Galaxy |

Changeset 90:6809c63d9161 (2022-01-25)

Previous changeset 89:3c9d4d976c47 (2021-11-05) Next changeset 91:f387cc1580c6 (2022-02-02)

Commit message:
"planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"

modified:
CHANGELOG.md
conda_environment.yml
remove_files.txt
shm_clonality.htm
shm_csr.htm
shm_csr.py
shm_csr.xml
shm_downloads.htm
shm_first.htm
shm_frequency.htm
shm_overview.htm
shm_selection.htm
shm_transition.htm
tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc
tests/test_shm_csr.py
tests/validation_data/shm_overview.txt
wrapper.sh

added:
build_container.sh
create_container_hash.py
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.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
tests/validation_data/tandems_by_id.txt

diff -r 3c9d4d976c47 -r 6809c63d9161 CHANGELOG.md
--- a/CHANGELOG.md Fri Nov 05 13:41:03 2021 +0000
+++ b/CHANGELOG.md Tue Jan 25 11:28:29 2022 +0000

@@ -1,3 +1,24 @@
+version 1.4.0
+-------------
++ Fix a bug where synonymous mutations where incorrectly parsed.
++ Use a container from biocontainers.
+
+version 1.3.3
+-------------
++ Fix a bug where tandem lengths were incorrectly calculated.
+
+version 1.3.2
+-------------
++ Fix a bug where the file removal process caused errors.
+
+version 1.3.1
+-------------
++ Fix issues with container discovery
+
+version 1.3.0
+-------------
++ Add missing dependencies to the requirements section.
+
version 1.2.0
-------------
+ Add a container in which the tool can execute.

diff -r 3c9d4d976c47 -r 6809c63d9161 build_container.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/build_container.sh Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+set -e
+DEFAULT_BASE_IMAGE="$1"
+
+python3 create_container_hash.py $DEFAULT_BASE_IMAGE
+mulled-build-files --namespace rhpvorderman build-and-test ./container_hash.tsv --verbose
+

diff -r 3c9d4d976c47 -r 6809c63d9161 conda_environment.yml
--- a/conda_environment.yml Fri Nov 05 13:41:03 2021 +0000
+++ b/conda_environment.yml Tue Jan 25 11:28:29 2022 +0000

@@ -17,7 +17,10 @@
   - r-seqinr=3.4_5
   - r-data.table=1.11.4
   - file=5.39
+  - bc=1.07.1
+  - findutils=4.6.0
+  - font-ttf-ubuntu=0.83
   # Test dependencies below
-  - pytest
+  - pytest=6.2.5
   # Add planemo so tool can be uploaded
-  - planemo
+  - planemo=0.74.9

diff -r 3c9d4d976c47 -r 6809c63d9161 create_container_hash.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/create_container_hash.py Tue Jan 25 11:28:29 2022 +0000

[

@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+
+import sys
+
+from xml.etree import ElementTree
+from xml.etree.ElementTree import Element
+
+DEFAULT_BASE_IMAGE = "bgruening/busybox-bash:0.1"
+def main():
+    try:
+        base_image = sys.argv[1]
+    except IndexError:
+        base_image = DEFAULT_BASE_IMAGE
+    tool = ElementTree.parse("shm_csr.xml").getroot()
+    requirements: Element = tool.find("requirements")
+    packages = []
+    for req in requirements.findall("requirement"):
+        if req.get("type") == "package":
+            name = req.text
+            version = req.get("version")
+            package_string = f"{name}={version}"
+            packages.append(package_string)
+    with open("container_hash.tsv", mode="wt") as container_hash_file:
+        container_hash_file.write("#targets\tbase_image\timage_build\n")
+        container_hash_file.write(",".join(packages) + f"\t{base_image}\t0\n")
+
+
+if __name__ == "__main__":
+    main()

diff -r 3c9d4d976c47 -r 6809c63d9161 remove_files.txt
--- a/remove_files.txt Fri Nov 05 13:41:03 2021 +0000
+++ b/remove_files.txt Tue Jan 25 11:28:29 2022 +0000

b'@@ -1,171 +1,160 @@\n-results/aa_histogram.txt\n-results/aa_histogram_absent.txt\n-results/aa_histogram_absent_IGA.txt\n-results/aa_histogram_absent_IGG.txt\n-results/aa_histogram_absent_IGM.txt\n-results/aa_histogram_count.txt\n-results/aa_histogram_count_IGA.txt\n-results/aa_histogram_count_IGG.txt\n-results/aa_histogram_count_IGM.txt\n-results/aa_histogram_IGA.txt\n-results/aa_histogram_IGG.txt\n-results/aa_histogram_IGM.txt\n-results/after_unique_filter.txt\n-results/all_mean_n.txt\n-results/all_mean_value.txt\n-results/all_median_n.txt\n-results/all_median_value.txt\n-results/all_sum_n.txt\n-results/all_sum_value.txt\n-results/before_filters.txt\n-results/before_unique_filter.txt\n-results/data_sum.txt\n-results/filtering_steps.txt\n-results/hotspot_analysis_mean.txt\n-results/hotspot_analysis_median.txt\n-results/hotspot_analysis_sum.txt\n-results/identified_genes.txt\n-results/IGA1_mean_n.txt\n-results/IGA1_mean_value.txt\n-results/IGA1_median_n.txt\n-results/IGA1_median_value.txt\n-results/IGA1_sum_n.txt\n-results/IGA1_sum_value.txt\n-results/IGA2_mean_n.txt\n-results/IGA2_mean_value.txt\n-results/IGA2_median_n.txt\n-results/IGA2_median_value.txt\n-results/IGA2_sum_n.txt\n-results/IGA2_sum_value.txt\n-results/IGA_mean_n.txt\n-results/IGA_mean_value.txt\n-results/IGA_median_n.txt\n-results/IGA_median_value.txt\n-results/IGA_sum_n.txt\n-results/IGA_sum_value.txt\n-results/IGE_mean_n.txt\n-results/IGE_mean_value.txt\n-results/IGE_median_n.txt\n-results/IGE_median_value.txt\n-results/IGE_sum_n.txt\n-results/IGE_sum_value.txt\n-results/IGG1_mean_n.txt\n-results/IGG1_mean_value.txt\n-results/IGG1_median_n.txt\n-results/IGG1_median_value.txt\n-results/IGG1_sum_n.txt\n-results/IGG1_sum_value.txt\n-results/IGG2_mean_n.txt\n-results/IGG2_mean_value.txt\n-results/IGG2_median_n.txt\n-results/IGG2_median_value.txt\n-results/IGG2_sum_n.txt\n-results/IGG2_sum_value.txt\n-results/IGG3_mean_n.txt\n-results/IGG3_mean_value.txt\n-results/IGG3_median_n.txt\n-results/IGG3_median_value.txt\n-results/IGG3_sum_n.txt\n-results/IGG3_sum_value.txt\n-results/IGG4_mean_n.txt\n-results/IGG4_mean_value.txt\n-results/IGG4_median_n.txt\n-results/IGG4_median_value.txt\n-results/IGG4_sum_n.txt\n-results/IGG4_sum_value.txt\n-results/IGG_mean_n.txt\n-results/IGG_mean_value.txt\n-results/IGG_median_n.txt\n-results/IGG_median_value.txt\n-results/IGG_sum_n.txt\n-results/IGG_sum_value.txt\n-results/IGM_mean_n.txt\n-results/IGM_mean_value.txt\n-results/IGM_median_n.txt\n-results/IGM_median_value.txt\n-results/IGM_sum_n.txt\n-results/IGM_sum_value.txt\n-results/matched_all_mean.txt\n-results/matched_all_median.txt\n-results/matched_IGA1_mean.txt\n-results/matched_IGA1_median.txt\n-results/matched_IGA2_mean.txt\n-results/matched_IGA2_median.txt\n-results/matched_IGA_mean.txt\n-results/matched_IGA_median.txt\n-results/matched_IGE_mean.txt\n-results/matched_IGE_median.txt\n-results/matched_IGG1_mean.txt\n-results/matched_IGG1_median.txt\n-results/matched_IGG2_mean.txt\n-results/matched_IGG2_median.txt\n-results/matched_IGG3_mean.txt\n-results/matched_IGG3_median.txt\n-results/matched_IGG4_mean.txt\n-results/matched_IGG4_median.txt\n-results/matched_IGG_mean.txt\n-results/matched_IGG_median.txt\n-results/matched_IGM_mean.txt\n-results/matched_IGM_median.txt\n-results/matched_unmatched_mean.txt\n-results/matched_unmatched_median.txt\n-results/matched_unmatched_sum.txt\n-results/mutationdict.txt\n-results/mutation_in_motifs.txt\n-results/mutations_mean.txt\n-results/mutations_median.txt\n-results/mutations_sum.txt\n-results/RGYW.txt\n-results/shm_overview_tandem_row.txt\n-results/tandem_frequency.txt\n-results/transitions_all_mean.txt\n-results/transitions_all_median.txt\n-results/transitions_IGA1_mean.txt\n-results/transitions_IGA1_median.txt\n-results/transitions_IGA2_mean.txt\n-results/transitions_IGA2_median.txt\n-results/transitions_IGA_mean.txt\n-results/transitions_IGA_median.txt\n-results/transitions_IGE_mean.txt\n-results/transitions_IGE_median.txt\n-results/transitions_IGG1_mean.txt\n-results/transitions_IGG1_median.txt\n-results/transitions_IGG2_mean.txt\n-results/transitions_IGG2_media'..b'e-o-db-IGA.txt\n-results/change_o/change-o-db-IGG.txt\n-results/change_o/change-o-db-IGM.txt\n-results/change_o/input.tab\n-aa.txt\n-aa_change_stats.txt\n-gapped_aa.txt\n-gapped_nt.txt\n-hotspots.txt\n-junction.txt\n-mutationanalysis.txt\n-mutationstats.txt\n-sequences.txt\n-summary.txt\n-Rplots.pdf\n+aa_histogram.txt\n+aa_histogram_absent.txt\n+aa_histogram_absent_IGA.txt\n+aa_histogram_absent_IGG.txt\n+aa_histogram_absent_IGM.txt\n+aa_histogram_count.txt\n+aa_histogram_count_IGA.txt\n+aa_histogram_count_IGG.txt\n+aa_histogram_count_IGM.txt\n+aa_histogram_IGA.txt\n+aa_histogram_IGG.txt\n+aa_histogram_IGM.txt\n+after_unique_filter.txt\n+all_mean_n.txt\n+all_mean_value.txt\n+all_median_n.txt\n+all_median_value.txt\n+all_sum_n.txt\n+all_sum_value.txt\n+before_filters.txt\n+before_unique_filter.txt\n+data_sum.txt\n+filtering_steps.txt\n+hotspot_analysis_mean.txt\n+hotspot_analysis_median.txt\n+hotspot_analysis_sum.txt\n+identified_genes.txt\n+IGA1_mean_n.txt\n+IGA1_mean_value.txt\n+IGA1_median_n.txt\n+IGA1_median_value.txt\n+IGA1_sum_n.txt\n+IGA1_sum_value.txt\n+IGA2_mean_n.txt\n+IGA2_mean_value.txt\n+IGA2_median_n.txt\n+IGA2_median_value.txt\n+IGA2_sum_n.txt\n+IGA2_sum_value.txt\n+IGA_mean_n.txt\n+IGA_mean_value.txt\n+IGA_median_n.txt\n+IGA_median_value.txt\n+IGA_sum_n.txt\n+IGA_sum_value.txt\n+IGE_mean_n.txt\n+IGE_mean_value.txt\n+IGE_median_n.txt\n+IGE_median_value.txt\n+IGE_sum_n.txt\n+IGE_sum_value.txt\n+IGG1_mean_n.txt\n+IGG1_mean_value.txt\n+IGG1_median_n.txt\n+IGG1_median_value.txt\n+IGG1_sum_n.txt\n+IGG1_sum_value.txt\n+IGG2_mean_n.txt\n+IGG2_mean_value.txt\n+IGG2_median_n.txt\n+IGG2_median_value.txt\n+IGG2_sum_n.txt\n+IGG2_sum_value.txt\n+IGG3_mean_n.txt\n+IGG3_mean_value.txt\n+IGG3_median_n.txt\n+IGG3_median_value.txt\n+IGG3_sum_n.txt\n+IGG3_sum_value.txt\n+IGG4_mean_n.txt\n+IGG4_mean_value.txt\n+IGG4_median_n.txt\n+IGG4_median_value.txt\n+IGG4_sum_n.txt\n+IGG4_sum_value.txt\n+IGG_mean_n.txt\n+IGG_mean_value.txt\n+IGG_median_n.txt\n+IGG_median_value.txt\n+IGG_sum_n.txt\n+IGG_sum_value.txt\n+IGM_mean_n.txt\n+IGM_mean_value.txt\n+IGM_median_n.txt\n+IGM_median_value.txt\n+IGM_sum_n.txt\n+IGM_sum_value.txt\n+matched_all_mean.txt\n+matched_all_median.txt\n+matched_IGA1_mean.txt\n+matched_IGA1_median.txt\n+matched_IGA2_mean.txt\n+matched_IGA2_median.txt\n+matched_IGA_mean.txt\n+matched_IGA_median.txt\n+matched_IGE_mean.txt\n+matched_IGE_median.txt\n+matched_IGG1_mean.txt\n+matched_IGG1_median.txt\n+matched_IGG2_mean.txt\n+matched_IGG2_median.txt\n+matched_IGG3_mean.txt\n+matched_IGG3_median.txt\n+matched_IGG4_mean.txt\n+matched_IGG4_median.txt\n+matched_IGG_mean.txt\n+matched_IGG_median.txt\n+matched_IGM_mean.txt\n+matched_IGM_median.txt\n+matched_unmatched_mean.txt\n+matched_unmatched_median.txt\n+matched_unmatched_sum.txt\n+mutationdict.txt\n+mutation_in_motifs.txt\n+mutations_mean.txt\n+mutations_median.txt\n+mutations_sum.txt\n+RGYW.txt\n+shm_overview_tandem_row.txt\n+tandem_frequency.txt\n+transitions_all_mean.txt\n+transitions_all_median.txt\n+transitions_IGA1_mean.txt\n+transitions_IGA1_median.txt\n+transitions_IGA2_mean.txt\n+transitions_IGA2_median.txt\n+transitions_IGA_mean.txt\n+transitions_IGA_median.txt\n+transitions_IGE_mean.txt\n+transitions_IGE_median.txt\n+transitions_IGG1_mean.txt\n+transitions_IGG1_median.txt\n+transitions_IGG2_mean.txt\n+transitions_IGG2_median.txt\n+transitions_IGG3_mean.txt\n+transitions_IGG3_median.txt\n+transitions_IGG4_mean.txt\n+transitions_IGG4_median.txt\n+transitions_IGG_mean.txt\n+transitions_IGG_median.txt\n+transitions_IGM_mean.txt\n+transitions_IGM_median.txt\n+transitions_unmatched_mean.txt\n+transitions_unmatched_median.txt\n+transitions_unmatched_sum.txt\n+unmatched_mean_n.txt\n+unmatched_mean_value.txt\n+unmatched_median_n.txt\n+unmatched_median_value.txt\n+unmatched_sum_n.txt\n+unmatched_sum_value.txt\n+change_o/change-o-db.txt\n+change_o/change-o-db-defined_first_clones.txt\n+change_o/change-o-db-defined_first_clones-IGA.txt\n+change_o/change-o-db-defined_first_clones-IGG.txt\n+change_o/change-o-db-defined_first_clones-IGM.txt\n+change_o/change-o-db-IGA.txt\n+change_o/change-o-db-IGG.txt\n+change_o/change-o-db-IGM.txt\n+change_o/input.tab\n'

diff -r 3c9d4d976c47 -r 6809c63d9161 shm_clonality.htm
--- a/shm_clonality.htm Fri Nov 05 13:41:03 2021 +0000
+++ b/shm_clonality.htm Tue Jan 25 11:28:29 2022 +0000

[

diff -r 3c9d4d976c47 -r 6809c63d9161 shm_csr.htm
--- a/shm_csr.htm Fri Nov 05 13:41:03 2021 +0000
+++ b/shm_csr.htm Tue Jan 25 11:28:29 2022 +0000

diff -r 3c9d4d976c47 -r 6809c63d9161 shm_csr.py
--- a/shm_csr.py Fri Nov 05 13:41:03 2021 +0000
+++ b/shm_csr.py Tue Jan 25 11:28:29 2022 +0000

[

b'@@ -2,15 +2,94 @@\n import logging\n import sys\n import os\n-import re\n+import typing\n+from typing import Optional\n \n from collections import defaultdict\n \n+REGION_FILTERS = ("leader", "FR1", "CDR1", "FR2", "CDR2")\n+\n+\n+class Mutation(typing.NamedTuple):\n+\t"""Represent a mutation type as a tuple"""\n+\tfrm: str # \'from\' is a reserved python keyword.\n+\twhere: int\n+\tto: str\n+\tfrmAA: Optional[str] = None\n+\twhereAA: Optional[int] = None\n+\ttoAA: Optional[str] = None\n+\tthing: Optional[str] = None # \'(---)\' or \'(+-+)\' etc. No idea\n+\n+\t@classmethod\n+\tdef from_string(cls, string: str):\n+\t\t# Complete mutation example: a88>g,I30>V(+ - +)\n+\t\t# Only nucleotide example: g303>t\n+\t\t# Including codon change:\n+\t\t# t169>g,Y57>D(- - -); Y57 tat 169-171 [ta 169-170]>D gac\n+\t\t# Including codon change (synonumous mutation):\n+\t\t# c114>t, Y38; Y38 tac 112-114 [tact 112-115]>Y tat\n+\t\tif \',\' in string:\n+\t\t\tnucleotide_change, aa_change = string.split(\',\', maxsplit=1) # type: str, Optional[str]\n+\t\telse:\n+\t\t\tnucleotide_change = string\n+\t\t\taa_change = None\n+\t\tfrm_part, to = nucleotide_change.split(\'>\', maxsplit=1)\n+\t\tfrm = frm_part[0]\n+\t\twhere = int(frm_part[1:])\n+\n+\t\tif aa_change is None:\n+\t\t\treturn cls(frm, where, to)\n+\n+\t\taa_change = aa_change.strip()\n+\t\t# The part after semicolon indicates the codon change. This part may\n+\t\t# not be present.\n+\t\tsemi_colon_index = aa_change.find(";")\n+\t\tif semi_colon_index == -1:\n+\t\t\tcodon_change = ""\n+\t\telse:\n+\t\t\tcodon_change = aa_change[semi_colon_index:]\n+\t\t\taa_change = aa_change[:semi_colon_index]\n+\t\tchange_operator_index = aa_change.find(">")\n+\t\tif change_operator_index == -1:\n+\t\t\t# Synonymous change\n+\t\t\tfrmAA_part = aa_change\n+\t\t\ttoAA_part = ""\n+\t\telse:\n+\t\t\tfrmAA_part, toAA_part = aa_change.split(\'>\', maxsplit=1) # type: str, str\n+\t\tfrmAA = frmAA_part[0]\n+\t\twhereAA = int(frmAA_part[1:])\n+\t\tif toAA_part:\n+\t\t\tbrace_start = toAA_part.index(\'(\')\n+\t\t\ttoAA = toAA_part[:brace_start]\n+\t\t\tthing = toAA_part[brace_start:] + codon_change\n+\t\telse:\n+\t\t\t# Synonymous mutation\n+\t\t\ttoAA = frmAA\n+\t\t\tthing = codon_change\n+\t\treturn cls(frm, where, to, frmAA, whereAA, toAA, thing)\n+\n+\n+class Hotspot(typing.NamedTuple):\n+\tstart: int\n+\tend: int\n+\tregion: str\n+\n+\t@classmethod\n+\tdef from_string(cls, string):\n+\t\t# Example: aa,40-41(FR1)\n+\t\tsequence, rest = string.split(\',\') # type: str, str\n+\t\tbrace_pos = rest.index(\'(\')\n+\t\tnumbers = rest[:brace_pos]\n+\t\tstart, end = numbers.split(\'-\')\n+\t\tregion = rest[brace_pos + 1:-1] # Remove the braces\n+\t\treturn cls(int(start), int(end), region)\n+\n+\n def main():\n \tparser = argparse.ArgumentParser()\n \tparser.add_argument("--input", help="The \'7_V-REGION-mutation-and-AA-change-table\' and \'10_V-REGION-mutation-hotspots\' merged together, with an added \'best_match\' annotation")\n \tparser.add_argument("--genes", help="The genes available in the \'best_match\' column")\n-\tparser.add_argument("--empty_region_filter", help="Where does the sequence start?", choices=[\'leader\', \'FR1\', \'CDR1\', \'FR2\'])\n+\tparser.add_argument("--empty_region_filter", help="Where does the sequence start?", choices=REGION_FILTERS)\n \tparser.add_argument("--output", help="Output file")\n \n \targs = parser.parse_args()\n@@ -23,12 +102,7 @@\n \tgenedic = dict()\n \n \tmutationdic = dict()\n-\tmutationMatcher = re.compile("^(.)(\\d+).(.),?[ ]?(.)?(\\d+)?.?(.)?(.?.?.?.?.?)?")\n-\tmutationMatcher = re.compile("^([actg])(\\d+).([actg]),?[ ]?([A-Z])?(\\d+)?.?([A-Z])?(.*)?")\n-\tmutationMatcher = re.compile("^([actg])(\\d+).([actg]),?[ ]?([A-Z])?(\\d+)?[>]?([A-Z;])?(.*)?")\n-\tmutationMatcher = re.compile(r"^([nactg])(\\d+).([nactg]),?[ ]?([A-Z*])?(\\d+)?[>]?([A-Z*;])?(.*)?")\n \tNAMatchResult = (None, None, None, None, None, None, \'\')\n-\tgeneMatchers = {gene: re.compile("^" + gene + ".*") for gene in genes}\n \tlinecount = 0\n \n \tIDIndex = 0\n@@ -42,20 +116,14 @@\n \tIDlist = []\n \tmutationList = []\n \tmutationListByID = {}\n-\tcdr1LengthDic = {}\n-\tcdr2LengthDic = {}\n+\tcdr1AALengthDic = {}\n+\tcdr2AALengthDic = {}\n \n-\tfr1LengthDict = {}\n-\tfr2LengthDict = {}\n-\tfr3LengthDict = {}\n+\tLengthDi'..b'gth)\n-\t\t\to.write("{0}\\t{1}\\t{2}\\t{3}\\t{4}\\t{5}\\t{6}\\n".format(ID,\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tstr(num_mutations),\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tstr(num_tandem_muts),\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tstr(region_length),\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tstr(round(expected_tandem_muts, 2)),\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tstr(longest_tandem[1]),\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tstr(tandem_muts)))\n+\t\t\t# String format and round disagree slightly (see 3.605).\n+\t\t\t# So round before formatting.\n+\t\t\to.write(f"{ID}\\t{num_mutations}\\t{num_tandem_muts}\\t{region_length}\\t"\n+\t\t\t\t\tf"{round(expected_tandem_muts, 2):.2f}\\t" \n+\t\t\t\t\tf"{longest_tandem[1]}\\t{tandem_muts}\\n")\n \t\t\tgene = genedic[ID]\n \t\t\tif gene.find("unmatched") == -1:\n \t\t\t\ttandem_sum_by_class[gene] += num_tandem_muts\n@@ -301,11 +366,11 @@\n \tabsentAACDR2Dic[9] = [60]\n \n \tabsentAA = [len(IDlist)] * (AALength-1)\n-\tfor k, cdr1Length in cdr1LengthDic.items():\n+\tfor k, cdr1Length in cdr1AALengthDic.items():\n \t\tfor c in absentAACDR1Dic[cdr1Length]:\n \t\t\tabsentAA[c] -= 1\n \n-\tfor k, cdr2Length in cdr2LengthDic.items():\n+\tfor k, cdr2Length in cdr2AALengthDic.items():\n \t\tfor c in absentAACDR2Dic[cdr2Length]:\n \t\t\tabsentAA[c] -= 1\n \n@@ -315,11 +380,11 @@\n \t\to.write("ID\\tcdr1length\\tcdr2length\\tbest_match\\t" + "\\t".join([str(x) for x in range(1,AALength)]) + "\\n")\n \t\tfor ID in IDlist:\n \t\t\tabsentAAbyID = [1] * (AALength-1)\n-\t\t\tcdr1Length = cdr1LengthDic[ID]\n+\t\t\tcdr1Length = cdr1AALengthDic[ID]\n \t\t\tfor c in absentAACDR1Dic[cdr1Length]:\n \t\t\t\tabsentAAbyID[c] -= 1\n \n-\t\t\tcdr2Length = cdr2LengthDic[ID]\n+\t\t\tcdr2Length = cdr2AALengthDic[ID]\n \t\t\tfor c in absentAACDR2Dic[cdr2Length]:\n \t\t\t\tabsentAAbyID[c] -= 1\n \t\t\to.write(ID + "\\t" + str(cdr1Length) + "\\t" + str(cdr2Length) + "\\t" + genedic[ID] + "\\t" + "\\t".join([str(x) for x in absentAAbyID]) + "\\n")\n@@ -333,7 +398,6 @@\n \t\t\to.write("TW (%)," + ("0,0,0\\n" * len(genes)))\n \t\tsys.exit()\n \n-\thotspotMatcher = re.compile("[actg]+,(\\d+)-(\\d+)\$(.*)\$")\n \tRGYWCount = {}\n \tWRCYCount = {}\n \tWACount = {}\n@@ -358,14 +422,10 @@\n \t\t\tlinesplt = line.split("\\t")\n \t\t\tgene = linesplt[best_matchIndex]\n \t\t\tID = linesplt[IDIndex]\n-\t\t\tRGYW = [(int(x), int(y), z) for (x, y, z) in\n-\t\t\t\t\t[hotspotMatcher.match(x).groups() for x in linesplt[aggctatIndex].split("|") if x]]\n-\t\t\tWRCY = [(int(x), int(y), z) for (x, y, z) in\n-\t\t\t\t\t[hotspotMatcher.match(x).groups() for x in linesplt[atagcctIndex].split("|") if x]]\n-\t\t\tWA = [(int(x), int(y), z) for (x, y, z) in\n-\t\t\t\t[hotspotMatcher.match(x).groups() for x in linesplt[ataIndex].split("|") if x]]\n-\t\t\tTW = [(int(x), int(y), z) for (x, y, z) in\n-\t\t\t\t[hotspotMatcher.match(x).groups() for x in linesplt[tatIndex].split("|") if x]]\n+\t\t\tRGYW = [Hotspot.from_string(x) for x in linesplt[aggctatIndex].split("|") if x]\n+\t\t\tWRCY = [Hotspot.from_string(x) for x in linesplt[atagcctIndex].split("|") if x]\n+\t\t\tWA = [Hotspot.from_string(x) for x in linesplt[ataIndex].split("|") if x]\n+\t\t\tTW = [Hotspot.from_string(x) for x in linesplt[tatIndex].split("|") if x]\n \t\t\tRGYWCount[ID], WRCYCount[ID], WACount[ID], TWCount[ID] = 0, 0, 0, 0\n \n \t\t\twith open(os.path.join(os.path.dirname(os.path.abspath(infile)), "RGYW.txt"), \'a\') as out_handle:\n@@ -417,7 +477,7 @@\n \t\t\t\t\t\t\t\tout_handle.write("{0}\\n".format(\n \t\t\t\t\t\t\t\t\t"\\t".join([\n \t\t\t\t\t\t\t\t\t\tID,\n-\t\t\t\t\t\t\t\t\t\twhere,\n+\t\t\t\t\t\t\t\t\t\tstr(where),\n \t\t\t\t\t\t\t\t\t\tregion,\n \t\t\t\t\t\t\t\t\t\tfrm,\n \t\t\t\t\t\t\t\t\t\tto,\n@@ -483,11 +543,10 @@\n \t\t\t\to.write(typ + " (%)")\n \t\t\t\tcurr = dic[typ]\n \t\t\t\tfor gene in genes:\n-\t\t\t\t\tgeneMatcher = geneMatchers[gene]\n-\t\t\t\t\tif valuedic[gene + "_" + fname] is 0:\n+\t\t\t\t\tif valuedic[gene + "_" + fname] == 0:\n \t\t\t\t\t\to.write(",0,0,0")\n \t\t\t\t\telse:\n-\t\t\t\t\t\tx, y, z = get_xyz([curr[x] for x in [y for y, z in genedic.items() if geneMatcher.match(z)]], gene, func, fname)\n+\t\t\t\t\t\tx, y, z = get_xyz([curr[x] for x in [y for y, z in genedic.items() if z.startswith(gene)]], gene, func, fname)\n \t\t\t\t\t\to.write("," + x + "," + y + "," + z)\n \t\t\t\tx, y, z = get_xyz([y for x, y in curr.items() if not genedic[x].startswith("unmatched")], "total", func, fname)\n \t\t\t\t#x, y, z = get_xyz([y for x, y in curr.iteritems()], "total", func, fname)\n'

diff -r 3c9d4d976c47 -r 6809c63d9161 shm_csr.xml
--- a/shm_csr.xml Fri Nov 05 13:41:03 2021 +0000
+++ b/shm_csr.xml Tue Jan 25 11:28:29 2022 +0000

@@ -1,4 +1,4 @@
-<tool id="shm_csr" name="SHM & CSR pipeline" version="1.3.0">
+<tool id="shm_csr" name="SHM & CSR pipeline" version="1.4.0">
<description></description>
<requirements>
<requirement type="package" version="3.7.1">python</requirement>
@@ -16,6 +16,9 @@
<requirement type="package" version="4.4.18">bash</requirement>
<requirement type="package" version="1.34">tar</requirement>
<requirement type="package" version="5.39">file</requirement>
+ <requirement type="package" version="4.6.0">findutils</requirement>
+ <requirement type="package" version="1.07.1">bc</requirement>
+ <requirement type="package" version="0.83">font-ttf-ubuntu</requirement>
</requirements>
<command interpreter="bash">
#if str ( $filter_unique.filter_unique_select ) == "remove":

diff -r 3c9d4d976c47 -r 6809c63d9161 shm_downloads.htm
--- a/shm_downloads.htm Fri Nov 05 13:41:03 2021 +0000
+++ b/shm_downloads.htm Tue Jan 25 11:28:29 2022 +0000

@@ -1,7 +1,7 @@
<html>

<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
<meta name=Generator content="Microsoft Word 14 (filtered)">
<style>
<!--
@@ -77,7 +77,7 @@
style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The SHM Overview
table as a dataset: Allows downloading of the SHM Overview
-table as a data set.� 
+table as a data set. 

Motif data per
@@ -97,7 +97,7 @@
every sequence: links to a page showing for each transcript the
sequence of the analysed region (as dependent on the sequence starts at filter),
-the assigned subclass and the number of sequenced A,C,G and T�s.
+the assigned subclass and the number of sequenced A,C,G and T’s.

The data used to
@@ -135,7 +135,7 @@
generate the frequency by class plot: Allows
downloading the data used to generate frequency by class plot included in the
-SHM frequency tab. �� 
+SHM frequency tab. 

The data for
@@ -145,7 +145,7 @@
>20% SHM. Information is provided for each subclass.

�
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> 

Transition
@@ -267,7 +267,7 @@
The data used to
generate the aa mutation frequency plot for IGE:� Provides the
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the
data used to generate the aa mutation frequency plot for all IGE sequences in
the antigen selection tab.

@@ -314,7 +314,7 @@
data:
Table output of the BASELINe analysis. Calculation of antigen selection as
performed by BASELINe are shown for each individual IGG sequence and the sum of
-all IGG sequences.�� 
+all IGG sequences. 

Baseline IGM PDF:Sequence overlap
between subclasses: Link to the overlap table as provided
-under the clonality overlap tab. �� 
+under the clonality overlap tab. 

The Change-O DB
@@ -388,7 +388,7 @@
style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
defined clones summary file: Gives a summary of the total number of
-clones in all sequences and their clone size. �� 
+clones in all sequences and their clone size. 

The Change-O DB
@@ -423,7 +423,7 @@
The Change-O DB
file with defined clones of IGM:�Downloads a table
+12.0pt;font-family:"Times New Roman","serif"'> Downloads a table
with the calculation of clonal relation between all IGM sequences. For each
individual transcript the results of the clonal assignment as provided by
Change-O are provided. Sequences with the same number in the CLONE column are

diff -r 3c9d4d976c47 -r 6809c63d9161 shm_first.htm
--- a/shm_first.htm Fri Nov 05 13:41:03 2021 +0000
+++ b/shm_first.htm Tue Jan 25 11:28:29 2022 +0000

diff -r 3c9d4d976c47 -r 6809c63d9161 shm_frequency.htm
--- a/shm_frequency.htm Fri Nov 05 13:41:03 2021 +0000
+++ b/shm_frequency.htm Tue Jan 25 11:28:29 2022 +0000

diff -r 3c9d4d976c47 -r 6809c63d9161 shm_overview.htm
--- a/shm_overview.htm Fri Nov 05 13:41:03 2021 +0000
+++ b/shm_overview.htm Tue Jan 25 11:28:29 2022 +0000

diff -r 3c9d4d976c47 -r 6809c63d9161 shm_selection.htm
--- a/shm_selection.htm Fri Nov 05 13:41:03 2021 +0000
+++ b/shm_selection.htm Tue Jan 25 11:28:29 2022 +0000

[

diff -r 3c9d4d976c47 -r 6809c63d9161 shm_transition.htm
--- a/shm_transition.htm Fri Nov 05 13:41:03 2021 +0000
+++ b/shm_transition.htm Tue Jan 25 11:28:29 2022 +0000

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA.pdf

Binary file test-output/IGA.pdf has changed

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA.png

Binary file test-output/IGA.png has changed

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA1_mean_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA1_mean_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+593
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA1_mean_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA1_mean_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+20.6
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA1_median_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA1_median_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+593
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA1_median_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA1_median_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+20
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA1_sum_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA1_sum_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+593
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA1_sum_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA1_sum_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+12223
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA2_mean_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA2_mean_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+324
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA2_mean_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA2_mean_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+17.8
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA2_median_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA2_median_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+324
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA2_median_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA2_median_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+16.5
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA2_sum_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA2_sum_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+324
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA2_sum_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA2_sum_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+5754
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA_mean_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA_mean_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+917
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA_mean_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA_mean_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+19.6
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA_median_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA_median_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+917
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA_median_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA_median_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+19
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA_pie.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA_pie.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,3 @@
+Gene Freq label
+IGA1 593 IGA1 - 593
+IGA2 324 IGA2 - 324

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA_sum_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA_sum_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+917
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGA_sum_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGA_sum_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+17977
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGE_mean_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGE_mean_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+0
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGE_mean_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGE_mean_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+0
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGE_median_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGE_median_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+0
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGE_median_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGE_median_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+0
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGE_sum_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGE_sum_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+0
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGE_sum_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGE_sum_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+0
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG.pdf

Binary file test-output/IGG.pdf has changed

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG.png

Binary file test-output/IGG.png has changed

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG1_mean_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG1_mean_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+274
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG1_mean_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG1_mean_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+20
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG1_median_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG1_median_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+274
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG1_median_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG1_median_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+18
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG1_sum_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG1_sum_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+274
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG1_sum_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG1_sum_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+5492
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG2_mean_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG2_mean_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+150
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG2_mean_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG2_mean_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+18.5
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG2_median_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG2_median_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+150
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG2_median_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG2_median_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+17
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG2_sum_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG2_sum_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+150
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG2_sum_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG2_sum_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+2777
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG3_mean_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG3_mean_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+26
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG3_mean_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG3_mean_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+14.9
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG3_median_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG3_median_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+26
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG3_median_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG3_median_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+13.5
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG3_sum_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG3_sum_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+26
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG3_sum_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG3_sum_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+388
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG4_mean_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG4_mean_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+19
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG4_mean_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG4_mean_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+19.9
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG4_median_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG4_median_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+19
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG4_median_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG4_median_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+18
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG4_sum_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG4_sum_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+19
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG4_sum_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG4_sum_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+379
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG_mean_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG_mean_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+469
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG_mean_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG_mean_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+19.3
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG_median_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG_median_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+469
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG_median_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG_median_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+18
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG_pie.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG_pie.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,5 @@
+Gene Freq label
+IGG1 274 IGG1 - 274
+IGG2 150 IGG2 - 150
+IGG3 26 IGG3 - 26
+IGG4 19 IGG4 - 19

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG_sum_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG_sum_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+469
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGG_sum_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGG_sum_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+9036
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGM_mean_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGM_mean_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+1
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGM_mean_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGM_mean_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+0
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGM_median_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGM_median_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+1
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGM_median_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGM_median_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+0
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGM_sum_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGM_sum_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+1
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/IGM_sum_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/IGM_sum_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+0
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/aa_id_mutations.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/aa_id_mutations.txt Tue Jan 25 11:28:29 2022 +0000

b'@@ -0,0 +1,1577 @@\n+ID\tbest_match\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t13\t14\t15\t16\t17\t18\t19\t20\t21\t22\t23\t24\t25\t26\t27\t28\t29\t30\t31\t32\t33\t34\t35\t36\t37\t38\t39\t40\t41\t42\t43\t44\t45\t46\t47\t48\t49\t50\t51\t52\t53\t54\t55\t56\t57\t58\t59\t60\t61\t62\t63\t64\t65\t66\t67\t68\t69\t70\t71\t72\t73\t74\t75\t76\t77\t78\t79\t80\t81\t82\t83\t84\t85\t86\t87\t88\t89\t90\t91\t92\t93\t94\t95\t96\t97\t98\t99\t100\t101\t102\t103\t104\n+JY8QFUQ01A0005\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\t1\t0\t0\t0\t1\t1\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\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+JY8QFUQ01A004N\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\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+JY8QFUQ01A006G\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\t1\t0\t0\t0\t0\t0\t0\t1\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t0\t2\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t2\t0\t0\t2\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+JY8QFUQ01A018V\tIGA1\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\t1\t2\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t1\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\t1\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t3\t0\t1\t0\n+JY8QFUQ01A019O\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\t1\t0\t0\t0\t0\t0\t2\t1\t1\t0\t0\t1\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\t1\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t2\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+JY8QFUQ01A01KX\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\t1\t0\t0\t1\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t1\t0\t0\t0\t0\t2\t0\t1\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t3\t0\t1\t2\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t0\n+JY8QFUQ01A0207\tIGG2\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\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t2\t1\t0\t0\t1\t0\t1\t0\t0\t1\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\t2\t0\t0\t0\n+JY8QFUQ01A02HL\tIGA1\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\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\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\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\n+JY8QFUQ01A02KS\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\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t2\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\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\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+JY8QFUQ01A02XZ\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\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\t1\t0\t0\t0\t1\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\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\n+JY8QFUQ01A03E3\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\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\t2\t0\t3\t1\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\t1\t0\t0\t0\t0\t0\t0\t0\t0\n+JY8QFUQ01A03N6\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\t1\t0\t0\t0\t0\t0\t2\t2\t0\t1\t1\t0\t0\t0\t0\t2\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t0\t0\t0\t0\t2\t0\t1\t0\t0\t0\t0\t0\t1\t0\t0\t0\t1\t2\t1\t0\t0\t1\t2\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t2\t0\t0\t0\n+JY8QFUQ01A08XO\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\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+JY8QFUQ01A0939\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\t0\t0\t0\t0\t0\t1\t1\t1\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\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\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'

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/absent_aa_id.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/absent_aa_id.txt Tue Jan 25 11:28:29 2022 +0000

b'@@ -0,0 +1,1577 @@\n+ID\tcdr1length\tcdr2length\tbest_match\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t13\t14\t15\t16\t17\t18\t19\t20\t21\t22\t23\t24\t25\t26\t27\t28\t29\t30\t31\t32\t33\t34\t35\t36\t37\t38\t39\t40\t41\t42\t43\t44\t45\t46\t47\t48\t49\t50\t51\t52\t53\t54\t55\t56\t57\t58\t59\t60\t61\t62\t63\t64\t65\t66\t67\t68\t69\t70\t71\t72\t73\t74\t75\t76\t77\t78\t79\t80\t81\t82\t83\t84\t85\t86\t87\t88\t89\t90\t91\t92\t93\t94\t95\t96\t97\t98\t99\t100\t101\t102\t103\t104\n+JY8QFUQ01A0005\t10\t7\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\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+JY8QFUQ01A004N\t10\t7\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\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+JY8QFUQ01A006G\t10\t7\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\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+JY8QFUQ01A018V\t10\t7\tIGA1\t1\t1\t1\t1\t1\t1\t1\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+JY8QFUQ01A019O\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\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+JY8QFUQ01A01KX\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\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+JY8QFUQ01A0207\t8\t8\tIGG2\t1\t1\t1\t1\t1\t1\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+JY8QFUQ01A02HL\t8\t8\tIGA1\t1\t1\t1\t1\t1\t1\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+JY8QFUQ01A02KS\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+JY8QFUQ01A02XZ\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\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+JY8QFUQ01A03E3\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+JY8QFUQ01A03N6\t9\t7\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\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\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+JY8QFUQ01A08XO\t10\t7\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\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+JY8QFUQ01A0939\t10\t9\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\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'

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/all_mean_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/all_mean_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+1387
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/all_mean_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/all_mean_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+19.5
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/all_median_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/all_median_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+1387
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/all_median_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/all_median_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+18
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/all_sum_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/all_sum_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+1387
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/all_sum_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/all_sum_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+27013
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/hotspot_analysis_mean.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/hotspot_analysis_mean.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,4 @@
+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

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/hotspot_analysis_median.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/hotspot_analysis_median.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,4 @@
+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

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/hotspot_analysis_sum.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/hotspot_analysis_sum.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,4 @@
+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

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/motif_per_seq.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/motif_per_seq.txt Tue Jan 25 11:28:29 2022 +0000

b'@@ -0,0 +1,1577 @@\n+ID\tRGYW\tWRCY\tWA\tTW\n+JY8QFUQ01A0005\t5.5\t2.5\t0.5\t0.5\n+JY8QFUQ01A004N\t5.5\t2.0\t2.5\t4.0\n+JY8QFUQ01A006G\t4.666666666666666\t2.333333333333333\t4.166666666666666\t3.833333333333333\n+JY8QFUQ01A018V\t6.666666666666667\t7.333333333333334\t3.0\t3.0\n+JY8QFUQ01A019O\t5.75\t2.083333333333333\t1.5833333333333333\t0.5833333333333333\n+JY8QFUQ01A01KX\t3.0000000000000004\t4.333333333333334\t5.833333333333333\t2.833333333333333\n+JY8QFUQ01A0207\t2.8333333333333335\t3.8333333333333335\t2.1666666666666665\t2.1666666666666665\n+JY8QFUQ01A02HL\t0.5\t2.5\t0.5\t0.5\n+JY8QFUQ01A02KS\t3.0\t3.3333333333333335\t3.3333333333333335\t0.3333333333333333\n+JY8QFUQ01A02XZ\t2.583333333333333\t0.5833333333333333\t0.9166666666666665\t1.9166666666666665\n+JY8QFUQ01A03E3\t3.75\t5.083333333333333\t1.7499999999999998\t1.4166666666666665\n+JY8QFUQ01A03N6\t6.499999999999999\t6.166666666666667\t5.833333333333332\t1.4999999999999998\n+JY8QFUQ01A08XO\t0\t0\t0\t0\n+JY8QFUQ01A0939\t2.5\t2.833333333333333\t2.333333333333333\t1.3333333333333333\n+JY8QFUQ01A09OY\t1.3333333333333333\t3.1666666666666665\t2.5\t1.0\n+JY8QFUQ01A0C2Y\t2.833333333333333\t2.0\t3.833333333333333\t0.3333333333333333\n+JY8QFUQ01A0C33\t4.333333333333333\t1.5\t2.333333333333333\t0.8333333333333333\n+JY8QFUQ01A0C4X\t2.666666666666667\t2.0\t1.6666666666666665\t1.6666666666666665\n+JY8QFUQ01A0D2K\t2.0\t0.5\t3.0\t2.5\n+JY8QFUQ01A0D5E\t5.0\t1.5\t1.5\t3.0\n+JY8QFUQ01A0DA8\t3.8333333333333335\t1.5\t5.833333333333333\t3.833333333333333\n+JY8QFUQ01A0DCS\t3.5\t5.166666666666667\t3.6666666666666665\t1.6666666666666665\n+JY8QFUQ01A0EF3\t0.25\t4.25\t0.75\t0.75\n+JY8QFUQ01A0ESJ\t2.333333333333333\t3.6666666666666665\t3.0\t1.9999999999999998\n+JY8QFUQ01A0FII\t1.5833333333333333\t2.25\t4.083333333333334\t2.0833333333333335\n+JY8QFUQ01A0FO5\t2.833333333333333\t0.8333333333333333\t1.3333333333333333\t1.0\n+JY8QFUQ01A0GVR\t6.666666666666667\t6.0\t4.666666666666666\t2.6666666666666665\n+JY8QFUQ01A0GVY\t4.833333333333333\t5.0\t3.333333333333333\t2.833333333333333\n+JY8QFUQ01A0HBK\t0\t0\t0\t0\n+JY8QFUQ01A0IZI\t4.583333333333333\t2.25\t1.5833333333333333\t2.5833333333333335\n+JY8QFUQ01A0LAJ\t3.833333333333333\t3.5\t6.333333333333333\t1.3333333333333333\n+JY8QFUQ01A0LBC\t3.833333333333334\t4.666666666666666\t6.499999999999999\t4.0\n+JY8QFUQ01A0LEW\t2.333333333333333\t1.0\t0.8333333333333333\t0.8333333333333333\n+JY8QFUQ01A0LZ5\t5.333333333333334\t4.666666666666666\t3.0\t1.0\n+JY8QFUQ01A0N2E\t0\t0\t0\t0\n+JY8QFUQ01A0N8H\t1.0\t3.333333333333333\t2.333333333333333\t0.3333333333333333\n+JY8QFUQ01A0OC8\t0.0\t1.0\t4.0\t2.0\n+JY8QFUQ01A0OMH\t2.8333333333333335\t2.5\t3.333333333333333\t2.333333333333333\n+JY8QFUQ01A0OTP\t3.6666666666666665\t1.6666666666666665\t3.5\t2.1666666666666665\n+JY8QFUQ01A0QXW\t0\t0\t0\t0\n+JY8QFUQ01A0RJS\t2.833333333333333\t2.0\t3.833333333333333\t0.3333333333333333\n+JY8QFUQ01A0S1H\t2.583333333333333\t4.583333333333333\t2.9166666666666665\t0.9166666666666665\n+JY8QFUQ01A0TAV\t0.0\t2.5\t2.5\t1.0\n+JY8QFUQ01A0TNI\t2.833333333333333\t4.833333333333333\t2.6666666666666665\t3.6666666666666665\n+JY8QFUQ01A0UZS\t3.8333333333333335\t5.833333333333334\t2.1666666666666665\t2.1666666666666665\n+JY8QFUQ01A0VIE\t2.25\t3.75\t3.75\t3.25\n+JY8QFUQ01A0WDV\t2.8333333333333335\t4.0\t3.833333333333333\t1.3333333333333333\n+JY8QFUQ01A0WZB\t3.0\t5.0\t3.5\t2.5\n+JY8QFUQ01A0X8W\t3.3333333333333335\t0.3333333333333333\t1.1666666666666665\t3.1666666666666665\n+JY8QFUQ01A0XE3\t3.0000000000000004\t4.333333333333334\t4.833333333333333\t2.833333333333333\n+JY8QFUQ01A0Z64\t3.3333333333333335\t2.3333333333333335\t1.1666666666666665\t1.1666666666666665\n+JY8QFUQ01A0ZW5\t6.0\t3.3333333333333335\t4.499999999999999\t2.1666666666666665\n+JY8QFUQ01A0ZX6\t2.0\t3.333333333333333\t0.8333333333333333\t0.8333333333333333\n+JY8QFUQ01A110D\t0.0\t3.0\t0.5\t0.5\n+JY8QFUQ01A12BY\t1.5\t3.166666666666667\t2.666666666666667\t0.6666666666666666\n+JY8QFUQ01A12KV\t4.833333333333333\t6.0\t3.833333333333333\t1.3333333333333333\n+JY8QFUQ01A12V0\t3.5\t3.5\t4.0\t1.0\n+JY8QFUQ01A14EE\t6.166666666666666\t2.0\t6.166666666666667\t4.666666666666667\n+JY8QFUQ01A152R\t1.5\t3.5\t3.5\t2.5\n+JY8QFUQ01A15L6\t5.999999999999999\t5.833333333333333\t5.333333333333333\t2.8333333333333335\n+JY8QFUQ01A15SR\t11.833333333333334\t6.166666666666666\t4.6666'..b'8QFUQ01C3QHH\t1.5\t1.5\t0.5\t2.5\n+JY8QFUQ01C4MHW\t1.8333333333333333\t1.8333333333333333\t2.333333333333333\t0.0\n+JY8QFUQ01C5Q2O\t2.1666666666666665\t0.8333333333333333\t0.6666666666666666\t1.3333333333333333\n+JY8QFUQ01C8QWZ\t1.8333333333333333\t1.5\t2.3333333333333335\t0.3333333333333333\n+JY8QFUQ01C92F8\t1.0\t3.333333333333333\t2.333333333333333\t0.3333333333333333\n+JY8QFUQ01C966Y\t0.8333333333333333\t1.5\t1.8333333333333333\t1.8333333333333333\n+JY8QFUQ01C98A9\t1.8333333333333333\t2.833333333333333\t1.3333333333333333\t0.0\n+JY8QFUQ01CANL1\t2.6666666666666665\t1.5\t2.6666666666666665\t3.1666666666666665\n+JY8QFUQ01CD8ZK\t6.166666666666666\t2.0\t6.166666666666667\t4.666666666666667\n+JY8QFUQ01CD9VK\t2.0\t3.3333333333333335\t0.3333333333333333\t0.3333333333333333\n+JY8QFUQ01CDZ5R\t2.25\t3.75\t3.75\t3.25\n+JY8QFUQ01CE8P9\t3.0833333333333335\t2.0833333333333335\t3.4166666666666665\t1.4166666666666665\n+JY8QFUQ01CF06T\t2.0\t3.333333333333333\t0.8333333333333333\t0.8333333333333333\n+JY8QFUQ01CG8U2\t2.833333333333333\t4.0\t0.8333333333333333\t0.3333333333333333\n+JY8QFUQ01CGLTX\t3.0\t2.5\t2.5\t2.0\n+JY8QFUQ01CGQFF\t3.3333333333333335\t2.5\t4.333333333333333\t2.833333333333333\n+JY8QFUQ01CHDDF\t6.0\t4.0\t2.0\t1.0\n+JY8QFUQ01CHKLB\t0.8333333333333333\t0.5\t2.333333333333333\t1.3333333333333333\n+JY8QFUQ01CHW93\t4.583333333333334\t2.5833333333333335\t0.9166666666666665\t0.9166666666666665\n+JY8QFUQ01CII5W\t2.6666666666666665\t5.166666666666666\t6.333333333333334\t3.833333333333333\n+JY8QFUQ01CINZT\t0.3333333333333333\t1.0\t1.3333333333333333\t0.3333333333333333\n+JY8QFUQ01CJLXK\t1.0\t5.0\t3.5\t1.4999999999999998\n+JY8QFUQ01CJT9B\t4.833333333333334\t6.0\t4.833333333333334\t2.333333333333333\n+JY8QFUQ01CK1VY\t9.666666666666666\t4.666666666666666\t2.5\t2.1666666666666665\n+JY8QFUQ01CKN3U\t1.9166666666666665\t3.25\t4.916666666666666\t2.9166666666666665\n+JY8QFUQ01CLP4K\t3.5\t4.833333333333334\t1.8333333333333333\t1.8333333333333333\n+JY8QFUQ01CNCW4\t0.5\t0.0\t0.5\t2.0\n+JY8QFUQ01CO019\t0.8333333333333333\t7.333333333333333\t4.166666666666666\t1.6666666666666665\n+JY8QFUQ01CPVUP\t2.833333333333333\t2.333333333333333\t5.166666666666666\t2.6666666666666665\n+JY8QFUQ01CPYJ0\t2.25\t3.25\t1.75\t1.75\n+JY8QFUQ01CQH14\t3.3333333333333335\t3.3333333333333335\t1.6666666666666665\t0.6666666666666666\n+JY8QFUQ01CST8T\t3.666666666666667\t2.0\t1.1666666666666665\t2.1666666666666665\n+JY8QFUQ01CU1XI\t3.8333333333333335\t3.5\t1.3333333333333333\t0.3333333333333333\n+JY8QFUQ01CU5CB\t1.8333333333333333\t3.5\t2.833333333333333\t0.8333333333333333\n+JY8QFUQ01CUGFD\t6.666666666666666\t4.0\t4.166666666666666\t4.166666666666667\n+JY8QFUQ01CURPS\t5.916666666666666\t4.583333333333334\t2.75\t1.7499999999999998\n+JY8QFUQ01CY2WW\t0.0\t1.0\t4.0\t2.0\n+JY8QFUQ01CY6MC\t3.0\t5.0\t1.0\t1.0\n+JY8QFUQ01CYWC2\t4.333333333333333\t2.0\t2.333333333333333\t1.3333333333333333\n+JY8QFUQ01DA9FW\t2.0\t2.0\t1.0\t0.0\n+JY8QFUQ01DA9S4\t0\t0\t0\t0\n+JY8QFUQ01DC4QI\t1.25\t5.75\t2.25\t0.75\n+JY8QFUQ01DC8OC\t6.583333333333333\t7.583333333333333\t3.916666666666667\t1.9166666666666665\n+JY8QFUQ01DCPGQ\t1.75\t1.75\t5.25\t2.25\n+JY8QFUQ01DEKWC\t3.5\t3.5\t1.0\t1.0\n+JY8QFUQ01DG2P7\t1.8333333333333333\t1.5\t2.3333333333333335\t0.3333333333333333\n+JY8QFUQ01DG5KX\t1.1666666666666665\t2.833333333333333\t1.9999999999999998\t3.0\n+JY8QFUQ01DG6GC\t1.5\t3.5000000000000004\t3.5\t1.4999999999999998\n+JY8QFUQ01DHXHT\t5.5\t2.0\t2.5\t4.0\n+JY8QFUQ01DI39D\t0.5\t0.0\t0.5\t2.0\n+JY8QFUQ01DIBNC\t0\t0\t0\t0\n+JY8QFUQ01DJFIZ\t6.416666666666666\t8.416666666666666\t4.083333333333334\t3.0833333333333335\n+JY8QFUQ01DLDLD\t0.3333333333333333\t0.5\t1.8333333333333333\t0.3333333333333333\n+JY8QFUQ01DMF0A\t6.916666666666666\t5.416666666666666\t6.249999999999999\t2.416666666666667\n+JY8QFUQ01DOVL5\t3.833333333333333\t3.333333333333333\t2.6666666666666665\t1.1666666666666665\n+JY8QFUQ01DPT8R\t0.8333333333333333\t0.8333333333333333\t1.3333333333333333\t1.0\n+JY8QFUQ01DUD3U\t6.833333333333333\t7.166666666666666\t4.0\t3.0\n+JY8QFUQ01DV4HU\t3.0\t5.333333333333334\t3.333333333333333\t3.3333333333333335\n+JY8QFUQ01DV8LF\t2.25\t0.25\t0.75\t1.75\n+JY8QFUQ01DVBU0\t2.1666666666666665\t0.8333333333333333\t0.6666666666666666\t1.3333333333333333\n+JY8QFUQ01DXDOM\t6.583333333333333\t4.75\t6.083333333333334\t3.583333333333333\n'

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/mutation_by_id.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/mutation_by_id.txt Tue Jan 25 11:28:29 2022 +0000

b'@@ -0,0 +1,1577 @@\n+Sequence.ID\tVRegionMutations\tVRegionNucleotides\ttransitionMutations\ttransversionMutations\ttransitionMutationsAtGC\ttransitionMutationsAtAT\tsilentMutationsFR\tnonSilentMutationsFR\tsilentMutationsCDR\tnonSilentMutationsCDR\n+JY8QFUQ01A0005\t18\t216\t12\t6\t11\t1\t6\t6\t2\t4\n+JY8QFUQ01A004N\t20\t216\t10\t10\t4\t6\t2\t10\t2\t6\n+JY8QFUQ01A006G\t32\t216\t20\t12\t11\t9\t10\t12\t3\t7\n+JY8QFUQ01A018V\t31\t216\t19\t12\t12\t7\t7\t14\t5\t5\n+JY8QFUQ01A019O\t19\t213\t10\t9\t6\t4\t2\t10\t0\t7\n+JY8QFUQ01A01KX\t29\t213\t18\t11\t8\t10\t6\t13\t3\t7\n+JY8QFUQ01A0207\t16\t213\t6\t10\t4\t2\t2\t8\t0\t6\n+JY8QFUQ01A02HL\t13\t213\t9\t4\t8\t1\t3\t5\t3\t2\n+JY8QFUQ01A02KS\t14\t213\t9\t5\t6\t3\t3\t7\t1\t3\n+JY8QFUQ01A02XZ\t10\t213\t6\t4\t3\t3\t3\t2\t1\t4\n+JY8QFUQ01A03E3\t21\t213\t14\t7\t8\t6\t4\t8\t3\t6\n+JY8QFUQ01A03N6\t39\t213\t22\t17\t11\t11\t8\t19\t2\t10\n+JY8QFUQ01A08XO\t0\t216\t0\t0\t0\t0\t0\t0\t0\t0\n+JY8QFUQ01A0939\t15\t222\t7\t8\t4\t3\t7\t3\t0\t5\n+JY8QFUQ01A09OY\t12\t213\t6\t6\t5\t1\t2\t5\t1\t4\n+JY8QFUQ01A0C2Y\t18\t213\t12\t6\t8\t4\t3\t4\t4\t7\n+JY8QFUQ01A0C33\t13\t213\t5\t8\t3\t2\t2\t3\t0\t8\n+JY8QFUQ01A0C4X\t13\t213\t4\t9\t3\t1\t2\t3\t0\t8\n+JY8QFUQ01A0D2K\t10\t213\t4\t6\t0\t4\t0\t2\t2\t6\n+JY8QFUQ01A0D5E\t28\t212\t14\t14\t11\t3\t5\t10\t2\t11\n+JY8QFUQ01A0DA8\t23\t213\t12\t11\t4\t8\t5\t11\t4\t3\n+JY8QFUQ01A0DCS\t22\t213\t12\t10\t6\t6\t4\t9\t0\t9\n+JY8QFUQ01A0EF3\t12\t213\t8\t4\t7\t1\t4\t3\t1\t4\n+JY8QFUQ01A0ESJ\t17\t213\t8\t9\t5\t3\t4\t7\t0\t6\n+JY8QFUQ01A0FII\t26\t213\t15\t11\t8\t7\t5\t9\t3\t9\n+JY8QFUQ01A0FO5\t11\t213\t6\t5\t2\t4\t4\t4\t0\t3\n+JY8QFUQ01A0GVR\t24\t216\t17\t7\t10\t7\t9\t5\t4\t6\n+JY8QFUQ01A0GVY\t30\t213\t22\t8\t15\t7\t8\t9\t4\t9\n+JY8QFUQ01A0HBK\t0\t213\t0\t0\t0\t0\t0\t0\t0\t0\n+JY8QFUQ01A0IZI\t18\t213\t11\t7\t7\t4\t3\t5\t0\t10\n+JY8QFUQ01A0LAJ\t29\t219\t15\t14\t8\t7\t4\t14\t1\t10\n+JY8QFUQ01A0LBC\t31\t213\t14\t17\t7\t7\t7\t12\t1\t11\n+JY8QFUQ01A0LEW\t9\t213\t5\t4\t2\t3\t2\t4\t3\t0\n+JY8QFUQ01A0LZ5\t20\t213\t14\t6\t11\t3\t4\t5\t2\t9\n+JY8QFUQ01A0N2E\t0\t213\t0\t0\t0\t0\t0\t0\t0\t0\n+JY8QFUQ01A0N8H\t13\t222\t9\t4\t5\t4\t2\t6\t0\t5\n+JY8QFUQ01A0OC8\t12\t212\t6\t6\t2\t4\t3\t5\t0\t4\n+JY8QFUQ01A0OMH\t26\t213\t16\t10\t12\t4\t9\t8\t2\t7\n+JY8QFUQ01A0OTP\t15\t209\t10\t5\t3\t7\t6\t4\t1\t4\n+JY8QFUQ01A0QXW\t0\t210\t0\t0\t0\t0\t0\t0\t0\t0\n+JY8QFUQ01A0RJS\t17\t212\t11\t6\t7\t4\t3\t4\t3\t7\n+JY8QFUQ01A0S1H\t16\t213\t10\t6\t4\t6\t5\t3\t5\t3\n+JY8QFUQ01A0TAV\t12\t213\t4\t8\t2\t2\t2\t5\t1\t4\n+JY8QFUQ01A0TNI\t24\t213\t12\t12\t7\t5\t8\t11\t0\t5\n+JY8QFUQ01A0UZS\t20\t213\t12\t8\t8\t4\t2\t11\t2\t5\n+JY8QFUQ01A0VIE\t23\t213\t16\t7\t8\t8\t5\t12\t1\t5\n+JY8QFUQ01A0WDV\t18\t210\t10\t8\t6\t4\t5\t7\t0\t6\n+JY8QFUQ01A0WZB\t34\t210\t20\t14\t11\t9\t11\t9\t3\t11\n+JY8QFUQ01A0X8W\t10\t213\t5\t5\t2\t3\t5\t1\t1\t3\n+JY8QFUQ01A0XE3\t27\t211\t17\t10\t8\t9\t6\t12\t2\t7\n+JY8QFUQ01A0Z64\t9\t213\t7\t2\t5\t2\t1\t3\t0\t5\n+JY8QFUQ01A0ZW5\t27\t216\t15\t12\t7\t8\t3\t13\t2\t9\n+JY8QFUQ01A0ZX6\t12\t213\t8\t4\t5\t3\t4\t3\t1\t4\n+JY8QFUQ01A110D\t14\t213\t8\t6\t6\t2\t3\t8\t1\t2\n+JY8QFUQ01A12BY\t14\t213\t6\t8\t4\t2\t1\t5\t1\t7\n+JY8QFUQ01A12KV\t29\t213\t17\t12\t11\t6\t8\t11\t1\t9\n+JY8QFUQ01A12V0\t28\t213\t18\t10\t13\t5\t6\t13\t2\t7\n+JY8QFUQ01A14EE\t30\t213\t20\t10\t8\t12\t8\t10\t1\t11\n+JY8QFUQ01A152R\t19\t213\t12\t7\t8\t4\t4\t7\t1\t7\n+JY8QFUQ01A15L6\t31\t215\t17\t14\t6\t11\t3\t17\t3\t8\n+JY8QFUQ01A15SR\t48\t216\t21\t27\t13\t8\t6\t17\t1\t24\n+JY8QFUQ01A16XV\t0\t213\t0\t0\t0\t0\t0\t0\t0\t0\n+JY8QFUQ01A17D9\t17\t213\t10\t7\t6\t4\t2\t7\t2\t6\n+JY8QFUQ01A17TV\t14\t210\t9\t5\t3\t6\t2\t7\t1\t4\n+JY8QFUQ01A18L5\t12\t213\t7\t5\t4\t3\t3\t3\t2\t4\n+JY8QFUQ01A1963\t12\t212\t8\t4\t5\t3\t2\t2\t1\t7\n+JY8QFUQ01A1ALH\t22\t216\t15\t7\t6\t9\t3\t10\t1\t8\n+JY8QFUQ01A1AYP\t14\t213\t6\t8\t4\t2\t5\t1\t2\t6\n+JY8QFUQ01A1BK7\t14\t213\t10\t4\t6\t4\t2\t5\t2\t5\n+JY8QFUQ01A1BT3\t24\t210\t16\t8\t11\t5\t7\t12\t2\t3\n+JY8QFUQ01A1CLZ\t18\t216\t11\t7\t8\t3\t6\t4\t1\t7\n+JY8QFUQ01A1CTT\t15\t213\t9\t6\t7\t2\t2\t4\t0\t9\n+JY8QFUQ01A1DJR\t14\t213\t11\t3\t8\t3\t2\t5\t2\t5\n+JY8QFUQ01A1DVA\t35\t213\t26\t9\t11\t15\t7\t11\t0\t17\n+JY8QFUQ01A1E6T\t14\t213\t7\t7\t6\t1\t3\t5\t0\t6\n+JY8QFUQ01A1GYW\t41\t210\t25\t16\t13\t12\t7\t25\t2\t7\n+JY8QFUQ01A1GZY\t26\t212\t16\t10\t7\t9\t5\t10\t3\t8\n+JY8QFUQ01A1ISV\t11\t213\t8\t3\t5\t3\t2\t5\t0\t4\n+JY8QFUQ01A1IV8\t24\t209\t13\t11\t7\t6\t4\t12\t0\t8\n+JY8QFUQ01A1IYG\t13\t210\t6\t7\t5\t1\t2\t5\t2\t4\n+JY8QFUQ01A1K37\t9\t213\t6\t3\t5\t1\t1\t2\t1\t5\n+JY8QFUQ01A1KQO\t20\t213\t12\t8\t6\t6\t2\t9\t3\t6\n+JY8QFUQ01A1L2W\t12\t213\t5\t7\t3\t2\t3\t7\t0\t2\n+JY8QFUQ01A1LNA\t14\t213\t7\t7\t5\t2\t5\t4\t0\t5\n+JY8QFUQ01A1MBV\t21\t213\t11\t10\t4\t7\t1\t10\t2\t8\n+JY8QFUQ01A1MJG\t17\t210\t11\t6\t8\t3\t5\t8\t0\t4\n+JY8QFUQ01A1MJU\t16\t213\t9\t7\t5\t4\t5\t8\t0\t3\n+JY8QFUQ01A1OLP\t38\t213\t22\t16\t14\t8\t9\t14\t4\t11\n+JY8QFUQ01A1PLD\t20\t213\t12\t8\t6\t6\t2\t9\t3\t6\n+JY8QFUQ01A1Q3N\t32\t213\t20\t12\t16\t4\t7\t17\t3\t5\n+JY8QFUQ01A1QLN\t11\t209\t7\t4\t4\t3\t2\t4\t2\t3\n+JY8QFUQ01A1R7K\t26\t212\t12\t14\t9\t3\t6\t14\t1\t5\n+JY8QFUQ01A1RAE\t16\t213\t6\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'

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/shm_overview_tandem_row.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/shm_overview_tandem_row.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+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

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/tandem_frequency.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/tandem_frequency.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,9 @@
+2 3292
+3 652
+4 143
+5 27
+6 11
+7 3
+8 2
+9 1
+10 1

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/tandems_by_id.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/tandems_by_id.txt Tue Jan 25 11:28:29 2022 +0000

[

b'@@ -0,0 +1,1553 @@\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'

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/unmatched.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/unmatched.txt Tue Jan 25 11:28:29 2022 +0000

[

b'@@ -0,0 +1,190 @@\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, IGA1\n+JY8QFUQ01C966Y\t89\t57\t[281, 282]\tunmatched, IGA2\n+JY8QFUQ01C98A9\t84\t57\t[292, 293]\tunmatched, IGA2\n+JY8QFUQ01CANL1\t79\t57\t[283, 285, 275]\tunmatched, IGA2\n+JY8QFUQ01CD8ZK\t68\t64\t[282, 273]\tunmatched, IGA2\n+JY8QFUQ01CD9VK\t5\t14\t[]\tunmatched, IGA1\n+JY8QFUQ01CDZ5R\t58\t100\t[288]\tunmatched, IGA1\n+JY8QFUQ01CE8P9\t89\t57\t[293, 294]\tunmatched, IGA2\n+JY8QFUQ01CF06T\t88\t64\t[283]\tunmatched, IGG1\n+JY8QFUQ01CG8U2\t95\t57\t[286, 288]\tunmatched, IGA2\n+JY8QFUQ01CGLTX\t89\t64\t[299, 298]\tunmatched, IGA1\n+JY8QFUQ01CGQFF\t84\t29\t[290, 292]\tunmatched, IGA1\n+JY8QFUQ01CHDDF\t89\t57\t[294, 295]\tunmatched, IGA2\n+JY8QFUQ01CHKLB\t84\t64\t[293]\tunmatched, IGA2\n+JY8QFUQ01CHW93\t0\t0\t[]\tunmatched, IGA1\n+JY8QFUQ01CII5W\t88\t64\t[289]\tunmatched, IGG1\n+JY8QFUQ01CINZT\t84\t64\t[284]\tunmatched, IGA2\n+JY8QFUQ01CJLXK\t84\t57\t[287, 286]\tunmatched, IGA2\n+JY8QFUQ01CJT9B\t68\t57\t[287, 290]\tunmatched, IGA2\n+JY8QFUQ01CK1VY\t84\t29\t[288, 290]\tunmatched, IGA1\n+JY8QFUQ01CKN3U\t88\t64\t[303]\tunmatched, IGG2\n+JY8QFUQ01CLP4K\t89\t57\t[281, 282]\tunmatched, IGA2\n+JY8QFUQ01CNCW4\t79\t64\t[267, 265, 266]\tunmatched, IGA1\n+JY8QFUQ01CO019\t50\t71\t[265]\tunmatched, IGG1\n+JY8QFUQ01CPVUP\t84\t57\t[288, 291]\tunmatched, IGA2\n+JY8QFUQ01CPYJ0\t84\t64\t[284, 287, 286]\tunmatched, IGA2\n+JY8QFUQ01CQH14\t75\t64\t[288]\tunmatched, IGG1\n+JY8QFUQ01CST8T\t84\t64\t[278, 280]\tunmatched, IGA2\n+JY8QFUQ01CU1XI\t84\t57\t[281, 282]\tunmatched, IGA2\n+JY8QFUQ01CU5CB\t79\t29\t[281, 282, 273]\tunmatched, IGA2\n+JY8QFUQ01CUGFD\t68\t57\t[293, 287]\tunmatched, IGA2\n+JY8QFUQ01CURPS\t74\t43\t[298, 299]\tunmatched, IGA2\n+JY8QFUQ01CY2WW\t84\t57\t[287, 289]\tunmatched, IGA2\n+JY8QFUQ01CY6MC\t79\t57\t[288, 289]\tunmatched, IGA2\n+JY8QFUQ01CYWC2\t89\t57\t[278, 279]\tunmatched, IGA2\n+JY8QFUQ01DA9FW\t89\t57\t[276, 277]\tunmatched, IGA2\n+JY8QFUQ01DA9S4\t56\t71\t[285]\tunmatched, IGG1\n+JY8QFUQ01DC4QI\t84\t57\t[284, 287]\tunmatched, IGA1\n+JY8QFUQ01DC8OC\t63\t43\t[275, 277]\tunmatched, IGA2\n+JY8QFUQ01DCPGQ\t56\t64\t[284]\tunmatched, IGG1\n+JY8QFUQ01DEKWC\t68\t50\t[295, 287, 296]\tunmatched, IGA2\n+JY8QFUQ01DG2P7\t79\t57\t[271, 272]\tunmatched, IGA2\n+JY8QFUQ01DG5KX\t42\t43\t[280]\tunmatched, IGA2\n+JY8QFUQ01DG6GC\t89\t57\t[296, 297]\tunmatched, IGA2\n+JY8QFUQ01DHXHT\t81\t57\t[295]\tunmatched, IGG1\n+JY8QFUQ01DI39D\t84\t64\t[267, 269]\tunmatched, IGA1\n+JY8QFUQ01DIBNC\t69\t79\t[319, 315]\tunmatched, IGG1\n+JY8QFUQ01DJFIZ\t88\t64\t[294]\tunmatched, IGG1\n+JY8QFUQ01DLDLD\t68\t86\t[281]\tunmatched, IGA1\n+JY8QFUQ01DMF0A\t68\t79\t[301]\tunmatched, IGA1\n+JY8QFUQ01DOVL5\t89\t57\t[302, 303]\tunmatched, IGA2\n+JY8QFUQ01DPT8R\t84\t57\t[271, 273]\tunmatched, IGA2\n+JY8QFUQ01DUD3U\t79\t64\t[279]\tunmatched, IGA2\n+JY8QFUQ01DV4HU\t62\t71\t[279, 280]\tunmatched, IGG2\n+JY8QFUQ01DV8LF\t89\t57\t[279, 280]\tunmatched, IGA2\n+JY8QFUQ01DVBU0\t74\t57\t[286, 285, 283]\tunmatched, IGA2\n+JY8QFUQ01DXDOM\t89\t57\t[283, 284]\tunmatched, IGA2\n'

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/unmatched_mean_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/unmatched_mean_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+189
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/unmatched_mean_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/unmatched_mean_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+18.4
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/unmatched_median_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/unmatched_median_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+189
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/unmatched_median_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/unmatched_median_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+16
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/unmatched_sum_n.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/unmatched_sum_n.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+189
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 test-output/unmatched_sum_value.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-output/unmatched_sum_value.txt Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,1 @@
+3486
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/.pytest_cache/.gitignore
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/.pytest_cache/.gitignore Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,2 @@
+# Created by pytest automatically.
+*

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/.pytest_cache/CACHEDIR.TAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/.pytest_cache/CACHEDIR.TAG Tue Jan 25 11:28:29 2022 +0000

@@ -0,0 +1,4 @@
+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

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/.pytest_cache/README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/.pytest_cache/README.md Tue Jan 25 11:28:29 2022 +0000

[

@@ -0,0 +1,8 @@
+# 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.

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/.pytest_cache/v/cache/lastfailed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/.pytest_cache/v/cache/lastfailed Tue Jan 25 11:28:29 2022 +0000

[

@@ -0,0 +1,3 @@
+{
+ "test_shm_csr.py::test_results_match_validation[shm_overview.txt]": true
+}
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/.pytest_cache/v/cache/nodeids
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/.pytest_cache/v/cache/nodeids Tue Jan 25 11:28:29 2022 +0000

[

@@ -0,0 +1,27 @@
+[
+  "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

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/.pytest_cache/v/cache/stepwise
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/.pytest_cache/v/cache/stepwise Tue Jan 25 11:28:29 2022 +0000

[

@@ -0,0 +1,1 @@
+[]
\ No newline at end of file

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc

Binary file tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc has changed

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/__pycache__/test_shm_csr.cpython-37.pyc

Binary file tests/__pycache__/test_shm_csr.cpython-37.pyc has changed

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/__pycache__/test_shm_csr.cpython-39-pytest-6.2.5.pyc

Binary file tests/__pycache__/test_shm_csr.cpython-39-pytest-6.2.5.pyc has changed

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/data/intermediate_files/RGYW.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/data/intermediate_files/RGYW.txt Tue Jan 25 11:28:29 2022 +0000

b'@@ -0,0 +1,501260 @@\n+JY8QFUQ01A0005\t2\t5\tFR1\n+JY8QFUQ01A0005\t8\t11\tFR1\n+JY8QFUQ01A0005\t82\t85\tCDR1\n+JY8QFUQ01A0005\t100\t103\tCDR1\n+JY8QFUQ01A0005\t106\t109\tCDR1\n+JY8QFUQ01A0005\t118\t121\tFR2\n+JY8QFUQ01A0005\t146\t149\tFR2\n+JY8QFUQ01A0005\t163\t166\tFR2-CDR2\n+JY8QFUQ01A0005\t190\t193\tCDR2\n+JY8QFUQ01A0005\t257\t260\tFR3\n+JY8QFUQ01A0005\t269\t272\tFR3\n+JY8QFUQ01A0005\t274\t277\tFR3\n+JY8QFUQ01A004N\t2\t5\tFR1\n+JY8QFUQ01A004N\t8\t11\tFR1\n+JY8QFUQ01A004N\t82\t85\tCDR1\n+JY8QFUQ01A004N\t100\t103\tCDR1\n+JY8QFUQ01A004N\t106\t109\tCDR1\n+JY8QFUQ01A004N\t118\t121\tFR2\n+JY8QFUQ01A004N\t146\t149\tFR2\n+JY8QFUQ01A004N\t163\t166\tFR2-CDR2\n+JY8QFUQ01A004N\t190\t193\tCDR2\n+JY8QFUQ01A004N\t269\t272\tFR3\n+JY8QFUQ01A004N\t274\t277\tFR3\n+JY8QFUQ01A004N\t297\t300\tFR3\n+JY8QFUQ01A006G\t2\t5\tFR1\n+JY8QFUQ01A006G\t8\t11\tFR1\n+JY8QFUQ01A006G\t82\t85\tCDR1\n+JY8QFUQ01A006G\t100\t103\tCDR1\n+JY8QFUQ01A006G\t106\t109\tCDR1\n+JY8QFUQ01A006G\t118\t121\tFR2\n+JY8QFUQ01A006G\t146\t149\tFR2\n+JY8QFUQ01A006G\t163\t166\tFR2-CDR2\n+JY8QFUQ01A006G\t190\t193\tCDR2\n+JY8QFUQ01A006G\t257\t260\tFR3\n+JY8QFUQ01A006G\t269\t272\tFR3\n+JY8QFUQ01A006G\t274\t277\tFR3\n+JY8QFUQ01A006G\t297\t300\tFR3\n+JY8QFUQ01A018V\t8\t11\tFR1\n+JY8QFUQ01A018V\t82\t85\tCDR1\n+JY8QFUQ01A018V\t103\t106\tCDR1\n+JY8QFUQ01A018V\t118\t121\tFR2\n+JY8QFUQ01A018V\t128\t131\tFR2\n+JY8QFUQ01A018V\t190\t193\tCDR2\n+JY8QFUQ01A018V\t237\t240\tFR3\n+JY8QFUQ01A018V\t257\t260\tFR3\n+JY8QFUQ01A018V\t269\t272\tFR3\n+JY8QFUQ01A018V\t274\t277\tFR3\n+JY8QFUQ01A019O\t8\t11\tFR1\n+JY8QFUQ01A019O\t24\t27\tFR1\n+JY8QFUQ01A019O\t73\t76\tFR1\n+JY8QFUQ01A019O\t85\t88\tCDR1\n+JY8QFUQ01A019O\t106\t109\tCDR1\n+JY8QFUQ01A019O\t118\t121\tFR2\n+JY8QFUQ01A019O\t253\t256\tFR3\n+JY8QFUQ01A019O\t274\t277\tFR3\n+JY8QFUQ01A01KX\t8\t11\tFR1\n+JY8QFUQ01A01KX\t31\t34\tFR1\n+JY8QFUQ01A01KX\t36\t39\tFR1\n+JY8QFUQ01A01KX\t103\t106\tCDR1\n+JY8QFUQ01A01KX\t118\t121\tFR2\n+JY8QFUQ01A01KX\t132\t135\tFR2\n+JY8QFUQ01A01KX\t146\t149\tFR2\n+JY8QFUQ01A01KX\t162\t165\tFR2\n+JY8QFUQ01A01KX\t172\t175\tCDR2\n+JY8QFUQ01A01KX\t187\t190\tCDR2\n+JY8QFUQ01A01KX\t224\t227\tFR3\n+JY8QFUQ01A0207\t8\t11\tFR1\n+JY8QFUQ01A0207\t31\t34\tFR1\n+JY8QFUQ01A0207\t36\t39\tFR1\n+JY8QFUQ01A0207\t103\t106\tCDR1\n+JY8QFUQ01A0207\t118\t121\tFR2\n+JY8QFUQ01A0207\t132\t135\tFR2\n+JY8QFUQ01A0207\t146\t149\tFR2\n+JY8QFUQ01A0207\t162\t165\tFR2\n+JY8QFUQ01A0207\t172\t175\tCDR2\n+JY8QFUQ01A0207\t187\t190\tCDR2\n+JY8QFUQ01A0207\t224\t227\tFR3\n+JY8QFUQ01A02HL\t8\t11\tFR1\n+JY8QFUQ01A02HL\t31\t34\tFR1\n+JY8QFUQ01A02HL\t36\t39\tFR1\n+JY8QFUQ01A02HL\t103\t106\tCDR1\n+JY8QFUQ01A02HL\t132\t135\tFR2\n+JY8QFUQ01A02HL\t146\t149\tFR2\n+JY8QFUQ01A02HL\t187\t190\tCDR2\n+JY8QFUQ01A02HL\t196\t199\tFR3\n+JY8QFUQ01A02HL\t297\t300\tFR3\n+JY8QFUQ01A02KS\t8\t11\tFR1\n+JY8QFUQ01A02KS\t31\t34\tFR1\n+JY8QFUQ01A02KS\t103\t106\tCDR1\n+JY8QFUQ01A02KS\t118\t121\tFR2\n+JY8QFUQ01A02KS\t132\t135\tFR2\n+JY8QFUQ01A02KS\t146\t149\tFR2\n+JY8QFUQ01A02KS\t170\t173\tCDR2\n+JY8QFUQ01A02KS\t297\t300\tFR3\n+JY8QFUQ01A02XZ\t8\t11\tFR1\n+JY8QFUQ01A02XZ\t31\t34\tFR1\n+JY8QFUQ01A02XZ\t36\t39\tFR1\n+JY8QFUQ01A02XZ\t103\t106\tCDR1\n+JY8QFUQ01A02XZ\t118\t121\tFR2\n+JY8QFUQ01A02XZ\t132\t135\tFR2\n+JY8QFUQ01A02XZ\t146\t149\tFR2\n+JY8QFUQ01A02XZ\t162\t165\tFR2\n+JY8QFUQ01A02XZ\t172\t175\tCDR2\n+JY8QFUQ01A02XZ\t187\t190\tCDR2\n+JY8QFUQ01A02XZ\t224\t227\tFR3\n+JY8QFUQ01A03E3\t8\t11\tFR1\n+JY8QFUQ01A03E3\t31\t34\tFR1\n+JY8QFUQ01A03E3\t36\t39\tFR1\n+JY8QFUQ01A03E3\t103\t106\tCDR1\n+JY8QFUQ01A03E3\t132\t135\tFR2\n+JY8QFUQ01A03E3\t146\t149\tFR2\n+JY8QFUQ01A03E3\t187\t190\tCDR2\n+JY8QFUQ01A03E3\t196\t199\tFR3\n+JY8QFUQ01A03E3\t297\t300\tFR3\n+JY8QFUQ01A03N6\t8\t11\tFR1\n+JY8QFUQ01A03N6\t106\t109\tCDR1\n+JY8QFUQ01A03N6\t146\t149\tFR2\n+JY8QFUQ01A03N6\t190\t193\tCDR2\n+JY8QFUQ01A03N6\t237\t240\tFR3\n+JY8QFUQ01A03N6\t257\t260\tFR3\n+JY8QFUQ01A03N6\t269\t272\tFR3\n+JY8QFUQ01A03N6\t274\t277\tFR3\n+JY8QFUQ01A08XO\t8\t11\tFR1\n+JY8QFUQ01A08XO\t82\t85\tCDR1\n+JY8QFUQ01A08XO\t103\t106\tCDR1\n+JY8QFUQ01A08XO\t118\t121\tFR2\n+JY8QFUQ01A08XO\t128\t131\tFR2\n+JY8QFUQ01A08XO\t161\t164\tFR2\n+JY8QFUQ01A08XO\t190\t193\tCDR2\n+JY8QFUQ01A08XO\t237\t240\tFR3\n+JY8QFUQ01A08XO\t257\t260\tFR3\n+JY8QFUQ01A08XO\t269\t272\tFR3\n+JY8QFUQ01A08XO\t274\t277\tFR3\n+JY8QFUQ01A0939\t3\t6\tFR1\n+JY8QFUQ01A0939\t8\t11\tFR1\n+JY8QFUQ01A0939\t14\t17\tFR1\n+JY8QFUQ01A0939\t100\t103\tCDR1\n+JY8QFUQ01A0939\t128\t131\tFR2\n+JY8QFUQ01A0939\t155\t158\tFR2\n+JY8QFUQ01A0939\t188\t191\tCDR2\n+JY8QFUQ01A0939\t204\t207\tFR3\n+JY8QFUQ01A0939\t257\t260\tFR3\n+JY8QFUQ01A0939\t269\t272\tFR3\n+JY8QFUQ01A0939\t29'..b'5\tFR2\n+JY8QFUQ01DG5KX\t146\t149\tFR2\n+JY8QFUQ01DG5KX\t162\t165\tFR2\n+JY8QFUQ01DG5KX\t187\t190\tCDR2\n+JY8QFUQ01DG5KX\t285\t288\tFR3\n+JY8QFUQ01DG5KX\t297\t300\tFR3\n+JY8QFUQ01DG6GC\t8\t11\tFR1\n+JY8QFUQ01DG6GC\t103\t106\tCDR1\n+JY8QFUQ01DG6GC\t132\t135\tFR2\n+JY8QFUQ01DG6GC\t139\t142\tFR2\n+JY8QFUQ01DG6GC\t146\t149\tFR2\n+JY8QFUQ01DG6GC\t159\t162\tFR2\n+JY8QFUQ01DG6GC\t187\t190\tCDR2\n+JY8QFUQ01DG6GC\t274\t277\tFR3\n+JY8QFUQ01DG6GC\t285\t288\tFR3\n+JY8QFUQ01DG6GC\t297\t300\tFR3\n+JY8QFUQ01DHXHT\t2\t5\tFR1\n+JY8QFUQ01DHXHT\t8\t11\tFR1\n+JY8QFUQ01DHXHT\t82\t85\tCDR1\n+JY8QFUQ01DHXHT\t100\t103\tCDR1\n+JY8QFUQ01DHXHT\t106\t109\tCDR1\n+JY8QFUQ01DHXHT\t118\t121\tFR2\n+JY8QFUQ01DHXHT\t146\t149\tFR2\n+JY8QFUQ01DHXHT\t163\t166\tFR2-CDR2\n+JY8QFUQ01DHXHT\t190\t193\tCDR2\n+JY8QFUQ01DHXHT\t269\t272\tFR3\n+JY8QFUQ01DHXHT\t274\t277\tFR3\n+JY8QFUQ01DHXHT\t297\t300\tFR3\n+JY8QFUQ01DI39D\t8\t11\tFR1\n+JY8QFUQ01DI39D\t12\t15\tFR1\n+JY8QFUQ01DI39D\t24\t27\tFR1\n+JY8QFUQ01DI39D\t72\t75\tFR1\n+JY8QFUQ01DI39D\t132\t135\tFR2\n+JY8QFUQ01DI39D\t146\t149\tFR2\n+JY8QFUQ01DI39D\t163\t166\tFR2-CDR2\n+JY8QFUQ01DI39D\t209\t212\tFR3\n+JY8QFUQ01DI39D\t220\t223\tFR3\n+JY8QFUQ01DI39D\t269\t272\tFR3\n+JY8QFUQ01DI39D\t274\t277\tFR3\n+JY8QFUQ01DIBNC\t8\t11\tFR1\n+JY8QFUQ01DIBNC\t82\t85\tCDR1\n+JY8QFUQ01DIBNC\t103\t106\tCDR1\n+JY8QFUQ01DIBNC\t118\t121\tFR2\n+JY8QFUQ01DIBNC\t128\t131\tFR2\n+JY8QFUQ01DIBNC\t161\t164\tFR2\n+JY8QFUQ01DIBNC\t190\t193\tCDR2\n+JY8QFUQ01DIBNC\t237\t240\tFR3\n+JY8QFUQ01DIBNC\t257\t260\tFR3\n+JY8QFUQ01DIBNC\t269\t272\tFR3\n+JY8QFUQ01DIBNC\t274\t277\tFR3\n+JY8QFUQ01DJFIZ\t8\t11\tFR1\n+JY8QFUQ01DJFIZ\t31\t34\tFR1\n+JY8QFUQ01DJFIZ\t36\t39\tFR1\n+JY8QFUQ01DJFIZ\t103\t106\tCDR1\n+JY8QFUQ01DJFIZ\t118\t121\tFR2\n+JY8QFUQ01DJFIZ\t132\t135\tFR2\n+JY8QFUQ01DJFIZ\t146\t149\tFR2\n+JY8QFUQ01DJFIZ\t162\t165\tFR2\n+JY8QFUQ01DJFIZ\t172\t175\tCDR2\n+JY8QFUQ01DJFIZ\t187\t190\tCDR2\n+JY8QFUQ01DJFIZ\t224\t227\tFR3\n+JY8QFUQ01DLDLD\t8\t11\tFR1\n+JY8QFUQ01DLDLD\t24\t27\tFR1\n+JY8QFUQ01DLDLD\t60\t63\tFR1\n+JY8QFUQ01DLDLD\t72\t75\tFR1\n+JY8QFUQ01DLDLD\t106\t109\tCDR1\n+JY8QFUQ01DLDLD\t146\t149\tFR2\n+JY8QFUQ01DLDLD\t187\t190\tCDR2\n+JY8QFUQ01DLDLD\t196\t199\tFR3\n+JY8QFUQ01DLDLD\t209\t212\tFR3\n+JY8QFUQ01DLDLD\t220\t223\tFR3\n+JY8QFUQ01DLDLD\t253\t256\tFR3\n+JY8QFUQ01DLDLD\t269\t272\tFR3\n+JY8QFUQ01DLDLD\t274\t277\tFR3\n+JY8QFUQ01DMF0A\t8\t11\tFR1\n+JY8QFUQ01DMF0A\t106\t109\tCDR1\n+JY8QFUQ01DMF0A\t146\t149\tFR2\n+JY8QFUQ01DMF0A\t190\t193\tCDR2\n+JY8QFUQ01DMF0A\t237\t240\tFR3\n+JY8QFUQ01DMF0A\t257\t260\tFR3\n+JY8QFUQ01DMF0A\t269\t272\tFR3\n+JY8QFUQ01DMF0A\t274\t277\tFR3\n+JY8QFUQ01DOVL5\t8\t11\tFR1\n+JY8QFUQ01DOVL5\t103\t106\tCDR1\n+JY8QFUQ01DOVL5\t112\t115\tCDR1\n+JY8QFUQ01DOVL5\t132\t135\tFR2\n+JY8QFUQ01DOVL5\t139\t142\tFR2\n+JY8QFUQ01DOVL5\t146\t149\tFR2\n+JY8QFUQ01DOVL5\t159\t162\tFR2\n+JY8QFUQ01DOVL5\t187\t190\tCDR2\n+JY8QFUQ01DOVL5\t285\t288\tFR3\n+JY8QFUQ01DOVL5\t297\t300\tFR3\n+JY8QFUQ01DPT8R\t8\t11\tFR1\n+JY8QFUQ01DPT8R\t31\t34\tFR1\n+JY8QFUQ01DPT8R\t36\t39\tFR1\n+JY8QFUQ01DPT8R\t103\t106\tCDR1\n+JY8QFUQ01DPT8R\t132\t135\tFR2\n+JY8QFUQ01DPT8R\t146\t149\tFR2\n+JY8QFUQ01DPT8R\t187\t190\tCDR2\n+JY8QFUQ01DPT8R\t196\t199\tFR3\n+JY8QFUQ01DPT8R\t297\t300\tFR3\n+JY8QFUQ01DUD3U\t8\t11\tFR1\n+JY8QFUQ01DUD3U\t31\t34\tFR1\n+JY8QFUQ01DUD3U\t36\t39\tFR1\n+JY8QFUQ01DUD3U\t103\t106\tCDR1\n+JY8QFUQ01DUD3U\t118\t121\tFR2\n+JY8QFUQ01DUD3U\t132\t135\tFR2\n+JY8QFUQ01DUD3U\t146\t149\tFR2\n+JY8QFUQ01DUD3U\t162\t165\tFR2\n+JY8QFUQ01DUD3U\t172\t175\tCDR2\n+JY8QFUQ01DUD3U\t187\t190\tCDR2\n+JY8QFUQ01DUD3U\t224\t227\tFR3\n+JY8QFUQ01DV4HU\t8\t11\tFR1\n+JY8QFUQ01DV4HU\t31\t34\tFR1\n+JY8QFUQ01DV4HU\t103\t106\tCDR1\n+JY8QFUQ01DV4HU\t118\t121\tFR2\n+JY8QFUQ01DV4HU\t132\t135\tFR2\n+JY8QFUQ01DV4HU\t146\t149\tFR2\n+JY8QFUQ01DV4HU\t170\t173\tCDR2\n+JY8QFUQ01DV4HU\t297\t300\tFR3\n+JY8QFUQ01DV8LF\t8\t11\tFR1\n+JY8QFUQ01DV8LF\t31\t34\tFR1\n+JY8QFUQ01DV8LF\t36\t39\tFR1\n+JY8QFUQ01DV8LF\t103\t106\tCDR1\n+JY8QFUQ01DV8LF\t132\t135\tFR2\n+JY8QFUQ01DV8LF\t146\t149\tFR2\n+JY8QFUQ01DV8LF\t187\t190\tCDR2\n+JY8QFUQ01DV8LF\t297\t300\tFR3\n+JY8QFUQ01DVBU0\t8\t11\tFR1\n+JY8QFUQ01DVBU0\t31\t34\tFR1\n+JY8QFUQ01DVBU0\t36\t39\tFR1\n+JY8QFUQ01DVBU0\t103\t106\tCDR1\n+JY8QFUQ01DVBU0\t132\t135\tFR2\n+JY8QFUQ01DVBU0\t146\t149\tFR2\n+JY8QFUQ01DVBU0\t187\t190\tCDR2\n+JY8QFUQ01DVBU0\t196\t199\tFR3\n+JY8QFUQ01DVBU0\t297\t300\tFR3\n+JY8QFUQ01DXDOM\t8\t11\tFR1\n+JY8QFUQ01DXDOM\t103\t106\tCDR1\n+JY8QFUQ01DXDOM\t112\t115\tCDR1\n+JY8QFUQ01DXDOM\t132\t135\tFR2\n+JY8QFUQ01DXDOM\t146\t149\tFR2\n+JY8QFUQ01DXDOM\t169\t172\tCDR2\n+JY8QFUQ01DXDOM\t184\t187\tCDR2\n+JY8QFUQ01DXDOM\t297\t300\tFR3\n'

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/data/intermediate_files/merged.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/data/intermediate_files/merged.txt Tue Jan 25 11:28:29 2022 +0000

[

b'@@ -0,0 +1,1577 @@\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"

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/data/intermediate_files/mutation_in_motifs.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/data/intermediate_files/mutation_in_motifs.txt Tue Jan 25 11:28:29 2022 +0000

b'@@ -0,0 +1,906816 @@\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(- - -)\n+JY8QFUQ01A006G\t269\tFR3\ta\tg\t90\tK\tR\tRGYW\t269\t272\t(+ + +)\n+JY8QFUQ01A006G\t269\tFR3\ta\tg\t90\tK\tR\tWRCY\t269\t272\t(+ + +)\n+JY8QFUQ01A006G\t269\tFR3\ta\tg\t90\tK\tR\tWA\t268\t269\t(+ + +)\n+JY8QFUQ01A006G\t271\tFR3\tc\tt\tNone\tNone\tNone\tRGYW\t269\t272\t\n+JY8QFUQ01A006G\t271\tFR3\tc\tt\tNone\tNone\tNone\tWRCY\t269\t272\t\n+JY8QFUQ01A006G\t276\tFR3\tc\tg\t92\tS\tR\tRGYW\t274\t277\t(- - -)\n+JY8QFUQ01A006G\t276\tFR3\tc\tg\t92\tS\tR\tWRCY\t274\t277\t(- - -)\n+JY8QFUQ01A006G\t306\tFR3\tt\tc\tNone\tNone\tNone\tTW\t306\t307\t\n+JY8QFUQ01A018V\t83\tCDR1\tg\tt\t28\tG\tV\tRGYW\t82\t85\t(- - -)\n+JY8QFUQ01A018V\t104\tCDR1\tg\ta\t35\tG\tE\tRGYW\t103\t106\t(- - -)\n+JY8QFUQ01A018V\t105\tCDR1\tt\tg\t35\tG\tE\tRGYW\t103\t106\t(- - -)\n+JY8QFUQ01A018V\t105\tCDR1\tt\tg\t35\tG\tE\tWA\t105\t106\t(- - -)\n+JY8QFUQ01A018V\t105\tCDR1\tt\tg\t35\tG\tE\tTW\t105\t106\t(- - -)\n+JY8QFUQ01A018V\t106\tCDR1\ta\tt\tNone\tNone\tNone\tRGYW\t103\t106\t\n+JY8QFUQ01A018V\t106\tCDR1\ta\tt\tNone\tNone\tNone\tWA\t105\t106\t\n+JY8QFUQ01A018V\t106\tCDR1\ta\tt\tNone\tNone\tNone\tTW\t105\t106\t\n+JY8QFUQ01A018V\t108\tCDR1\tt\tc\tNone\tNone\tNone\tTW\t108\t109\t\n+JY8QFUQ01A018V\t111\tCDR1\tc\tt\tNone\tNone\tNone\tWRCY\t109\t112'..b'103\t106\t(+ - -)\n+JY8QFUQ01DV4HU\t104\tCDR1\tg\tc\t35\tS\tP\tRGYW\t103\t106\t(+ - -)\n+JY8QFUQ01DV4HU\t108\tCDR1\tc\ta\t36\tS\tR\tWRCY\t106\t109\t(- - -)\n+JY8QFUQ01DV4HU\t111\tCDR1\tt\tc\tNone\tNone\tNone\tTW\t111\t112\tNone\n+JY8QFUQ01DV4HU\t119\tFR2\tg\ta\t40\tS\tN\tRGYW\t118\t121\t(- - -)\n+JY8QFUQ01DV4HU\t119\tFR2\tg\ta\t40\tS\tN\tWRCY\t118\t121\t(- - -)\n+JY8QFUQ01DV4HU\t120\tFR2\tc\tt\t40\tS\tN\tRGYW\t118\t121\t(- - -)\n+JY8QFUQ01DV4HU\t120\tFR2\tc\tt\t40\tS\tN\tWRCY\t118\t121\t(- - -)\n+JY8QFUQ01DV4HU\t193\tCDR2\ta\tg\t65\tK\tE\tWA\t193\t194\t(+ - -)\n+JY8QFUQ01DV4HU\t196\tFR3\tt\ta\t66\tY\tN\tWRCY\t196\t199\t(- - -)\n+JY8QFUQ01DV4HU\t196\tFR3\tt\ta\t66\tY\tN\tWA\t196\t197\t(- - -)\n+JY8QFUQ01DV4HU\t196\tFR3\tt\ta\t66\tY\tN\tTW\t196\t197\t(- - -)\n+JY8QFUQ01DV4HU\t200\tFR3\ta\tt\t67\tY\tF\tWA\t199\t200\t(- + -)\n+JY8QFUQ01DV4HU\t200\tFR3\ta\tt\t67\tY\tF\tTW\t199\t200\t(- + -)\n+JY8QFUQ01DV4HU\t245\tFR3\ta\tg\t82\tN\tS\tWA\t244\t245\t(- - -)\n+JY8QFUQ01DV4HU\t255\tFR3\tc\tt\tNone\tNone\tNone\tWRCY\t253\t256\tNone\n+JY8QFUQ01DV4HU\t263\tFR3\ta\tc\t88\tY\tS\tWA\t262\t263\t(+ - -)\n+JY8QFUQ01DV4HU\t263\tFR3\ta\tc\t88\tY\tS\tTW\t262\t263\t(+ - -)\n+JY8QFUQ01DV4HU\t287\tFR3\tc\tt\t96\tA\tV\tWRCY\t285\t288\t(+ - +)\n+JY8QFUQ01DV4HU\t309\tFR3\tc\tt\tNone\tNone\tNone\tWRCY\t307\t310\tNone\n+JY8QFUQ01DV8LF\t106\tCDR1\ta\tc\t36\tS\tR\tRGYW\t103\t106\t(- - -)\n+JY8QFUQ01DV8LF\t106\tCDR1\ta\tc\t36\tS\tR\tWRCY\t106\t109\t(- - -)\n+JY8QFUQ01DV8LF\t106\tCDR1\ta\tc\t36\tS\tR\tWA\t105\t106\t(- - -)\n+JY8QFUQ01DV8LF\t106\tCDR1\ta\tc\t36\tS\tR\tTW\t105\t106\t(- - -)\n+JY8QFUQ01DV8LF\t147\tFR2\tg\tc\tNone\tNone\tNone\tRGYW\t146\t149\tNone\n+JY8QFUQ01DV8LF\t171\tCDR2\tt\ta\t57\tN\tK\tWA\t171\t172\t(+ - -)\n+JY8QFUQ01DV8LF\t171\tCDR2\tt\ta\t57\tN\tK\tTW\t171\t172\t(+ - -)\n+JY8QFUQ01DV8LF\t188\tCDR2\tg\tt\t63\tS\tI\tRGYW\t187\t190\t(- - -)\n+JY8QFUQ01DV8LF\t306\tFR3\tt\tc\tNone\tNone\tNone\tTW\t306\t307\tNone\n+JY8QFUQ01DVBU0\t167\tCDR2\tt\tg\t56\tI\tS\tTW\t167\t168\t(- - -)\n+JY8QFUQ01DVBU0\t188\tCDR2\tg\tc\t63\tS\tT\tRGYW\t187\t190\t(+ - +)\n+JY8QFUQ01DVBU0\t190\tCDR2\ta\tg\t64\tS\tD\tRGYW\t187\t190\t(- - -)\n+JY8QFUQ01DVBU0\t190\tCDR2\ta\tg\t64\tS\tD\tWA\t189\t190\t(- - -)\n+JY8QFUQ01DVBU0\t190\tCDR2\ta\tg\t64\tS\tD\tTW\t189\t190\t(- - -)\n+JY8QFUQ01DVBU0\t196\tFR3\ta\tg\t66\tS\tA\tRGYW\t196\t199\t(- + -)\n+JY8QFUQ01DVBU0\t196\tFR3\ta\tg\t66\tS\tA\tWRCY\t196\t199\t(- + -)\n+JY8QFUQ01DVBU0\t196\tCDR2\ta\tg\t66\tS\tA\tWA\t195\t196\t(- + -)\n+JY8QFUQ01DVBU0\t197\tFR3\tg\tc\t66\tS\tA\tRGYW\t196\t199\t(- + -)\n+JY8QFUQ01DVBU0\t197\tFR3\tg\tc\t66\tS\tA\tWRCY\t196\t199\t(- + -)\n+JY8QFUQ01DXDOM\t104\tCDR1\tg\tc\t35\tS\tT\tRGYW\t103\t106\t(+ - +)\n+JY8QFUQ01DXDOM\t106\tCDR1\ta\tg\t36\tS\tG\tRGYW\t103\t106\t(+ + -)\n+JY8QFUQ01DXDOM\t106\tCDR1\ta\tg\t36\tS\tG\tWRCY\t106\t109\t(+ + -)\n+JY8QFUQ01DXDOM\t106\tCDR1\ta\tg\t36\tS\tG\tWA\t105\t106\t(+ + -)\n+JY8QFUQ01DXDOM\t106\tCDR1\ta\tg\t36\tS\tG\tTW\t105\t106\t(+ + -)\n+JY8QFUQ01DXDOM\t108\tCDR1\tc\tt\t36\tS\tG\tWRCY\t106\t109\t(+ + -)\n+JY8QFUQ01DXDOM\t110\tCDR1\ta\tt\t37\tY\tF\tWA\t109\t110\t(- + -)\n+JY8QFUQ01DXDOM\t110\tCDR1\ta\tt\t37\tY\tF\tTW\t109\t110\t(- + -)\n+JY8QFUQ01DXDOM\t113\tCDR1\tg\tc\t38\tS\tT\tRGYW\t112\t115\t(+ - +)\n+JY8QFUQ01DXDOM\t115\tCDR1\ta\tg\t39\tM\tV\tRGYW\t112\t115\t(+ - -)\n+JY8QFUQ01DXDOM\t119\tFR2\ta\tt\t40\tN\tI\tWRCY\t118\t121\t(- - -)\n+JY8QFUQ01DXDOM\t119\tFR2\ta\tt\t40\tN\tI\tWA\t118\t119\t(- - -)\n+JY8QFUQ01DXDOM\t168\tCDR2\tt\tc\t56\tI\tV\tWA\t168\t169\t(+ - +)\n+JY8QFUQ01DXDOM\t168\tCDR2\tt\tc\t56\tI\tV\tTW\t167\t168\t(+ - +)\n+JY8QFUQ01DXDOM\t170\tCDR2\tg\tc\t57\tS\tT\tRGYW\t169\t172\t(+ - +)\n+JY8QFUQ01DXDOM\t187\tCDR2\ta\tg\t63\tS\tG\tRGYW\t184\t187\t(+ + -)\n+JY8QFUQ01DXDOM\t187\tCDR2\ta\tg\t63\tS\tG\tWA\t186\t187\t(+ + -)\n+JY8QFUQ01DXDOM\t187\tCDR2\ta\tg\t63\tS\tG\tTW\t186\t187\t(+ + -)\n+JY8QFUQ01DXDOM\t190\tCDR2\tt\tc\t64\tY\tL\tWA\t190\t191\t(- - -)\n+JY8QFUQ01DXDOM\t190\tCDR2\tt\tc\t64\tY\tL\tTW\t189\t190\t(- - -)\n+JY8QFUQ01DXDOM\t191\tCDR2\ta\tt\t64\tY\tL\tWA\t190\t191\t(- - -)\n+JY8QFUQ01DXDOM\t194\tCDR2\tt\tc\t65\tI\tT\tWA\t194\t195\t(- - -)\n+JY8QFUQ01DXDOM\t194\tCDR2\tt\tc\t65\tI\tT\tTW\t194\t195\t(- - -)\n+JY8QFUQ01DXDOM\t195\tCDR2\ta\tg\t65\tI\tT\tWA\t194\t195\t(- - -)\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'

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/data/intermediate_files/mutationdict.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/data/intermediate_files/mutationdict.txt Tue Jan 25 11:28:29 2022 +0000

b'@@ -0,0 +1,41750 @@\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'

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/test_shm_csr.py
--- a/tests/test_shm_csr.py Fri Nov 05 13:41:03 2021 +0000
+++ b/tests/test_shm_csr.py Tue Jan 25 11:28:29 2022 +0000

[

@@ -24,23 +24,38 @@
import sys
import tempfile
from pathlib import Path
+from xml.etree import ElementTree
+from xml.etree.ElementTree import Element

import pytest

-GIT_ROOT = str(Path(__file__).parent.parent.absolute())
+GIT_ROOT = Path(__file__).parent.parent.absolute()
TEST_DIR = Path(__file__).parent
TEST_DATA_DIR = TEST_DIR / "data"
VALIDATION_DATA_DIR = TEST_DIR / "validation_data"
CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"

+def get_container():
+    tool = ElementTree.parse(GIT_ROOT / "shm_csr.xml").getroot()
+    requirements: Element = tool.find("requirements")
+    container = requirements.find("container")
+    return container.text
+
+
@pytest.fixture(scope="module")
def shm_csr_result():
-    temp_dir = tempfile.mktemp()
-    shutil.copytree(GIT_ROOT, temp_dir)
+    temp_dir = Path(tempfile.mkdtemp())
+    tool_dir = temp_dir / "shm_csr"
+    shutil.copytree(GIT_ROOT, tool_dir)
+    working_dir = temp_dir / "working"
+    working_dir.mkdir(parents=True)
+    output_dir = temp_dir / "outputs"
+    output_dir.mkdir(parents=True)
+    wrapper = str(tool_dir / "wrapper.sh")
     input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2)
-    out_files_path = os.path.join(temp_dir, "results")
-    out_file = os.path.join(out_files_path, "result.html")
+    out_files_path = output_dir / "results"
+    out_file = out_files_path / "result.html"
     infile_name = "input_data"
     functionality = "productive"
     unique = "Sequence.ID"
@@ -57,11 +72,11 @@
     fast = 'no'
     cmd = [
         "bash",
-        "wrapper.sh",
+        wrapper,
         input,
         "custom",
-        out_file,
-        out_files_path,
+        str(out_file),
+        str(out_files_path),
         infile_name,
         "-",
         functionality,
@@ -78,10 +93,25 @@
         empty_region_filter,
         fast
     ]
-    subprocess.run(cmd, cwd=temp_dir, stdout=sys.stdout, stderr=sys.stderr,
-                   check=True)
+    docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
+                  "--rm",  # Remove container after running
+                  "-v", f"{input}:{input}",
+                  "-w", str(working_dir),
+                  # Run as current user which allows deletion of files.
+                  # It also mitigates some security considerations
+                  "-u", f"{os.getuid()}:{os.getgid()}",
+                  # Run with default seccomp profile to mitigate mitigation slowdown
+                  # http://mamememo.blogspot.com/2020/05/cpu-intensive-rubypython-code-runs.html
+                  # This knocks down test runtime from 8 to 6 minutes.
+                  "--security-opt", "seccomp=unconfined",
+                  # Use a mulled container generated with `planemo mull`
+                  "quay.io/biocontainers/mulled-v2-f7d31c9d7424063a492fc0e5ecbf89bc757c0107:2b50bdd4d8c1fefc6ec24b0753fad0dcecec843b-0"
+                  ] + cmd
+    with open(temp_dir / "stderr", "wt") as stderr_file:
+        with open(temp_dir / "stdout", "wt") as stdout_file:
+            subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
+                           stderr=stderr_file, check=True)
     yield Path(out_files_path)
-    #shutil.rmtree(temp_dir)

def test_check_output(shm_csr_result):
@@ -90,13 +120,17 @@

@pytest.mark.parametrize("filename", os.listdir(VALIDATION_DATA_DIR))
def test_results_match_validation(shm_csr_result, filename):
-    if filename == "shm_overview.txt":
-        # TODO: Fix errors in shm_overview.
-        return
     with open(Path(shm_csr_result, filename)) as result_h:
         with open(Path(VALIDATION_DATA_DIR, filename)) as validate_h:
             for line in result_h:
-                assert line == validate_h.readline()
+                # Skip two faulty lines in shm_overview.
+                # TODO: Fix the issue.
+                validation_line = validate_h.readline()
+                if filename == "shm_overview.txt":
+                    if (line.startswith("RGYW (%)") or
+                            line.startswith("WRCY (%)")):
+                        continue
+                assert line == validation_line

def test_nt_overview(shm_csr_result):

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/validation_data/shm_overview.txt
--- a/tests/validation_data/shm_overview.txt Fri Nov 05 13:41:03 2021 +0000
+++ b/tests/validation_data/shm_overview.txt Tue Jan 25 11:28:29 2022 +0000

@@ -11,7 +11,7 @@
CDR R/S (ratio) 5901 1203 4.9 3873 855 4.5 2028 348 5.8 2962 605 4.9 1717 381 4.5 998 174 5.7 126 30 4.2 121 20 6 0 0 0 0 0 8863 1808 4.9 1208 223 5.4
nt in FR 151127 195251 77.4 97738 126298 77.4 53389 68953 77.4 77252 99835 77.4 45155 58332 77.4 24674 31881 77.4 4289 5570 77 3134 4052 77.3 165 213 77.5 0 0 0 228544 295299 77.4 31179 40247 77.5
nt in CDR 44124 195251 22.6 28560 126298 22.6 15564 68953 22.6 22583 99835 22.6 13177 58332 22.6 7207 31881 22.6 1281 5570 23 918 4052 22.7 48 213 22.5 0 0 0 66755 295299 22.6 9068 40247 22.5
-Tandems/Expected (ratio) 2438 2262.33 1.08 1680 1601.93 1.05 758 660.41 1.15 1212 1128.79 1.07 769 710.06 1.08 357 321.62 1.11 43 45.72 0.94 43 51.4 0.84 0 0 0 0 0 0 3650 3391.13 1.08 482 411.6 1.17
+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 3650 2880.54 1.27 482 349.88 1.38
RGYW (%) 3163 17977 17.6 2186 12223 17.9 978 5754 17 1524 9036 16.9 911 5492 16.6 485 2777 17.5 63 388 16.2 65 379 17.2 0 0 0 0 0 0 4687 27013 17.4 602 3486 17.3
WRCY (%) 2984 17977 16.6 2060 12223 16.9 924 5754 16.1 1445 9036 16 888 5492 16.2 455 2777 16.4 52 388 13.4 50 379 13.2 0 0 0 0 0 0 4429 27013 16.4 614 3486 17.6
WA (%) 2610 17977 14.5 1715 12223 14 895 5754 15.6 1420 9036 15.7 859 5492 15.6 433 2777 15.6 67 388 17.3 61 379 16.1 0 0 0 0 0 0 4030 27013 14.9 540 3486 15.5

diff -r 3c9d4d976c47 -r 6809c63d9161 tests/validation_data/tandems_by_id.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/validation_data/tandems_by_id.txt Tue Jan 25 11:28:29 2022 +0000

[

diff -r 3c9d4d976c47 -r 6809c63d9161 wrapper.sh
--- a/wrapper.sh Fri Nov 05 13:41:03 2021 +0000
+++ b/wrapper.sh Tue Jan 25 11:28:29 2022 +0000

@@ -895,15 +895,26 @@
echo "---------------- remove_files----------------"
echo "---------------- remove_files---------------- " >> $log

-rm -r -v -f results/baseline
-rm -r -v -f files
-filename='remove_files.txt'
+rm -r -v -f $outdir/baseline
+rm -r -v -f $PWD/files
+rm -v $PWD/aa.txt
+rm -v $PWD/aa_change_stats.txt
+rm -v $PWD/gapped_aa.txt
+rm -v $PWD/gapped_nt.txt
+rm -v $PWD/hotspots.txt
+rm -v $PWD/junction.txt
+rm -v $PWD/mutationanalysis.txt
+rm -v $PWD/mutationstats.txt
+rm -v $PWD/sequences.txt
+rm -v $PWD/summary.txt
+rm -v $PWD/Rplots.pdf
+
+filename="$dir/remove_files.txt"

while read file; do
- rm -v -f $file
+ rm -v -f $outdir/$file
done < "$filename"

-
echo "---------------- Done! ----------------"
echo "---------------- Done! ---------------- " >> $outdir/log.html