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -18.4 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/unmatched_median_n.txt --- a/test-output/unmatched_median_n.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -189 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/unmatched_median_value.txt --- a/test-output/unmatched_median_value.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -16 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/unmatched_sum_n.txt --- a/test-output/unmatched_sum_n.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -189 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f test-output/unmatched_sum_value.txt --- a/test-output/unmatched_sum_value.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -3486 \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f tests/.pytest_cache/.gitignore --- a/tests/.pytest_cache/.gitignore Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -# Created by pytest automatically. -* |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f tests/.pytest_cache/CACHEDIR.TAG --- a/tests/.pytest_cache/CACHEDIR.TAG Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -Signature: 8a477f597d28d172789f06886806bc55 -# This file is a cache directory tag created by pytest. -# For information about cache directory tags, see: -# http://www.bford.info/cachedir/spec.html |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f tests/.pytest_cache/README.md --- a/tests/.pytest_cache/README.md Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,8 +0,0 @@ -# pytest cache directory # - -This directory contains data from the pytest's cache plugin, -which provides the `--lf` and `--ff` options, as well as the `cache` fixture. - -**Do not** commit this to version control. - -See [the docs](https://docs.pytest.org/en/stable/cache.html) for more information. |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f tests/.pytest_cache/v/cache/lastfailed --- a/tests/.pytest_cache/v/cache/lastfailed Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,3 +0,0 @@ -{ - "test_shm_csr.py::test_results_match_validation[shm_overview.txt]": true -} \ No newline at end of file |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f tests/.pytest_cache/v/cache/nodeids --- a/tests/.pytest_cache/v/cache/nodeids Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,27 +0,0 @@ -[ - "test_shm_csr.py::test_check_output", - "test_shm_csr.py::test_nt_overview", - "test_shm_csr.py::test_results_match_validation[IGA_pie.txt]", - "test_shm_csr.py::test_results_match_validation[IGG_pie.txt]", - "test_shm_csr.py::test_results_match_validation[aa_histogram_sum.txt]", - "test_shm_csr.py::test_results_match_validation[aa_histogram_sum_IGA.txt]", - "test_shm_csr.py::test_results_match_validation[aa_histogram_sum_IGG.txt]", - "test_shm_csr.py::test_results_match_validation[absolute_mutations.txt]", - "test_shm_csr.py::test_results_match_validation[frequency_ranges_classes.txt]", - "test_shm_csr.py::test_results_match_validation[frequency_ranges_subclasses.txt]", - "test_shm_csr.py::test_results_match_validation[mutation_by_id.txt]", - "test_shm_csr.py::test_results_match_validation[relative_mutations.txt]", - "test_shm_csr.py::test_results_match_validation[scatter.txt]", - "test_shm_csr.py::test_results_match_validation[shm_overview.txt]", - "test_shm_csr.py::test_results_match_validation[tandems_by_id.txt]", - "test_shm_csr.py::test_results_match_validation[transitions_IGA1_sum.txt]", - "test_shm_csr.py::test_results_match_validation[transitions_IGA2_sum.txt]", - "test_shm_csr.py::test_results_match_validation[transitions_IGA_sum.txt]", - "test_shm_csr.py::test_results_match_validation[transitions_IGE_sum.txt]", - "test_shm_csr.py::test_results_match_validation[transitions_IGG1_sum.txt]", - "test_shm_csr.py::test_results_match_validation[transitions_IGG2_sum.txt]", - "test_shm_csr.py::test_results_match_validation[transitions_IGG3_sum.txt]", - "test_shm_csr.py::test_results_match_validation[transitions_IGG4_sum.txt]", - "test_shm_csr.py::test_results_match_validation[transitions_IGG_sum.txt]", - "test_shm_csr.py::test_results_match_validation[transitions_all_sum.txt]" -] \ No newline at end of file |
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| diff -r f387cc1580c6 -r cf8ad181628f tests/.pytest_cache/v/cache/stepwise --- a/tests/.pytest_cache/v/cache/stepwise Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -[] \ No newline at end of file |
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| diff -r f387cc1580c6 -r cf8ad181628f tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc |
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| Binary file tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc has changed |
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| diff -r f387cc1580c6 -r cf8ad181628f tests/__pycache__/test_shm_csr.cpython-39-pytest-6.2.5.pyc |
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| Binary file tests/__pycache__/test_shm_csr.cpython-39-pytest-6.2.5.pyc has changed |
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| diff -r f387cc1580c6 -r cf8ad181628f tests/__pycache__/test_shm_csr.cpython-39-pytest-7.2.0.pyc |
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| Binary file tests/__pycache__/test_shm_csr.cpython-39-pytest-7.2.0.pyc has changed |
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| diff -r f387cc1580c6 -r cf8ad181628f tests/data/intermediate_files/RGYW.txt --- a/tests/data/intermediate_files/RGYW.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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|
| b |
| diff -r f387cc1580c6 -r cf8ad181628f tests/data/intermediate_files/merged.txt --- a/tests/data/intermediate_files/merged.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1577 +0,0 @@\n-Sequence.ID\tSequence.number\tFunctionality\tV.GENE.and.allele\tV.REGION.score\tV.REGION.identity..\tV.REGION.identity.nt\tV.REGION.identity....with.ins.del.events.\tV.REGION.identity.nt..with.ins.del.events.\tJ.GENE.and.allele\tJ.REGION.score\tJ.REGION.identity..\tJ.REGION.identity.nt\tD.GENE.and.allele\tD.REGION.reading.frame\tCDR1.IMGT.length\tCDR2.IMGT.length\tCDR3.IMGT.length\tCDR.IMGT.lengths\tFR.IMGT.lengths\tAA.JUNCTION\tJUNCTION.frame\tOrientation\tFunctionality.comment\tV.REGION.potential.ins.del\tJ.GENE.and.allele.comment\tV.REGION.insertions\tV.REGION.deletions\tSequence\tX\tbest_match\tnt_hit_percentage\tchunk_hit_percentage\tstart_locations\tV.REGION\tFR1.IMGT\tCDR1.IMGT\tFR2.IMGT\tCDR2.IMGT\tFR3.IMGT\tCDR3.IMGT\tV.REGION.Nb.of.positions.including.IMGT.gaps..nt.\tV.REGION.Nb.of.nucleotides\tV.REGION.Nb.of.identical.nucleotides\tV.REGION.Nb.of.mutations\tV.REGION.Nb.of.silent.mutations\tV.REGION.Nb.of.nonsilent.mutations\tV.REGION.a.g\tV.REGION.g.a\tV.REGION.c.t\tV.REGION.t.c\tV.REGION.a.c\tV.REGION.c.a\tV.REGION.a.t\tV.REGION.t.a\tV.REGION.g.c\tV.REGION.c.g\tV.REGION.g.t\tV.REGION.t.g\tFR1.IMGT.Nb.of.positions.including.IMGT.gaps..nt.\tFR1.IMGT.Nb.of.nucleotides\tFR1.IMGT.Nb.of.identical.nucleotides\tFR1.IMGT.Nb.of.mutations\tFR1.IMGT.Nb.of.silent.mutations\tFR1.IMGT.Nb.of.nonsilent.mutations\tFR1.IMGT.a.g\tFR1.IMGT.g.a\tFR1.IMGT.c.t\tFR1.IMGT.t.c\tFR1.IMGT.a.c\tFR1.IMGT.c.a\tFR1.IMGT.a.t\tFR1.IMGT.t.a\tFR1.IMGT.g.c\tFR1.IMGT.c.g\tFR1.IMGT.g.t\tFR1.IMGT.t.g\tCDR1.IMGT.Nb.of.positions.including.IMGT.gaps..nt.\tCDR1.IMGT.Nb.of.nucleotides\tCDR1.IMGT.Nb.of.identical.nucleotides\tCDR1.IMGT.Nb.of.mutations\tCDR1.IMGT.Nb.of.silent.mutations\tCDR1.IMGT.Nb.of.nonsilent.mutations\tCDR1.IMGT.a.g\tCDR1.IMGT.g.a\tCDR1.IMGT.c.t\tCDR1.IMGT.t.c\tCDR1.IMGT.a.c\tCDR1.IMGT.c.a\tCDR1.IMGT.a.t\tCDR1.IMGT.t.a\tCDR1.IMGT.g.c\tCDR1.IMGT.c.g\tCDR1.IMGT.g.t\tCDR1.IMGT.t.g\tFR2.IMGT.Nb.of.positions.including.IMGT.gaps..nt.\tFR2.IMGT.Nb.of.nucleotides\tFR2.IMGT.Nb.of.identical.nucleotides\tFR2.IMGT.Nb.of.mutations\tFR2.IMGT.Nb.of.silent.mutations\tFR2.IMGT.Nb.of.nonsilent.mutations\tFR2.IMGT.a.g\tFR2.IMGT.g.a\tFR2.IMGT.c.t\tFR2.IMGT.t.c\tFR2.IMGT.a.c\tFR2.IMGT.c.a\tFR2.IMGT.a.t\tFR2.IMGT.t.a\tFR2.IMGT.g.c\tFR2.IMGT.c.g\tFR2.IMGT.g.t\tFR2.IMGT.t.g\tCDR2.IMGT.Nb.of.positions.including.IMGT.gaps..nt.\tCDR2.IMGT.Nb.of.nucleotides\tCDR2.IMGT.Nb.of.identical.nucleotides\tCDR2.IMGT.Nb.of.mutations\tCDR2.IMGT.Nb.of.silent.mutations\tCDR2.IMGT.Nb.of.nonsilent.mutations\tCDR2.IMGT.a.g\tCDR2.IMGT.g.a\tCDR2.IMGT.c.t\tCDR2.IMGT.t.c\tCDR2.IMGT.a.c\tCDR2.IMGT.c.a\tCDR2.IMGT.a.t\tCDR2.IMGT.t.a\tCDR2.IMGT.g.c\tCDR2.IMGT.c.g\tCDR2.IMGT.g.t\tCDR2.IMGT.t.g\tFR3.IMGT.Nb.of.positions.including.IMGT.gaps..nt.\tFR3.IMGT.Nb.of.nucleotides\tFR3.IMGT.Nb.of.identical.nucleotides\tFR3.IMGT.Nb.of.mutations\tFR3.IMGT.Nb.of.silent.mutations\tFR3.IMGT.Nb.of.nonsilent.mutations\tFR3.IMGT.a.g\tFR3.IMGT.g.a\tFR3.IMGT.c.t\tFR3.IMGT.t.c\tFR3.IMGT.a.c\tFR3.IMGT.c.a\tFR3.IMGT.a.t\tFR3.IMGT.t.a\tFR3.IMGT.g.c\tFR3.IMGT.c.g\tFR3.IMGT.g.t\tFR3.IMGT.t.g\tCDR3.IMGT.Nb.of.positions.including.IMGT.gaps..nt.\tCDR3.IMGT.Nb.of.nucleotides\tCDR3.IMGT.Nb.of.identical.nucleotides\tCDR3.IMGT.Nb.of.mutations\tCDR3.IMGT.Nb.of.silent.mutations\tCDR3.IMGT.Nb.of.nonsilent.mutations\tCDR3.IMGT.a.g\tCDR3.IMGT.g.a\tCDR3.IMGT.c.t\tCDR3.IMGT.t.c\tCDR3.IMGT.a.c\tCDR3.IMGT.c.a\tCDR3.IMGT.a.t\tCDR3.IMGT.t.a\tCDR3.IMGT.g.c\tCDR3.IMGT.c.g\tCDR3.IMGT.g.t\tCDR3.IMGT.t.g\tX.a.t.a\tt.a.t.\tX.a.g.g.c.t..a.t.\tX.a.t..a.g.c.c.t.\tFR1.IMGT.seq\tCDR1.IMGT.seq\tFR2.IMGT.seq\tCDR2.IMGT.seq\tFR3.IMGT.seq\tCDR3.IMGT.seq\tCDR3.IMGT.AA\tVGene\tDGene\tJGene\tunique.def\tVRegionMutations\tVRegionNucleotides\ttransitionMutations\ttransversionMutations\ttransitionMutationsAtGC\ttotalMutationsAtGC\ttransitionMutationsAtAT\ttotalMutationsAtAT\tsilentMutationsFR\tsilentMutationsCDR\tnonSilentMutationsFR\tnonSilentMutationsCDR\n-JY8QFUQ01A0005\t14683\tproductive\tHomsap IGHV4-39*03 F\t929\t91.36\t201/220 nt\tNA\t\tHomsap IGHJ3*01 F\t232\t96\t48/50 nt\tHomsap IGHD3-22*01 F\t3\t10\t7\t17\t10.7.17\t[1.17.38.11]\tCARSITLTVVVMNDAFDVW\tin-frame\t+\t\t\t\t\t\ttctccggtggctccatcaacagtagaaattattattggggctggatccgccagcccccagggaagggtttggagtg'..b"ected insertion/deletion\tThe submitted sequence and the closest germline V-GENE allele show different CDR2-IMGT amino acid lengths (7 AA in JY8QFUQ01DXDOM ; 8 AA in Homsap_IGHV3-21*01), and low V-REGION identity (83,26% ) this may indicate potential nucleotide insertion(s) and/or deletion(s) which are not dealt in this release\t\tin FR3-IMGT at codon 81 of V-REGION: 'G' (1 nucleotides at position 144 to 144 in the user submitted sequence), (cause frameshift);\t\tcctctggattcagtttcactggttttaccgtgatctgggtccgccaggctccaaggaaggggctggaatggatctcatccgtcactactaatggtctcacgtactacgcagactcagtagagggccgattcaacatctccaggGgacaacgccaacaatttagtgtttctgcaaatgaacagcctgagagtcgaggacactggtgtatattattgtgcgagagataaagtgatctctgccggacgggacgtctggggccaagggaccacggtcaccgtctcctcaacatccccgaccagccccaaggtcttcccgctgagcctcgacagcaccccccgaagatgggaacgtggtcgtcgcatgcctggtccagggcttcttcccccc\tNA\tunmatched, IGA2\t57\t89\t[283, 284]\tc86>g,T29>S(+ - +)|c87>t,T29>S(+ - +)|g104>c,S35>T(+ - +)|a106>g,S36>G(+ + -)|c108>t,S36>G(+ + -)|a110>t,Y37>F(- + -)|g113>c,S38>T(+ - +)|a115>g,M39>V(+ - -)|a119>t,N40>I(- - -)|g139>a,G47>R(- - -)|g153>a|g157>a,V53>I(+ - +)|a166>g,I56>V(+ - +)|t168>c,I56>V(+ - +)|g170>c,S57>T(+ - +)|g173>c,S58>T(+ - +)|g176>a,S59>N(- - -)|a187>g,S63>G(+ + -)|t190>c,Y64>L(- - -)|a191>t,Y64>L(- - -)|t194>c,I65>T(- - -)|a195>g,I65>T(- - -)|g213>a|a214>g,K72>E(+ - -)|c230>a,T77>N(- + -)|a240>g|g252>c,K84>N(+ - -)|c255>t|c257>t,S86>L(- - -)|c259>g,L87>V(+ - +)|a263>t,Y88>F(- + -)|c287>t,A96>V(+ - +)|g297>t|c299>g,A100>G(- + -)|g303>a|c309>t|\t\tc86>g,T29>S(+ - +)|c87>t,T29>S(+ - +)|g104>c,S35>T(+ - +)|a106>g,S36>G(+ + -)|c108>t,S36>G(+ + -)|a110>t,Y37>F(- + -)|g113>c,S38>T(+ - +)|\ta115>g,M39>V(+ - -)|a119>t,N40>I(- - -)|g139>a,G47>R(- - -)|g153>a|g157>a,V53>I(+ - +)|\ta166>g,I56>V(+ - +)|t168>c,I56>V(+ - +)|g170>c,S57>T(+ - +)|g173>c,S58>T(+ - +)|g176>a,S59>N(- - -)|a187>g,S63>G(+ + -)|t190>c,Y64>L(- - -)|a191>t,Y64>L(- - -)|t194>c,I65>T(- - -)|a195>g,I65>T(- - -)|\tg213>a|a214>g,K72>E(+ - -)|c230>a,T77>N(- + -)|a240>g|g252>c,K84>N(+ - -)|c255>t|c257>t,S86>L(- - -)|c259>g,L87>V(+ - +)|a263>t,Y88>F(- + -)|c287>t,A96>V(+ - +)|g297>t|c299>g,A100>G(- + -)|g303>a|c309>t|\t\t320\t223\t187\t36\t7\t29\t7\t6\t6\t3\t0\t1\t4\t0\t5\t3\t1\t0\t78\t5\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t36\t24\t17\t7\t0\t7\t1\t0\t2\t0\t0\t0\t1\t0\t2\t1\t0\t0\t51\t51\t46\t5\t1\t4\t1\t3\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t30\t21\t11\t10\t0\t10\t3\t1\t0\t3\t0\t0\t1\t0\t2\t0\t0\t0\t117\t114\t100\t14\t6\t8\t2\t2\t4\t0\t0\t1\t1\t0\t1\t2\t1\t0\t8\t8\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\taa,40-41(FR1)|ta,105-106(CDR1)|ta,109-110(CDR1)|ta,111-112(CDR1)|aa,118-119(FR2)|aa,142-143(FR2)|ta,168-169(CDR2)|ta,171-172(CDR2)|ta,174-175(CDR2)|ta,186-187(CDR2)|ta,190-191(CDR2)|ta,194-195(CDR2)|ta,196-197(FR3)|ta,199-200(FR3)|aa,214-215(FR3)|aa,244-245(FR3)|aa,250-251(FR3)|aa,253-254(FR3)|ta,262-263(FR3)|aa,269-270(FR3)|aa,274-275(FR3)|ta,304-305(FR3)|ta,307-308(FR3)|\ttt,82-83(CDR1)|tt,88-89(CDR1)|ta,105-106(CDR1)|ta,109-110(CDR1)|ta,111-112(CDR1)|tt,167-168(CDR2)|ta,171-172(CDR2)|ta,174-175(CDR2)|ta,186-187(CDR2)|tt,189-190(CDR2)|ta,194-195(CDR2)|ta,196-197(FR3)|ta,199-200(FR3)|tt,226-227(FR3)|ta,262-263(FR3)|ta,304-305(FR3)|tt,306-307(FR3)|\tagct,8-11(FR1)|agta,103-106(CDR1)|agca,112-115(CDR1)|ggct,132-135(FR2)|ggct,146-149(FR2)|agta,169-172(CDR2)|agta,184-187(CDR2)|ggct,297-300(FR3)|\tagct,8-11(FR1)|agcc,41-44(FR1)|agcc,72-75(FR1)|agct,106-109(CDR1)|aact,118-121(FR2)|tact,196-199(FR3)|aact,253-256(FR3)|agcc,277-280(FR3)|agcc,285-288(FR3)|tact,307-310(FR3)|\tcctct\tggattcagtttcactggttttacc\tgtgatctgggtccgccaggctccaaggaaggggctggaatggatctcatcc\tgtcactactaatggtctcacg\ttactacgcagactcagtagagggccgattcaacatctccagggacaacgccaacaatttagtgtttctgcaaatgaacagcctgagagtcgaggacactggtgtatattattgt\tgcgagagataaagtgatctctgccggacgggacgtc\tARDKVISAGRDV\tIGHV3-21\tIGHD2-15\tIGHJ6\tggattcagtttcactggttttacc gtgatctgggtccgccaggctccaaggaaggggctggaatggatctcatcc gtcactactaatggtctcacg tactacgcagactcagtagagggccgattcaacatctccagggacaacgccaacaatttagtgtttctgcaaatgaacagcctgagagtcgaggacactggtgtatattattgt gcgagagataaagtgatctctgccggacgggacgtc unmatched\t36\t210\t22\t14\t12\t22\t10\t14\t7\t0\t12\t17\n" |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f tests/data/intermediate_files/mutation_in_motifs.txt --- a/tests/data/intermediate_files/mutation_in_motifs.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,906816 +0,0 @@\n-JY8QFUQ01A0005\t105\tCDR1\tt\ta\t35\tS\tR\tWA\t105\t106\t(- - -)\n-JY8QFUQ01A0005\t105\tCDR1\tt\ta\t35\tS\tR\tTW\t105\t106\t(- - -)\n-JY8QFUQ01A0005\t107\tCDR1\tg\ta\t36\tS\tN\tRGYW\t106\t109\t(- - -)\n-JY8QFUQ01A0005\t111\tCDR1\tc\tt\tNone\tNone\tNone\tWRCY\t109\t112\t\n-JY8QFUQ01A0005\t147\tFR2\tg\tt\tNone\tNone\tNone\tRGYW\t146\t149\t\n-JY8QFUQ01A0005\t148\tFR2\tc\tt\tNone\tNone\tNone\tRGYW\t146\t149\t\n-JY8QFUQ01A0005\t164\tFR2-CDR2\tg\ta\t55\tS\tN\tRGYW\t163\t166\t(- - -)\n-JY8QFUQ01A0005\t191\tCDR2\tg\ta\t64\tS\tN\tRGYW\t190\t193\t(- - -)\n-JY8QFUQ01A0005\t204\tFR3\tc\tt\tNone\tNone\tNone\tWRCY\t202\t205\t\n-JY8QFUQ01A0005\t275\tFR3\tg\tc\t92\tS\tT\tRGYW\t274\t277\t(+ - +)\n-JY8QFUQ01A0005\t275\tFR3\tg\tc\t92\tS\tT\tWRCY\t274\t277\t(+ - +)\n-JY8QFUQ01A004N\t102\tCDR1\tt\tg\t34\tS\tR\tRGYW\t100\t103\t(- - -)\n-JY8QFUQ01A004N\t102\tCDR1\tt\tg\t34\tS\tR\tWA\t102\t103\t(- - -)\n-JY8QFUQ01A004N\t102\tCDR1\tt\tg\t34\tS\tR\tTW\t102\t103\t(- - -)\n-JY8QFUQ01A004N\t106\tCDR1\ta\tg\t36\tS\tA\tRGYW\t106\t109\t(- + -)\n-JY8QFUQ01A004N\t106\tCDR1\ta\tg\t36\tS\tA\tWA\t105\t106\t(- + -)\n-JY8QFUQ01A004N\t106\tCDR1\ta\tg\t36\tS\tA\tTW\t105\t106\t(- + -)\n-JY8QFUQ01A004N\t107\tCDR1\tg\tc\t36\tS\tA\tRGYW\t106\t109\t(- + -)\n-JY8QFUQ01A004N\t108\tCDR1\tt\tc\t36\tS\tA\tRGYW\t106\t109\t(- + -)\n-JY8QFUQ01A004N\t108\tCDR1\tt\tc\t36\tS\tA\tTW\t108\t109\t(- + -)\n-JY8QFUQ01A004N\t164\tFR2-CDR2\tg\tc\t55\tS\tT\tRGYW\t163\t166\t(+ - +)\n-JY8QFUQ01A004N\t165\tFR2-CDR2\tt\tc\t55\tS\tT\tRGYW\t163\t166\t(+ - +)\n-JY8QFUQ01A004N\t165\tFR2-CDR2\tt\tc\t55\tS\tT\tWA\t165\t166\t(+ - +)\n-JY8QFUQ01A004N\t165\tFR2-CDR2\tt\tc\t55\tS\tT\tTW\t165\t166\t(+ - +)\n-JY8QFUQ01A004N\t191\tCDR2\tg\tc\t64\tS\tT\tRGYW\t190\t193\t(+ - +)\n-JY8QFUQ01A004N\t200\tFR3\ta\tc\t67\tY\tS\tWA\t199\t200\t(+ - -)\n-JY8QFUQ01A004N\t200\tFR3\ta\tc\t67\tY\tS\tTW\t199\t200\t(+ - -)\n-JY8QFUQ01A004N\t204\tFR3\tc\tt\tNone\tNone\tNone\tWRCY\t202\t205\t\n-JY8QFUQ01A004N\t234\tFR3\ta\tg\t78\tI\tM\tWA\t233\t234\t(+ + -)\n-JY8QFUQ01A004N\t234\tFR3\ta\tg\t78\tI\tM\tTW\t233\t234\t(+ + -)\n-JY8QFUQ01A004N\t240\tFR3\ta\tg\t80\tV\tL\tWA\t239\t240\t(+ - +)\n-JY8QFUQ01A004N\t240\tFR3\ta\tg\t80\tV\tL\tTW\t239\t240\t(+ - +)\n-JY8QFUQ01A004N\t259\tFR3\tt\ta\t87\tF\tI\tTW\t259\t260\t(+ - -)\n-JY8QFUQ01A004N\t275\tFR3\tg\ta\t92\tS\tN\tRGYW\t274\t277\t(- - -)\n-JY8QFUQ01A004N\t275\tFR3\tg\ta\t92\tS\tN\tWRCY\t274\t277\t(- - -)\n-JY8QFUQ01A004N\t276\tFR3\tc\tt\t92\tS\tN\tRGYW\t274\t277\t(- - -)\n-JY8QFUQ01A004N\t276\tFR3\tc\tt\t92\tS\tN\tWRCY\t274\t277\t(- - -)\n-JY8QFUQ01A006G\t83\tCDR1\tg\ta\t28\tG\tD\tRGYW\t82\t85\t(- - -)\n-JY8QFUQ01A006G\t106\tCDR1\ta\tc\t36\tS\tH\tRGYW\t106\t109\t(+ - -)\n-JY8QFUQ01A006G\t106\tCDR1\ta\tc\t36\tS\tH\tWA\t105\t106\t(+ - -)\n-JY8QFUQ01A006G\t106\tCDR1\ta\tc\t36\tS\tH\tTW\t105\t106\t(+ - -)\n-JY8QFUQ01A006G\t107\tCDR1\tg\ta\t36\tS\tH\tRGYW\t106\t109\t(+ - -)\n-JY8QFUQ01A006G\t143\tFR2\ta\tg\t48\tK\tR\tWA\t142\t143\t(+ + +)\n-JY8QFUQ01A006G\t147\tFR2\tg\ta\tNone\tNone\tNone\tRGYW\t146\t149\t\n-JY8QFUQ01A006G\t169\tCDR2\tt\tc\t57\tY\tH\tWA\t169\t170\t(+ - -)\n-JY8QFUQ01A006G\t169\tCDR2\tt\tc\t57\tY\tH\tTW\t169\t170\t(+ - -)\n-JY8QFUQ01A006G\t171\tCDR2\tt\tc\t57\tY\tH\tTW\t171\t172\t(+ - -)\n-JY8QFUQ01A006G\t174\tCDR2\tt\tc\tNone\tNone\tNone\tWA\t174\t175\t\n-JY8QFUQ01A006G\t174\tCDR2\tt\tc\tNone\tNone\tNone\tTW\t174\t175\t\n-JY8QFUQ01A006G\t205\tFR3\tc\tt\t69\tP\tW\tWRCY\t202\t205\t(- - -)\n-JY8QFUQ01A006G\t240\tFR3\ta\tg\tNone\tNone\tNone\tWA\t239\t240\t\n-JY8QFUQ01A006G\t240\tFR3\ta\tg\tNone\tNone\tNone\tTW\t239\t240\t\n-JY8QFUQ01A006G\t251\tFR3\ta\tg\t84\tK\tS\tWA\t250\t251\t(- - 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-)\n-JY8QFUQ01DXDOM\t195\tCDR2\ta\tg\t65\tI\tT\tTW\t194\t195\t(- - -)\n-JY8QFUQ01DXDOM\t214\tFR3\ta\tg\t72\tK\tE\tWA\t214\t215\t(+ - -)\n-JY8QFUQ01DXDOM\t255\tFR3\tc\tt\tNone\tNone\tNone\tWRCY\t253\t256\tNone\n-JY8QFUQ01DXDOM\t263\tFR3\ta\tt\t88\tY\tF\tWA\t262\t263\t(- + -)\n-JY8QFUQ01DXDOM\t263\tFR3\ta\tt\t88\tY\tF\tTW\t262\t263\t(- + -)\n-JY8QFUQ01DXDOM\t287\tFR3\tc\tt\t96\tA\tV\tWRCY\t285\t288\t(+ - +)\n-JY8QFUQ01DXDOM\t297\tFR3\tg\tt\tNone\tNone\tNone\tRGYW\t297\t300\tNone\n-JY8QFUQ01DXDOM\t299\tFR3\tc\tg\t100\tA\tG\tRGYW\t297\t300\t(- + -)\n-JY8QFUQ01DXDOM\t309\tFR3\tc\tt\tNone\tNone\tNone\tWRCY\t307\t310\tNone\n' |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f tests/data/intermediate_files/mutationdict.txt --- a/tests/data/intermediate_files/mutationdict.txt Wed Feb 02 10:57:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,41750 +0,0 @@\n-JY8QFUQ01A0005_CDR1\tg\t92\ta\tS\t31\tN\t(- - -)\n-JY8QFUQ01A0005_CDR1\tt\t105\ta\tS\t35\tR\t(- - -)\n-JY8QFUQ01A0005_CDR1\tg\t107\ta\tS\t36\tN\t(- - -)\n-JY8QFUQ01A0005_CDR1\tc\t111\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A0005_CDR1\tc\t114\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A0005_FR2\tg\t147\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A0005_FR2\tc\t148\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A0005_FR2\tg\t162\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01A0005_FR2\tg\t164\ta\tS\t55\tN\t(- - -)\n-JY8QFUQ01A0005_CDR2\tg\t191\ta\tS\t64\tN\t(- - -)\n-JY8QFUQ01A0005_FR2-CDR2\tg\t147\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A0005_FR2-CDR2\tc\t148\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A0005_FR2-CDR2\tg\t162\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01A0005_FR2-CDR2\tg\t164\ta\tS\t55\tN\t(- - -)\n-JY8QFUQ01A0005_FR2-CDR2\tg\t191\ta\tS\t64\tN\t(- - -)\n-JY8QFUQ01A0005_FR3\tc\t204\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A0005_FR3\ta\t232\tg\tI\t78\tV\t(+ - +)\n-JY8QFUQ01A0005_FR3\tc\t245\tg\tT\t82\tR\t(- - -)\n-JY8QFUQ01A0005_FR3\tc\t249\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A0005_FR3\tc\t261\tg\tF\t87\tL\t(+ - -)\n-JY8QFUQ01A0005_FR3\tg\t275\tc\tS\t92\tT\t(+ - +)\n-JY8QFUQ01A0005_FR3\tg\t280\tc\tV\t94\tL\t(+ - +)\n-JY8QFUQ01A0005_FR3\tg\t303\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01A004N_CDR1\ta\t88\tg\tI\t30\tV\t(+ - +)\n-JY8QFUQ01A004N_CDR1\tc\t93\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A004N_CDR1\tt\t102\tg\tS\t34\tR\t(- - -)\n-JY8QFUQ01A004N_CDR1\ta\t106\tg\tS\t36\tA\t(- + -)\n-JY8QFUQ01A004N_CDR1\tg\t107\tc\tS\t36\tA\t(- + -)\n-JY8QFUQ01A004N_CDR1\tt\t108\tc\tS\t36\tA\t(- + -)\n-JY8QFUQ01A004N_FR2\tg\t164\tc\tS\t55\tT\t(+ - +)\n-JY8QFUQ01A004N_FR2\tt\t165\tc\tS\t55\tT\t(+ - +)\n-JY8QFUQ01A004N_CDR2\tg\t191\tc\tS\t64\tT\t(+ - +)\n-JY8QFUQ01A004N_CDR2\tc\t195\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01A004N_FR2-CDR2\tg\t164\tc\tS\t55\tT\t(+ - +)\n-JY8QFUQ01A004N_FR2-CDR2\tt\t165\tc\tS\t55\tT\t(+ - +)\n-JY8QFUQ01A004N_FR2-CDR2\tg\t191\tc\tS\t64\tT\t(+ - +)\n-JY8QFUQ01A004N_FR2-CDR2\tc\t195\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01A004N_FR3\ta\t200\tc\tY\t67\tS\t(+ - -)\n-JY8QFUQ01A004N_FR3\tc\t204\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A004N_FR3\tg\t221\tc\tS\t74\tT\t(+ - +)\n-JY8QFUQ01A004N_FR3\ta\t234\tg\tI\t78\tM\t(+ + -)\n-JY8QFUQ01A004N_FR3\tg\t238\tt\tV\t80\tL\t(+ - +)\n-JY8QFUQ01A004N_FR3\ta\t240\tg\tV\t80\tL\t(+ - +)\n-JY8QFUQ01A004N_FR3\tt\t259\ta\tF\t87\tI\t(+ - -)\n-JY8QFUQ01A004N_FR3\tg\t275\ta\tS\t92\tN\t(- - -)\n-JY8QFUQ01A004N_FR3\tc\t276\tt\tS\t92\tN\t(- - -)\n-JY8QFUQ01A004N_FR3\tg\t303\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_CDR1\tg\t83\ta\tG\t28\tD\t(- - -)\n-JY8QFUQ01A006G_CDR1\tc\t93\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_CDR1\tg\t104\tc\tS\t35\tT\t(+ - +)\n-JY8QFUQ01A006G_CDR1\ta\t106\tc\tS\t36\tH\t(+ - -)\n-JY8QFUQ01A006G_CDR1\tg\t107\ta\tS\t36\tH\t(+ - -)\n-JY8QFUQ01A006G_CDR1\tc\t114\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR2\tc\t129\tg\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR2\ta\t143\tg\tK\t48\tR\t(+ + +)\n-JY8QFUQ01A006G_FR2\tg\t147\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR2\ta\t157\tg\tI\t53\tV\t(+ - +)\n-JY8QFUQ01A006G_CDR2\tt\t169\tc\tY\t57\tH\t(+ - -)\n-JY8QFUQ01A006G_CDR2\tt\t171\tc\tY\t57\tH\t(+ - -)\n-JY8QFUQ01A006G_CDR2\tt\t174\tc\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_CDR2\tg\t176\tc\tS\t59\tT\t(+ - +)\n-JY8QFUQ01A006G_FR2-CDR2\tc\t129\tg\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR2-CDR2\ta\t143\tg\tK\t48\tR\t(+ + +)\n-JY8QFUQ01A006G_FR2-CDR2\tg\t147\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR2-CDR2\ta\t157\tg\tI\t53\tV\t(+ - +)\n-JY8QFUQ01A006G_FR2-CDR2\tt\t169\tc\tY\t57\tH\t(+ - -)\n-JY8QFUQ01A006G_FR2-CDR2\tt\t171\tc\tY\t57\tH\t(+ - -)\n-JY8QFUQ01A006G_FR2-CDR2\tt\t174\tc\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR2-CDR2\tg\t176\tc\tS\t59\tT\t(+ - +)\n-JY8QFUQ01A006G_FR3\tc\t205\tt\tP\t69\tW\t(- - -)\n-JY8QFUQ01A006G_FR3\tc\t206\tg\tP\t69\tW\t(- - -)\n-JY8QFUQ01A006G_FR3\ta\t220\tc\tS\t74\tH\t(+ - -)\n-JY8QFUQ01A006G_FR3\tg\t221\ta\tS\t74\tH\t(+ - -)\n-JY8QFUQ01A006G_FR3\ta\t229\tt\tT\t77\tS\t(+ - +)\n-JY8QFUQ01A006G_FR3\tc\t231\tt\tT\t77\tS\t(+ - +)\n-JY8QFUQ01A006G_FR3\tc\t237\tg\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR3\ta\t240\tg\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR3\tg\t246\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR3\tc\t249\tg\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR3\ta\t251\tg\tK\t84\tS\t(- - -)\n-JY8QFUQ01A006G_FR3\tg\t252\tt\tK\t84\tS\t(- - -)\n-JY8QFUQ01A006G_FR3\ta\t269\tg\tK\t90\tR\t(+ + +)\n-JY8QFUQ01A006G_FR3\tc\t271\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR3\tc\t276\tg\tS\t92\tR\t(- - -)\n-JY8QFUQ01A006G_FR3\ta\t291\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR3\tg\t303\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01A006G_FR3\tt\t'..b'e\n-JY8QFUQ01DV4HU_FR3\tc\t287\tt\tA\t96\tV\t(+ - +)\n-JY8QFUQ01DV4HU_FR3\tg\t303\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01DV4HU_FR3\tc\t309\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01DV4HU_FR3\tt\t312\tc\tNone\tNone\tNone\tNone\n-JY8QFUQ01DV8LF_CDR1\ta\t106\tc\tS\t36\tR\t(- - -)\n-JY8QFUQ01DV8LF_FR2\tg\t147\tc\tNone\tNone\tNone\tNone\n-JY8QFUQ01DV8LF_CDR2\tt\t171\ta\tN\t57\tK\t(+ - -)\n-JY8QFUQ01DV8LF_CDR2\tg\t188\tt\tS\t63\tI\t(- - -)\n-JY8QFUQ01DV8LF_FR2-CDR2\tg\t147\tc\tNone\tNone\tNone\tNone\n-JY8QFUQ01DV8LF_FR2-CDR2\tt\t171\ta\tN\t57\tK\t(+ - -)\n-JY8QFUQ01DV8LF_FR2-CDR2\tg\t188\tt\tS\t63\tI\t(- - -)\n-JY8QFUQ01DV8LF_FR3\tc\t259\tg\tL\t87\tV\t(+ - +)\n-JY8QFUQ01DV8LF_FR3\tt\t306\tc\tNone\tNone\tNone\tNone\n-JY8QFUQ01DVBU0_CDR1\tc\t86\tt\tT\t29\tI\t(- - -)\n-JY8QFUQ01DVBU0_FR2\tc\t159\tg\tNone\tNone\tNone\tNone\n-JY8QFUQ01DVBU0_CDR2\tt\t167\tg\tI\t56\tS\t(- - -)\n-JY8QFUQ01DVBU0_CDR2\tt\t174\tc\tNone\tNone\tNone\tNone\n-JY8QFUQ01DVBU0_CDR2\ta\t176\tg\tD\t59\tG\t(- - -)\n-JY8QFUQ01DVBU0_CDR2\tt\t177\tg\tD\t59\tG\t(- - -)\n-JY8QFUQ01DVBU0_CDR2\tg\t188\tc\tS\t63\tT\t(+ - +)\n-JY8QFUQ01DVBU0_CDR2\ta\t190\tg\tS\t64\tD\t(- - -)\n-JY8QFUQ01DVBU0_CDR2\tg\t191\ta\tS\t64\tD\t(- - -)\n-JY8QFUQ01DVBU0_FR2-CDR2\tc\t159\tg\tNone\tNone\tNone\tNone\n-JY8QFUQ01DVBU0_FR2-CDR2\tt\t167\tg\tI\t56\tS\t(- - -)\n-JY8QFUQ01DVBU0_FR2-CDR2\tt\t174\tc\tNone\tNone\tNone\tNone\n-JY8QFUQ01DVBU0_FR2-CDR2\ta\t176\tg\tD\t59\tG\t(- - -)\n-JY8QFUQ01DVBU0_FR2-CDR2\tt\t177\tg\tD\t59\tG\t(- - -)\n-JY8QFUQ01DVBU0_FR2-CDR2\tg\t188\tc\tS\t63\tT\t(+ - +)\n-JY8QFUQ01DVBU0_FR2-CDR2\ta\t190\tg\tS\t64\tD\t(- - -)\n-JY8QFUQ01DVBU0_FR2-CDR2\tg\t191\ta\tS\t64\tD\t(- - -)\n-JY8QFUQ01DVBU0_FR3\ta\t196\tg\tS\t66\tA\t(- + -)\n-JY8QFUQ01DVBU0_FR3\tg\t197\tc\tS\t66\tA\t(- + -)\n-JY8QFUQ01DVBU0_FR3\ta\t238\tc\tNone\tNone\tNone\tNone\n-JY8QFUQ01DVBU0_FR3\tc\t248\tg\tA\t83\tG\t(- + -)\n-JY8QFUQ01DVBU0_FR3\tc\t249\tg\tA\t83\tG\t(- + -)\n-JY8QFUQ01DVBU0_FR3\tg\t303\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01DXDOM_CDR1\tc\t86\tg\tT\t29\tS\t(+ - +)\n-JY8QFUQ01DXDOM_CDR1\tc\t87\tt\tT\t29\tS\t(+ - +)\n-JY8QFUQ01DXDOM_CDR1\tg\t104\tc\tS\t35\tT\t(+ - +)\n-JY8QFUQ01DXDOM_CDR1\ta\t106\tg\tS\t36\tG\t(+ + -)\n-JY8QFUQ01DXDOM_CDR1\tc\t108\tt\tS\t36\tG\t(+ + -)\n-JY8QFUQ01DXDOM_CDR1\ta\t110\tt\tY\t37\tF\t(- + -)\n-JY8QFUQ01DXDOM_CDR1\tg\t113\tc\tS\t38\tT\t(+ - +)\n-JY8QFUQ01DXDOM_FR2\ta\t115\tg\tM\t39\tV\t(+ - -)\n-JY8QFUQ01DXDOM_FR2\ta\t119\tt\tN\t40\tI\t(- - -)\n-JY8QFUQ01DXDOM_FR2\tg\t139\ta\tG\t47\tR\t(- - -)\n-JY8QFUQ01DXDOM_FR2\tg\t153\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01DXDOM_FR2\tg\t157\ta\tV\t53\tI\t(+ - +)\n-JY8QFUQ01DXDOM_CDR2\ta\t166\tg\tI\t56\tV\t(+ - +)\n-JY8QFUQ01DXDOM_CDR2\tt\t168\tc\tI\t56\tV\t(+ - +)\n-JY8QFUQ01DXDOM_CDR2\tg\t170\tc\tS\t57\tT\t(+ - +)\n-JY8QFUQ01DXDOM_CDR2\tg\t173\tc\tS\t58\tT\t(+ - +)\n-JY8QFUQ01DXDOM_CDR2\tg\t176\ta\tS\t59\tN\t(- - -)\n-JY8QFUQ01DXDOM_CDR2\ta\t187\tg\tS\t63\tG\t(+ + -)\n-JY8QFUQ01DXDOM_CDR2\tt\t190\tc\tY\t64\tL\t(- - -)\n-JY8QFUQ01DXDOM_CDR2\ta\t191\tt\tY\t64\tL\t(- - -)\n-JY8QFUQ01DXDOM_CDR2\tt\t194\tc\tI\t65\tT\t(- - -)\n-JY8QFUQ01DXDOM_CDR2\ta\t195\tg\tI\t65\tT\t(- - -)\n-JY8QFUQ01DXDOM_FR2-CDR2\ta\t115\tg\tM\t39\tV\t(+ - -)\n-JY8QFUQ01DXDOM_FR2-CDR2\ta\t119\tt\tN\t40\tI\t(- - -)\n-JY8QFUQ01DXDOM_FR2-CDR2\tg\t139\ta\tG\t47\tR\t(- - -)\n-JY8QFUQ01DXDOM_FR2-CDR2\tg\t153\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01DXDOM_FR2-CDR2\tg\t157\ta\tV\t53\tI\t(+ - +)\n-JY8QFUQ01DXDOM_FR2-CDR2\ta\t166\tg\tI\t56\tV\t(+ - +)\n-JY8QFUQ01DXDOM_FR2-CDR2\tt\t168\tc\tI\t56\tV\t(+ - +)\n-JY8QFUQ01DXDOM_FR2-CDR2\tg\t170\tc\tS\t57\tT\t(+ - +)\n-JY8QFUQ01DXDOM_FR2-CDR2\tg\t173\tc\tS\t58\tT\t(+ - +)\n-JY8QFUQ01DXDOM_FR2-CDR2\tg\t176\ta\tS\t59\tN\t(- - -)\n-JY8QFUQ01DXDOM_FR2-CDR2\ta\t187\tg\tS\t63\tG\t(+ + -)\n-JY8QFUQ01DXDOM_FR2-CDR2\tt\t190\tc\tY\t64\tL\t(- - -)\n-JY8QFUQ01DXDOM_FR2-CDR2\ta\t191\tt\tY\t64\tL\t(- - -)\n-JY8QFUQ01DXDOM_FR2-CDR2\tt\t194\tc\tI\t65\tT\t(- - -)\n-JY8QFUQ01DXDOM_FR2-CDR2\ta\t195\tg\tI\t65\tT\t(- - -)\n-JY8QFUQ01DXDOM_FR3\tg\t213\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01DXDOM_FR3\ta\t214\tg\tK\t72\tE\t(+ - -)\n-JY8QFUQ01DXDOM_FR3\tc\t230\ta\tT\t77\tN\t(- + -)\n-JY8QFUQ01DXDOM_FR3\ta\t240\tg\tNone\tNone\tNone\tNone\n-JY8QFUQ01DXDOM_FR3\tg\t252\tc\tK\t84\tN\t(+ - -)\n-JY8QFUQ01DXDOM_FR3\tc\t255\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01DXDOM_FR3\tc\t257\tt\tS\t86\tL\t(- - -)\n-JY8QFUQ01DXDOM_FR3\tc\t259\tg\tL\t87\tV\t(+ - +)\n-JY8QFUQ01DXDOM_FR3\ta\t263\tt\tY\t88\tF\t(- + -)\n-JY8QFUQ01DXDOM_FR3\tc\t287\tt\tA\t96\tV\t(+ - +)\n-JY8QFUQ01DXDOM_FR3\tg\t297\tt\tNone\tNone\tNone\tNone\n-JY8QFUQ01DXDOM_FR3\tc\t299\tg\tA\t100\tG\t(- + -)\n-JY8QFUQ01DXDOM_FR3\tg\t303\ta\tNone\tNone\tNone\tNone\n-JY8QFUQ01DXDOM_FR3\tc\t309\tt\tNone\tNone\tNone\tNone\n' |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f tests/test_shm_csr.py --- a/tests/test_shm_csr.py Wed Feb 02 10:57:36 2022 +0000 +++ b/tests/test_shm_csr.py Mon Dec 12 12:32:44 2022 +0000 |
| [ |
| @@ -69,7 +69,11 @@ filter_unique_count = '2' class_filter = '70_70' empty_region_filter = 'FR1' - fast = 'no' + # Skip baseline and changeo by default. These tools cannot be modified + # anyway and take most of the test time to execute. The environment + # variable can be set to "no" on the CI so the code path is tested + # at the time a PR is ready. + fast = os.environ.get("SHM_CSR_FAST", "yes") cmd = [ "bash", wrapper, |
| b |
| diff -r f387cc1580c6 -r cf8ad181628f wrapper.sh --- a/wrapper.sh Wed Feb 02 10:57:36 2022 +0000 +++ b/wrapper.sh Mon Dec 12 12:32:44 2022 +0000 |
| [ |
| b'@@ -24,7 +24,10 @@\n \n #exec 5> debug_output.txt\n #BASH_XTRACEFD="5"\n-#PS4=\'$(date +%s.%N) $LINENO: \'\n+## Busybox date does not support \'+%s.%N\'. So use the slower python instead.\n+## Using -S python does not do \'import site\' which shortens the command\n+## to 10 milliseconds.\n+#PS4=\'$(python -Sc "import time; print(time.time())") $LINENO: \'\n #set -x\n \n mkdir -p $outdir\n@@ -84,107 +87,13 @@\n \n Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1\n \n-if [[ "${naive_output}" == "yes" ]] || [[ "$fast" == "no" ]] ; then\n-\n-\techo "---------------- creating new IMGT zips ----------------"\n-\techo "---------------- creating new IMGT zips ----------------<br />" >> $log\n-\n-\tmkdir $outdir/new_IMGT\n-\n-\tcp $PWD/summary.txt "$outdir/new_IMGT/1_Summary.txt"\n-\tcp $PWD/gapped_nt.txt "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"\n-\tcp $PWD/sequences.txt "$outdir/new_IMGT/3_Nt-sequences.txt"\n-\tcp $PWD/gapped_aa.txt "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"\n-\tcp $PWD/aa.txt "$outdir/new_IMGT/5_AA-sequences.txt"\n-\tcp $PWD/junction.txt "$outdir/new_IMGT/6_Junction.txt"\n-\tcp $PWD/mutationanalysis.txt "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"\n-\tcp $PWD/mutationstats.txt "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"\n-\tcp $PWD/aa_change_stats.txt "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"\n-\tcp $PWD/hotspots.txt "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"\n-\n-\tmkdir $outdir/new_IMGT_IGA\n-\tcp $outdir/new_IMGT/* $outdir/new_IMGT_IGA\n-\n-\tmkdir $outdir/new_IMGT_IGA1\n-\tcp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1\n-\n-\tmkdir $outdir/new_IMGT_IGA2\n-\tcp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2\n-\n-\tmkdir $outdir/new_IMGT_IGG\n-\tcp $outdir/new_IMGT/* $outdir/new_IMGT_IGG\n-\n-\tmkdir $outdir/new_IMGT_IGG1\n-\tcp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1\n-\n-\tmkdir $outdir/new_IMGT_IGG2\n-\tcp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2\n-\n-\tmkdir $outdir/new_IMGT_IGG3\n-\tcp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3\n-\n-\tmkdir $outdir/new_IMGT_IGG4\n-\tcp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4\n-\n-\tmkdir $outdir/new_IMGT_IGM\n-\tcp $outdir/new_IMGT/* $outdir/new_IMGT_IGM\n-\n-\tmkdir $outdir/new_IMGT_IGE\n-\tcp $outdir/new_IMGT/* $outdir/new_IMGT_IGE\n-\n-\tRscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1\n+echo "---------------- creating new IMGT zips ----------------"\n+echo "---------------- creating new IMGT zips ----------------<br />" >> $log\n \n-\tRscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1\n-\tRscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1\n-\tRscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1\n-\n-\tRscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1\n-\tRscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1\n-\tRscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1\n-\tRscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1\n-\tRscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1\n-\n-\tRscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1\n-\n-\tRscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1\n-\n-\n-\ttmp="$PWD"\n-\tcd $outdir/new_IMGT/ #tar weirdness...\n-\ttar -cJf ../new_IMGT.txz *\n-\n-\tcd $outdir/new_IMGT_IGA/\n-\ttar -cJf ../new_IMGT_IGA.txz *\n-\n-\tcd $outdir/new_IMGT_IGA1/\n-\ttar -cJf ../new_IMGT_IGA1.txz *\n+python $dir/split_imgt_file.py --outdir $outdir $input $outdir/merged.txt \\\n+ --prefix new_IMGT \\\n+ - IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE\n \n-\tcd $outdir/new_IMGT_IGA2/\n-\ttar -cJf ../new_IMGT_IGA2.txz *\n-\n-\tcd $outdir/new_IMGT_IGG/\n-\ttar -cJf ../new_'..b'tdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-defined_clones-summary-IGM.txt\n \t\tRscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-db-defined_first_clones-IGM.txt 2>&1\n \t\t\n-\t\tmkdir $outdir/new_IMGT_IGM_changeo\n-\t\tcp $outdir/new_IMGT/* $outdir/new_IMGT_IGM_changeo\n-\t\t\n-\t\tRscript $dir/new_imgt.r $outdir/new_IMGT_IGM_changeo $outdir/change_o/change-o-db-defined_first_clones-IGM.txt "-" 2>&1\n-\t\t\n-\t\tcd $outdir/new_IMGT_IGM_changeo\n-\t\ttar -cJf ../new_IMGT_IGM_first_seq_of_clone.txz *\n-\t\t\n-\t\trm -rf $outdir/new_IMGT_IGM_changeo\n-\t\t\n-\t\tcd $outdir/change_o\n+ python $dir/split_imgt_file.py --outdir $outdir --prefix new_IMGT_IGM_first_seq_of_clone \\\n+ $outdir/new_IMGT.txz $outdir/change_o/change-o-db-defined_first_clones-IGM.txt \\\n+ "-"\n+\n \telse\n \t\techo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"\n \t\techo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"\n \tfi\n \n-\tif [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then\n+\tif [[ "$(count_imgt_lines $outdir/new_IMGT_IGE.txz)" -gt "1" ]]; then\n \t\tbash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt\n \t\tbash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGE.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-defined_clones-summary-IGE.txt\n \t\tRscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-db-defined_first_clones-IGE.txt 2>&1\n \t\t\n-\t\tmkdir $outdir/new_IMGT_IGE_changeo\n-\t\tcp $outdir/new_IMGT/* $outdir/new_IMGT_IGE_changeo\n-\t\t\n-\t\tRscript $dir/new_imgt.r $outdir/new_IMGT_IGE_changeo $outdir/change_o/change-o-db-defined_first_clones-IGE.txt "-" 2>&1\n-\t\t\n-\t\tcd $outdir/new_IMGT_IGE_changeo\n-\t\ttar -cJf ../new_IMGT_IGE_first_seq_of_clone.txz *\n-\t\t\n-\t\trm -rf $outdir/new_IMGT_IGE_changeo\n-\t\t\n-\t\tcd $outdir/change_o\n+ python $dir/split_imgt_file.py --outdir $outdir --prefix new_IMGT_IGE_first_seq_of_clone \\\n+ $outdir/new_IMGT.txz $outdir/change_o/change-o-db-defined_first_clones-IGE.txt \\\n+ "-"\n+\n \telse\n \t\techo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"\n \t\techo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"\n \tfi\n \n \tcd "$tmp"\n-\t\n-\trm -rf $outdir/new_IMGT\n-\trm -rf $outdir/new_IMGT_IGA/\n-\trm -rf $outdir/new_IMGT_IGA1/\n-\trm -rf $outdir/new_IMGT_IGA2/\n-\trm -rf $outdir/new_IMGT_IGG/\n-\trm -rf $outdir/new_IMGT_IGG1/\n-\trm -rf $outdir/new_IMGT_IGG2/\n-\trm -rf $outdir/new_IMGT_IGG3/\n-\trm -rf $outdir/new_IMGT_IGG4/\n-\trm -rf $outdir/new_IMGT_IGM/\n-\trm -rf $outdir/new_IMGT_IGE/\n \n \techo "<div class=\'tabbertab\' title=\'Clonal Relation\' style=\'width: 7000px;\'>" >> $output #clonality tab\n \n@@ -860,7 +744,8 @@\n echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href=\'new_IMGT_IGG4.txz\' download=\'new_IMGT_IGG4.txz\' >Download</a></td></tr>" >> $output\n echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href=\'new_IMGT_IGM.txz\' download=\'new_IMGT_IGM.txz\' >Download</a></td></tr>" >> $output\n echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href=\'new_IMGT_IGE.txz\' download=\'new_IMGT_IGE.txz\' >Download</a></td></tr>" >> $output\n-\n+echo "<tr><td>An IMGT archive with just the matched and filtered naive IGM sequences (mutations below 2%)</td><td><a href=\'new_IMGT_IGM_NAIVE.txz\' download=\'new_IMGT_IGM_NAIVE.txz\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>An IMGT archive with just the matched and filtered naive memory IGM sequences (mutations 2% or higher)</td><td><a href=\'new_IMGT_IGM_NAIVE_MEMORY.txz\' download=\'new_IMGT_IGM_NAIVE_MEMORY.txz\' >Download</a></td></tr>" >> $output\n echo "</table>" >> $output\n \n echo "<br />" >> $output\n' |
