| Previous changeset 98:d714f5ea83d7 (2024-01-10) |
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Commit message:
planemo upload commit 0d652311f9c4ccc26b27eebc44a3ae91a72e57b0 |
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modified:
CHANGELOG.md shm_csr.xml wrapper.sh |
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added:
tests/__pycache__/test_shm_csr.cpython-311-pytest-8.3.4.pyc tests/data/10_V-REGION-mutation-hotspots.txt tests/data/11_Parameters.txt tests/data/1_Summary.txt tests/data/2_IMGT-gapped-nt-sequences.txt tests/data/3_Nt-sequences.txt tests/data/4_IMGT-gapped-AA-sequences.txt tests/data/5_AA-sequences.txt tests/data/6_Junction.txt tests/data/7_V-REGION-mutation-and-AA-change-table.txt tests/data/8_V-REGION-nt-mutation-statistics.txt tests/data/9_V-REGION-AA-change-statistics.txt tests/data/CONTROL_NWK377_PB_IGHC_MID1_40nt_2.tar.gz tests/data/CONTROL_NWK377_PB_IGHC_MID1_40nt_2.tar.xz tests/data/README.txt |
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| diff -r d714f5ea83d7 -r 5b79485234e1 CHANGELOG.md --- a/CHANGELOG.md Wed Jan 10 12:32:47 2024 +0000 +++ b/CHANGELOG.md Mon Feb 03 13:37:26 2025 +0000 |
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| @@ -1,3 +1,7 @@ +version 1.10.1 +------------------ ++ Fix a bug that is caused by a wrong bash variable. + version 1.10.0 ------------------ + Fix crashing baseline when only unproductive sequences are present. |
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| diff -r d714f5ea83d7 -r 5b79485234e1 shm_csr.xml --- a/shm_csr.xml Wed Jan 10 12:32:47 2024 +0000 +++ b/shm_csr.xml Mon Feb 03 13:37:26 2025 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="shm_csr" name="SHM & CSR pipeline" version="1.10.0" profile="16.04"> +<tool id="shm_csr" name="SHM & CSR pipeline" version="1.10.1" profile="16.04"> <description></description> <requirements> <requirement type="package" version="3.7.1">python</requirement> |
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| diff -r d714f5ea83d7 -r 5b79485234e1 tests/__pycache__/test_shm_csr.cpython-311-pytest-8.3.4.pyc |
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| Binary file tests/__pycache__/test_shm_csr.cpython-311-pytest-8.3.4.pyc has changed |
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| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/10_V-REGION-mutation-hotspots.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/10_V-REGION-mutation-hotspots.txt Mon Feb 03 13:37:26 2025 +0000 |
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| b'@@ -0,0 +1,22434 @@\n+Sequence number\tSequence ID\tFunctionality\tV-GENE and allele\t(a/t)a\tt(a/t)\t(a/g)g(c/t)(a/t)\t(a/t)(a/g)c(c/t)\t\n+1\tJY8QFUQ01DD1I8\tNo results\t\n+2\tJY8QFUQ01BR14W\tunknown\tHomsap IGHV3-16*01 ORF, or Homsap IGHV3-16*02 ORF or Homsap IGHV3-19*01 P or Homsap IGHV3-21*01 F or Homsap IGHV3-21*02 F or Homsap IGHV3-21*03 F or Homsap IGHV3-21*04 F or Homsap IGHV3-35*01 ORF or Homsap IGHV3-48*01 F or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\tta,5-6(FR1)|aa,8-9(FR1)|ta,38-39(FR1)|ta,105-106(CDR1)|aa,118-119(FR2)|aa,130-131()|aa,141-142()|ta,158-159()|ta,168-169()|aa,175-176()|ta,189-190()|ta,199-200()|aa,214-215()|aa,244-245()|aa,253-254()|ta,262-263()|aa,269-270()|aa,271-272()|aa,274-275()|ta,304-305()|ta,307-308()|aa,318-319()|\tta,5-6(FR1)|tt,34-35(FR1)|ta,38-39(FR1)|tt,82-83(CDR1)|tt,88-89(CDR1)|ta,105-106(CDR1)|ta,158-159()|tt,167-168()|tt,171-172()|ta,189-190()|ta,199-200()|tt,226-227()|tt,246-247()|ta,262-263()|ta,304-305()|tt,306-307()|\tggta,3-6(FR1)|ggct,31-34(FR1)|ggta,36-39(FR1)|agta,103-106(CDR1)|ggct,132-135()|ggct,146-149()|ggta,156-159()|agtt,169-172()|ggca,184-187()|ggct,297-300()|\taact,8-11(FR1)|agcc,41-44(FR1)|agcc,72-75(FR1)|aact,118-121(FR2)|aact,253-256()|agcc,285-288()|tact,307-310()|\t\n+3\tJY8QFUQ01DI33C\tNo results\t\n+4\tJY8QFUQ01AHA5U\tNo results\t\n+5\tJY8QFUQ01C6E2Q\tNo results\t\n+6\tJY8QFUQ01DTOF7\tNo results\t\n+7\tJY8QFUQ01DTQZ4\tNo results\t\n+8\tJY8QFUQ01CH7HW\tNo results\t\n+9\tJY8QFUQ01DRIUN\tNo results\t\n+10\tJY8QFUQ01DMFB3\tNo results\t\n+11\tJY8QFUQ01DBKZ5\tNo results\t\n+12\tJY8QFUQ01ALILW\tNo results\t\n+13\tJY8QFUQ01DQT5M\tNo results\t\n+14\tJY8QFUQ01CU1U5\tNo results\t\n+15\tJY8QFUQ01AZ7M4\tNo results\t\n+16\tJY8QFUQ01BJI4T\tNo results\t\n+17\tJY8QFUQ01A8WKP\tNo results\t\n+18\tJY8QFUQ01CDRAH\tNo results\t\n+19\tJY8QFUQ01BSZTH\tNo results\t\n+20\tJY8QFUQ01COV1I\tNo results\t\n+21\tJY8QFUQ01BYN3R\tNo results\t\n+22\tJY8QFUQ01BB6L9\tunknown\tHomsap IGHV3-74*01 F, or Homsap IGHV3-74*02 F or Homsap IGHV3-74*03 F\tta,35-36(FR1)|ta,105-106(CDR1)|ta,109-110(CDR1)|aa,131-132(FR2)|aa,142-143()|ta,165-166()|ta,168-169()|ta,171-172()|ta,189-190()|aa,195-196()|ta,199-200()|aa,214-215()|aa,244-245()|aa,250-251()|aa,253-254()|ta,262-263()|aa,269-270()|aa,274-275()|ta,304-305()|ta,307-308()|aa,315-316()|\ttt,34-35(FR1)|tt,38-39(FR1)|tt,82-83(CDR1)|tt,88-89(CDR1)|ta,105-106(CDR1)|ta,109-110(CDR1)|ta,165-166()|tt,167-168()|ta,171-172()|ta,189-190()|ta,199-200()|tt,226-227()|ta,262-263()|ta,304-305()|tt,306-307()|\tagct,8-11(FR1)|ggct,31-34(FR1)|agtt,36-39(FR1)|agta,103-106(CDR1)|agct,132-135(FR2)|ggct,146-149()|agta,187-190()|agct,196-199()|ggct,297-300()|\tagct,8-11(FR1)|agcc,41-44(FR1)|agcc,72-75(FR1)|agct,106-109(CDR1)|agct,132-135(FR2)|agct,196-199()|agcc,285-288()|tact,307-310()|\t\n+23\tJY8QFUQ01AK5S0\tNo results\t\n+24\tJY8QFUQ01A3U3N\tNo results\t\n+25\tJY8QFUQ01DMJ3V\tNo results\t\n+26\tJY8QFUQ01DULTP\tNo results\t\n+27\tJY8QFUQ01DXFUU\tNo results\t\n+28\tJY8QFUQ01BDHX9\tNo results\t\n+29\tJY8QFUQ01BFXXE\tNo results\t\n+30\tJY8QFUQ01DA0S9\tNo results\t\n+31\tJY8QFUQ01A8RD7\tNo results\t\n+32\tJY8QFUQ01DUD3G\tunknown\tHomsap IGHV3-20*01 F, or Homsap IGHV3-20*02 ORF\tta,38-39(FR1)|ta,109-110(CDR1)|aa,131-132()|aa,142-143()|ta,165-166()|ta,168-169()|aa,175-176()|ta,189-190()|ta,199-200()|aa,214-215()|aa,244-245()|aa,250-251()|aa,253-254()|ta,262-263()|aa,269-270()|aa,274-275()|ta,304-305()|\tta,38-39(FR1)|tt,82-83(CDR1)|tt,88-89(CDR1)|tt,108-109(CDR1)|ta,165-166()|tt,167-168()|tt,171-172()|ta,189-190()|tt,198-199()|tt,226-227()|ta,262-263()|tt,301-302()|ta,304-305()|\tagct,8-11(FR1)|ggta,36-39(FR1)|ggca,112-115(CDR1)|agct,118-121(FR2)|agct,132-135()|ggct,146-149()|ggta,163-166()|ggta,187-190()|ggtt,196-199()|\tagct,8-11(FR1)|agcc,72-75(FR1)|agct,118-121(FR2)|agct,132-135()|aact,253-256()|agcc,285-288()|\t\n+33\tJY8QFUQ01BAEVW\tunknown\tHomsap IGHV3-48*01 F, or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\tta,38-39(FR1)|ta,105-106(CDR1)|ta,109-110(CDR1)|ta,111-112(CDR1)|aa,118-119(FR2)|aa,142-143(FR2)|ta,163-164(FR2)|ta,168-169(CDR2)|ta,171-172(CDR2)|ta,174-175(CDR2)|ta,186-187(CDR2)|ta,189-190(CDR2)|ta,194-195(CDR2)|ta,'..b')|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)|tt,164-165(FR2)|ta,167-168(CDR2)|ta,172-173(CDR2)|ta,189-190(CDR2)|ta,192-193(CDR2)|ta,196-197(FR3)|ta,199-200(FR3)|tt,226-227(FR3)|tt,246-247(FR3)|ta,262-263(FR3)|ta,304-305(FR3)|tt,306-307(FR3)|\tagct,8-11(FR1)|agta,103-106(CDR1)|ggca,112-115(CDR1)|ggct,132-135(FR2)|ggca,139-142(FR2)|ggct,146-149(FR2)|ggca,159-162(FR2)|agta,187-190(CDR2)|ggct,297-300(FR3)|\tagct,8-11(FR1)|agcc,41-44(FR1)|agct,106-109(CDR1)|tact,196-199(FR3)|agcc,277-280(FR3)|agcc,285-288(FR3)|tact,307-310(FR3)|\t\n+22431\tJY8QFUQ01BLN4B\tproductive\tHomsap IGHV3-33*01 F, or Homsap IGHV3-33*06 F\tta,105-106(CDR1)|ta,109-110(CDR1)|aa,142-143(FR2)|ta,165-166(FR2-CDR2)|ta,167-168(CDR2)|ta,172-173(CDR2)|aa,186-187(CDR2)|ta,189-190(CDR2)|ta,192-193(CDR2)|aa,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)|tt,164-165(FR2)|ta,167-168(CDR2)|ta,172-173(CDR2)|ta,189-190(CDR2)|ta,192-193(CDR2)|ta,196-197(FR3)|ta,199-200(FR3)|tt,226-227(FR3)|tt,246-247(FR3)|ta,262-263(FR3)|ta,304-305(FR3)|tt,306-307(FR3)|\tagct,8-11(FR1)|agta,103-106(CDR1)|ggca,112-115(CDR1)|ggct,132-135(FR2)|ggca,139-142(FR2)|ggct,146-149(FR2)|ggca,159-162(FR2)|ggta,170-173(CDR2)|agta,187-190(CDR2)|ggct,297-300(FR3)|\tagct,8-11(FR1)|agcc,41-44(FR1)|agct,106-109(CDR1)|tact,196-199(FR3)|agcc,277-280(FR3)|agcc,285-288(FR3)|tact,307-310(FR3)|\t\n+22432\tJY8QFUQ01ARNFI\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tta,38-39(FR1)|ta,109-110(CDR1)|aa,142-143(FR2)|ta,165-166(FR2-CDR2)|ta,168-169(CDR2)|ta,174-175(CDR2)|ta,189-190(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,302-303(FR3)|ta,304-305(FR3)|ta,307-308(FR3)|aa,316-317(CDR3)|\ttt,13-14(FR1)|tt,34-35(FR1)|ta,38-39(FR1)|tt,82-83(CDR1)|tt,88-89(CDR1)|ta,109-110(CDR1)|ta,165-166(FR2-CDR2)|tt,167-168(CDR2)|ta,174-175(CDR2)|ta,189-190(CDR2)|ta,196-197(FR3)|ta,199-200(FR3)|tt,226-227(FR3)|tt,246-247(FR3)|ta,262-263(FR3)|ta,302-303(FR3)|ta,304-305(FR3)|tt,306-307(FR3)|\tagct,8-11(FR1)|ggct,31-34(FR1)|ggta,36-39(FR1)|agca,103-106(CDR1)|agct,118-121(FR2)|ggct,132-135(FR2)|ggct,146-149(FR2)|agct,162-165(FR2)|ggta,172-175(CDR2)|ggta,187-190(CDR2)|ggtt,224-227(FR3)|\tagct,8-11(FR1)|agcc,41-44(FR1)|agcc,72-75(FR1)|agct,106-109(CDR1)|tgcc,111-114(CDR1)|agct,118-121(FR2)|agct,162-165(FR2)|tact,196-199(FR3)|agcc,277-280(FR3)|agcc,285-288(FR3)|tact,307-310(FR3)|\t\n+22433\tJY8QFUQ01CDTOM\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tta,38-39(FR1)|ta,109-110(CDR1)|aa,142-143(FR2)|ta,165-166(FR2-CDR2)|ta,168-169(CDR2)|ta,174-175(CDR2)|ta,189-190(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,302-303(FR3)|ta,304-305(FR3)|ta,307-308(FR3)|aa,316-317(CDR3)|\ttt,13-14(FR1)|tt,34-35(FR1)|ta,38-39(FR1)|tt,82-83(CDR1)|tt,88-89(CDR1)|ta,109-110(CDR1)|ta,165-166(FR2-CDR2)|tt,167-168(CDR2)|ta,174-175(CDR2)|ta,189-190(CDR2)|ta,196-197(FR3)|ta,199-200(FR3)|tt,226-227(FR3)|tt,246-247(FR3)|ta,262-263(FR3)|ta,302-303(FR3)|ta,304-305(FR3)|tt,306-307(FR3)|\tagct,8-11(FR1)|ggct,31-34(FR1)|ggta,36-39(FR1)|agca,103-106(CDR1)|agct,118-121(FR2)|ggct,132-135(FR2)|ggct,146-149(FR2)|agct,162-165(FR2)|ggta,172-175(CDR2)|ggta,187-190(CDR2)|ggtt,224-227(FR3)|\tagct,8-11(FR1)|agcc,41-44(FR1)|agcc,72-75(FR1)|agct,106-109(CDR1)|tgcc,111-114(CDR1)|agct,118-121(FR2)|agct,162-165(FR2)|tact,196-199(FR3)|agcc,277-280(FR3)|agcc,285-288(FR3)|tact,307-310(FR3)|\t\n' 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| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/11_Parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/11_Parameters.txt Mon Feb 03 13:37:26 2025 +0000 |
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| @@ -0,0 +1,10 @@ +Date Sat Apr 02 10:28:34 CEST 2016 +IMGT/V-QUEST programme version 3.3.6 +IMGT/V-QUEST reference directory release 201606-4 +Species Homo sapiens +Receptor type or locus IGH +IMGT/V-QUEST reference directory set F+ORF+in-frame P +Search for insertions and deletions yes +Nb of nucleotides to add (or exclude) in 3' of the V-REGION for the evaluation of the alignment score 0 +Nb of nucleotides to exclude in 5' of the V-REGION for the evaluation of the nb of mutations 0 +Number of submitted sequences 22433 |
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| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/1_Summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/1_Summary.txt Mon Feb 03 13:37:26 2025 +0000 |
| [ |
| b'@@ -0,0 +1,22434 @@\n+Sequence number\tSequence ID\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\t\n+1\tJY8QFUQ01DD1I8\tNo results\t\n+2\tJY8QFUQ01BR14W\tunknown (see comment)\tHomsap IGHV3-16*01 ORF, or Homsap IGHV3-16*02 ORF or Homsap IGHV3-19*01 P or Homsap IGHV3-21*01 F or Homsap IGHV3-21*02 F or Homsap IGHV3-21*03 F or Homsap IGHV3-21*04 F or Homsap IGHV3-35*01 ORF or Homsap IGHV3-48*01 F or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t134\t88.24\t30/34 nt\t\t\t\t\t\t\t\t\t8\tX\tX\t8.X.X\t[1.2.X.X]\t\tnull\t+\tNo rearrangement found\t\t\t\t\ttctggattcaccttcagcaaccataacatgaact\t\n+3\tJY8QFUQ01DI33C\tNo results\t\n+4\tJY8QFUQ01AHA5U\tNo results\t\n+5\tJY8QFUQ01C6E2Q\tNo results\t\n+6\tJY8QFUQ01DTOF7\tNo results\t\n+7\tJY8QFUQ01DTQZ4\tNo results\t\n+8\tJY8QFUQ01CH7HW\tNo results\t\n+9\tJY8QFUQ01DRIUN\tNo results\t\n+10\tJY8QFUQ01DMFB3\tNo results\t\n+11\tJY8QFUQ01DBKZ5\tNo results\t\n+12\tJY8QFUQ01ALILW\tNo results\t\n+13\tJY8QFUQ01DQT5M\tNo results\t\n+14\tJY8QFUQ01CU1U5\tNo results\t\n+15\tJY8QFUQ01AZ7M4\tNo results\t\n+16\tJY8QFUQ01BJI4T\tNo results\t\n+17\tJY8QFUQ01A8WKP\tNo results\t\n+18\tJY8QFUQ01CDRAH\tNo results\t\n+19\tJY8QFUQ01BSZTH\tNo results\t\n+20\tJY8QFUQ01COV1I\tNo results\t\n+21\tJY8QFUQ01BYN3R\tNo results\t\n+22\tJY8QFUQ01BB6L9\tunknown (see comment)\tHomsap IGHV3-74*01 F, or Homsap IGHV3-74*02 F or Homsap IGHV3-74*03 F\t121\t69.81\t37/53 nt\t\t\t\t\t\t\t\t\t8\tX\tX\t8.X.X\t[1.8.X.X]\t\tnull\t+\tNo rearrangement found\t\t\t\t\ttccggattcacctttagtagttactggatgcactgggtccagggcttcttccc\t\n+23\tJY8QFUQ01AK5S0\tNo results\t\n+24\tJY8QFUQ01A3U3N\tNo results\t\n+25\tJY8QFUQ01DMJ3V\tNo results\t\n+26\tJY8QFUQ01DULTP\tNo results\t\n+27\tJY8QFUQ01DXFUU\tNo results\t\n+28\tJY8QFUQ01BDHX9\tNo results\t\n+29\tJY8QFUQ01BFXXE\tNo results\t\n+30\tJY8QFUQ01DA0S9\tNo results\t\n+31\tJY8QFUQ01A8RD7\tNo results\t\n+32\tJY8QFUQ01DUD3G\tunknown (see comment)\tHomsap IGHV3-20*01 F, or Homsap IGHV3-20*02 ORF\t167\t94.59\t35/37 nt\t\t\t\t\t\t\t\t\t8\tX\tX\t8.X.X\t[1.3.X.X]\t\tnull\t+\tNo rearrangement found\t\t\t\t\tctctggattcacctttggttattatggcatgagctgg\t\n+33\tJY8QFUQ01BAEVW\tunknown (see comment)\tHomsap IGHV3-48*01 F, or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F (see comment)\t412\t81.97\t100/122 nt\t\t\t\t\t\t\t\t\t8\t8\tX\t8.8.X\t[1.17.6.X]\t\tnull\t+\tNo rearrangement found\tLow V-REGION identity (81,97% ) this may indicate potential nucleotide insertion(s) and/or deletion(s) which are not dealt in this release\t\t\t\tctctggatttgccctcagtgactatgccatgcactgggtccgccaggctccagggaaggggctggagtggattgcatacattagtgtttctacttacaccattttctacgcagagtctgtta\t\n+34\tJY8QFUQ01C5VTQ\tNo results\t\n+35\tJY8QFUQ01DV0LO\tunknown (see comment)\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*02 F or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t442\t93.07\t94/101 nt\t\t\t\t\t\t\t\t\t8\t7\tX\t8.7.X\t[1.17.X.X]\t\tnull\t+\tNo rearrangement found\t\t\t\t\tctctggattcacctttggcagctatatcatgagctgggtccgccaggctccagggaaggggctggagtgggtctcagctattagtggtaggggtgttgaca\t\n+36\tJY8QFUQ01BQV49\tNo results\t\n+37\tJY8QFUQ01BG2BI\tNo results\t\n+38\tJY8QFUQ01DDCUU\tunknown (see comment)\tHomsap IGHV3-15*01 F, or Homsap IGHV3-15*02 F (see comment)\t709\t79.73\t177/222 nt\t\t\tHomsap IGHJ4*03 F (see comment)\t20\t61.54\t8/13 nt\t\t\t8\t10\tX\t8.10.X\t[1.17.38.X]\t\tnull\t+\tRearranged sequence but no junction found\tLow V-REGION identity (79,73% ) this may indicate potential nucleotide insertion(s) and/or deletion(s) which are not dealt in this release\t The JUNCTION has not been identified: the results for J-GENE may be unreliable.\t\t\ttctggattcactgtcaataacgcctggatgacctgggtccgccaggctccagggaaggggctggagtgggttggccgtattagaagcaaaactgatggcgggacagcagactacgctccatttgtggacgacagattcaccatttcaacagatgattcaaaaatcacgttgtatctcctcagcatccccgaccagcccaaggtcttcccgctgagcctctgcagcacccagccagatgggaacg'..b"cattttgatatctggagccaagggacaatggtcaccgtctcttcagcatcccccgaccagcccccaaggtcttcccgctgagcctctgcagcacccagccagatgggaacgtggtcatcgcctgcctggtccagggcttcttcccccca\t\n+22429\tJY8QFUQ01C1IBJ\tunproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t950\t93.12\t203/218 nt\t92.2\t201/218 nt\tHomsap IGHJ4*02 F\t123\t72.92\t35/48 nt\tHomsap IGHD4-17*01 F\t3\t8\t8\tX\t8.8.X\t[1.17.38.11]\tCARFGPLTRPDY##\tout-of-frame\t+\t\t\t\tin CDR1-IMGT at codon 30 of V-REGION: 'T' (1 nucleotides at position 15 to 15 in the user submitted sequence), (cause frameshift);in FR2-IMGT at codon 48 of V-REGION: 'GA' (2 nucleotides at position 58 to 59 in the user submitted sequence), (cause frameshift);\t\tcctctggattcaccTtttaccaactatggcatgagctgggtccgccaggctccagggGAagggggctggagtgggtctcaggtattagtggtagtggtgataccacataccacgcagactccgtgcagggccgattcaccatctccagagacaactccaagaacactctgtatctgcaaatgaacagtctgagagtcgaggacacggccgtttattactgtgcgagattcggcccacttactcgacctgactactgggggccagggaactttggtcaccgtctcctcagcatccccgaccagccccaaggtcttcccgctgagcctccgacagcacccccccgaagatgggaacgtggtcgtcgcatgcctggtccagggcttcttccccca\t\n+22430\tJY8QFUQ01B48C0\tproductive\tHomsap IGHV3-33*05 F (see comment)\t699\t80.0\t176/220 nt\t\t\tHomsap IGHJ4*02 F\t186\t87.5\t42/48 nt\tHomsap IGHD5-12*01 F\t3\t8\t8\t13\t8.8.13\t[2.17.38.11]\tCVKGRGYNDYGLDYW\tin-frame\t-\t\tLow V-REGION identity (80,00% ) this may indicate potential nucleotide insertion(s) and/or deletion(s) which are not dealt in this release\t\t\t\tgcgtctgggattctccttcagcaattatgccatccactgggtccgccaggctccaggcaaggggctggagtgggtggcgaccatttcatatgatattaataaaagatattatgcagagtccgtgaggggccgattcaccctctccagagacaattccaagaacactctcgatctgctcatggatacccttcggttcgacgacacggctgtctattattgtgttaaaggacgtggatacaatgactacggcctcgactactggggcccgggaaccctgctcaccgtctcctcagcctccaccaagggcccatcggtcttcccccctggcaccctcctccaagagcacctctggggggcacagcggccctgggctgcctggtcaaggactacttccccgaaccggtgacggtgtcgtggaactca\t\n+22431\tJY8QFUQ01BLN4B\tproductive\tHomsap IGHV3-33*01 F, or Homsap IGHV3-33*06 F\t851\t88.07\t192/218 nt\t\t\tHomsap IGHJ6*01 F (see comment)\t171\t74.6\t47/63 nt\tHomsap IGHD2-2*01 F\t1\t8\t8\t13\t8.8.13\t[1.17.38.11]\tCVSDRELHYQHLDVW\tin-frame\t+\t\t\t Other possibilities: Homsap_IGHJ3*01 (shorter alignment but highest percentage of identity)\t\t\tcgtctggattcaacttcaatagttttggcatgcactgggtccgccaggctccgggcaagggactggagtgggtggcaaacatatggtatgatggaggtagtcaacactatgcagacctcgtgaagggccgattcaccatctctagagacaattccaagaacatcttgttcctgcaaatgagcgacctgagagccgaggacacggctgtttattattgtgtgagcgatagagaactccattaccagcatttggacgtctggggtcaagggaccacggtcatcgtctcatcagcctccaccaagggcccatcggtcttccccctggcaccctcctccaagagcacctctgggggccacagcggccctgggctgcctggtcaaggactacttccccgaaccggtgacggtgtcgtggaactcag\t\n+22432\tJY8QFUQ01ARNFI\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t860\t88.53\t193/218 nt\t\t\tHomsap IGHJ4*02 F\t186\t87.5\t42/48 nt\tHomsap IGHD2-15*01 F\t3\t8\t8\t14\t8.8.14\t[1.17.38.11]\tCAKEEGATGVYYVDHW\tin-frame\t+\t\t\t\t\t\tcctctggattcacctttaccacctccgccatggcctgggtccgccaggttccagggaaggggctggagtgggtctcaactattagacctagtggtgagagaacctactacgcagagtccgtgaggggccgcttcaccatctccagagacaattccgagaacacgttgtatctacaactgaacaacctgagagtcgaggacacggccatatattactgtgcgaaggaggaaggtgctactggagtctattatgttgaccactggggccagggaacccgggtcaccgtctcctcatcctccaccaagggcccatcggtcttccccctggcgccctgctccaggagcacctccgagagcacagcggccctgggctgcctggtcaaggactacttccccgaaccggtgacggtgtcgtggaactcag\t\n+22433\tJY8QFUQ01CDTOM\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t959\t93.58\t204/218 nt\t\t\tHomsap IGHJ6*02 F\t220\t83.87\t52/62 nt\tHomsap IGHD5-12*01 F\t2\t8\t8\t13\t8.8.13\t[1.17.38.11]\tCARGPRSRGYGMDVW\tin-frame\t+\t\t\t\t\t\tcctctggattcaccttcaacaactatgccatgagttgggtccgccaggctccagggaaggggctggaatgggtctcaactattactagtggtggtggtagtacattgtacgcagactccgtgaagggccggttcaccatctccagagacaatttcaaggacacgctgtatctgcaaatgaacagcctgagagccgaggacacggccgtatattactgtgcgagagggcctcgatcgcgcggctacggtatggacgtctggggccaagggaccacggtcaccgtctcctcagcctccaccaagggcccatcggtcttccccctggcaccctcctccaagagcacctctgggggcacagcgcccctggggcgcctggtcaaggactaccttccccgaaccggtgagtgtcgtggaact\t\n" |
| b |
| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/2_IMGT-gapped-nt-sequences.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/2_IMGT-gapped-nt-sequences.txt Mon Feb 03 13:37:26 2025 +0000 |
| b |
| b'@@ -0,0 +1,22434 @@\n+Sequence number\tSequence ID\tFunctionality\tV-GENE and allele\tJ-GENE and allele\tD-GENE and allele\tV-D-J-REGION\tV-J-REGION\tV-REGION\tFR1-IMGT\tCDR1-IMGT\tFR2-IMGT\tCDR2-IMGT\tFR3-IMGT\tCDR3-IMGT\tJUNCTION\tJ-REGION\tFR4-IMGT\t\n+1\tJY8QFUQ01DD1I8\tNo results\t\n+2\tJY8QFUQ01BR14W\tunknown\tHomsap IGHV3-16*01 ORF, or Homsap IGHV3-16*02 ORF or Homsap IGHV3-19*01 P or Homsap IGHV3-21*01 F or Homsap IGHV3-21*02 F or Homsap IGHV3-21*03 F or Homsap IGHV3-21*04 F or Homsap IGHV3-35*01 ORF or Homsap IGHV3-48*01 F or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t\t\t\t\t...........................................................................tctggattcaccttc............agcaaccataacatgaact\t...........................................................................tct\tggattcaccttc............agcaaccataac\tatgaac\t\t\t\t\t\t\t\n+3\tJY8QFUQ01DI33C\tNo results\t\n+4\tJY8QFUQ01AHA5U\tNo results\t\n+5\tJY8QFUQ01C6E2Q\tNo results\t\n+6\tJY8QFUQ01DTOF7\tNo results\t\n+7\tJY8QFUQ01DTQZ4\tNo results\t\n+8\tJY8QFUQ01CH7HW\tNo results\t\n+9\tJY8QFUQ01DRIUN\tNo results\t\n+10\tJY8QFUQ01DMFB3\tNo results\t\n+11\tJY8QFUQ01DBKZ5\tNo results\t\n+12\tJY8QFUQ01ALILW\tNo results\t\n+13\tJY8QFUQ01DQT5M\tNo results\t\n+14\tJY8QFUQ01CU1U5\tNo results\t\n+15\tJY8QFUQ01AZ7M4\tNo results\t\n+16\tJY8QFUQ01BJI4T\tNo results\t\n+17\tJY8QFUQ01A8WKP\tNo results\t\n+18\tJY8QFUQ01CDRAH\tNo results\t\n+19\tJY8QFUQ01BSZTH\tNo results\t\n+20\tJY8QFUQ01COV1I\tNo results\t\n+21\tJY8QFUQ01BYN3R\tNo results\t\n+22\tJY8QFUQ01BB6L9\tunknown\tHomsap IGHV3-74*01 F, or Homsap IGHV3-74*02 F or Homsap IGHV3-74*03 F\t\t\t\t\t...........................................................................tccggattcaccttt............agtagttactggatgcactgggtccagggcttcttccc\t...........................................................................tcc\tggattcaccttt............agtagttactgg\tatgcactgggtccagggcttcttc\t\t\t\t\t\t\t\n+23\tJY8QFUQ01AK5S0\tNo results\t\n+24\tJY8QFUQ01A3U3N\tNo results\t\n+25\tJY8QFUQ01DMJ3V\tNo results\t\n+26\tJY8QFUQ01DULTP\tNo results\t\n+27\tJY8QFUQ01DXFUU\tNo results\t\n+28\tJY8QFUQ01BDHX9\tNo results\t\n+29\tJY8QFUQ01BFXXE\tNo results\t\n+30\tJY8QFUQ01DA0S9\tNo results\t\n+31\tJY8QFUQ01A8RD7\tNo results\t\n+32\tJY8QFUQ01DUD3G\tunknown\tHomsap IGHV3-20*01 F, or Homsap IGHV3-20*02 ORF\t\t\t\t\t..........................................................................ctctggattcaccttt............ggttattatggcatgagctgg\t..........................................................................ctct\tggattcaccttt............ggttattatggc\tatgagctgg\t\t\t\t\t\t\t\n+33\tJY8QFUQ01BAEVW\tunknown\tHomsap IGHV3-48*01 F, or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t\t\t\t\t..........................................................................ctctggatttgccctc............agtgactatgccatgcactgggtccgccaggctccagggaaggggctggagtggattgcatacattagtgtttct......acttacaccattttctacgcagagtctgtta\t..........................................................................ctct\tggatttgccctc............agtgactatgcc\tatgcactgggtccgccaggctccagggaaggggctggagtggattgcatac\tattagtgtttct......acttacaccatt\tttctacgcagagtctgtt\t\t\t\t\t\n+34\tJY8QFUQ01C5VTQ\tNo results\t\n+35\tJY8QFUQ01DV0LO\tunknown\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*02 F or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t\t\t\t\t..........................................................................ctctggattcaccttt............ggcagctatatcatgagctgggtccgccaggctccagggaaggggctggagtgggtctcagctattagtggtagg......ggtgttgaca\t..........................................................................ctct\tggattcaccttt............ggcagctatatc\tatgagctgggtccgccaggctccagggaaggggctggagtgggtctcagct\tattagtggtagg......ggtgttgac\t\t\t\t\t\t\n+36\tJY8QFUQ01BQV49\tNo results\t\n+37\tJY8QFUQ01BG2BI\tNo results\t\n+38\tJY8QFUQ01DDCUU\tunknown\tHomsap IGHV3-15*01 F, or Homsap IGHV3-15*02 F\tHomsap IGHJ4*03 F\t\t...........................................................................tctggattcactgtc............aataacgcctggatgacctgggtccgccaggctccagggaaggggctggagtgggttggccgtattagaagcaaaactgatggcgggacagcagactacgctccatttgtggac...gacagattcaccatttcaacagatgattcaaaaatcacgttgtatctcctcagcatccccgaccagcccaaggtcttcccgctgagcctctgcagcacccagccaga'..b'ap IGHV3-33*01 F, or Homsap IGHV3-33*06 F\tHomsap IGHJ6*01 F\tHomsap IGHD2-2*01 F\t.........................................................................cgtctggattcaacttc............aatagttttggcatgcactgggtccgccaggctccgggcaagggactggagtgggtggcaaacatatggtatgat......ggaggtagtcaacactatgcagacctcgtgaag...ggccgattcaccatctctagagacaattccaagaacatcttgttcctgcaaatgagcgacctgagagccgaggacacggctgtttattattgtgtgagcgatagagaactccattaccagcatttggacgtctggggtcaagggaccacggtcatcgtctcatcag\t\t.........................................................................cgtctggattcaacttc............aatagttttggcatgcactgggtccgccaggctccgggcaagggactggagtgggtggcaaacatatggtatgat......ggaggtagtcaacactatgcagacctcgtgaag...ggccgattcaccatctctagagacaattccaagaacatcttgttcctgcaaatgagcgacctgagagccgaggacacggctgtttattattgtgtgagcga\t.........................................................................cgtct\tggattcaacttc............aatagttttggc\tatgcactgggtccgccaggctccgggcaagggactggagtgggtggcaaac\tatatggtatgat......ggaggtagtcaa\tcactatgcagacctcgtgaag...ggccgattcaccatctctagagacaattccaagaacatcttgttcctgcaaatgagcgacctgagagccgaggacacggctgtttattattgt\tgtgagcgatagagaactccattaccagcatttggacgtc\ttgtgtgagcgatagagaactccattaccagcatttggacgtctgg\ttggacgtctggggtcaagggaccacggtcatcgtctcatcag\ttggggtcaagggaccacggtcatcgtctcatcag\t\n+22432\tJY8QFUQ01ARNFI\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ4*02 F\tHomsap IGHD2-15*01 F\t.........................................................................cctctggattcaccttt............accacctccgccatggcctgggtccgccaggttccagggaaggggctggagtgggtctcaactattagacctagt......ggtgagagaacctactacgcagagtccgtgagg...ggccgcttcaccatctccagagacaattccgagaacacgttgtatctacaactgaacaacctgagagtcgaggacacggccatatattactgtgcgaaggaggaaggtgctactggagtctattatgttgaccactggggccagggaacccgggtcaccgtctcctcat\t\t.........................................................................cctctggattcaccttt............accacctccgccatggcctgggtccgccaggttccagggaaggggctggagtgggtctcaactattagacctagt......ggtgagagaacctactacgcagagtccgtgagg...ggccgcttcaccatctccagagacaattccgagaacacgttgtatctacaactgaacaacctgagagtcgaggacacggccatatattactgtgcgaagga\t.........................................................................cctct\tggattcaccttt............accacctccgcc\tatggcctgggtccgccaggttccagggaaggggctggagtgggtctcaact\tattagacctagt......ggtgagagaacc\ttactacgcagagtccgtgagg...ggccgcttcaccatctccagagacaattccgagaacacgttgtatctacaactgaacaacctgagagtcgaggacacggccatatattactgt\tgcgaaggaggaaggtgctactggagtctattatgttgaccac\ttgtgcgaaggaggaaggtgctactggagtctattatgttgaccactgg\tttgaccactggggccagggaacccgggtcaccgtctcctcat\ttggggccagggaacccgggtcaccgtctcctcat\t\n+22433\tJY8QFUQ01CDTOM\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ6*02 F\tHomsap IGHD5-12*01 F\t.........................................................................cctctggattcaccttc............aacaactatgccatgagttgggtccgccaggctccagggaaggggctggaatgggtctcaactattactagtggt......ggtggtagtacattgtacgcagactccgtgaag...ggccggttcaccatctccagagacaatttcaaggacacgctgtatctgcaaatgaacagcctgagagccgaggacacggccgtatattactgtgcgagagggcctcgatcgcgcggctacggtatggacgtctggggccaagggaccacggtcaccgtctcctca\t\t.........................................................................cctctggattcaccttc............aacaactatgccatgagttgggtccgccaggctccagggaaggggctggaatgggtctcaactattactagtggt......ggtggtagtacattgtacgcagactccgtgaag...ggccggttcaccatctccagagacaatttcaaggacacgctgtatctgcaaatgaacagcctgagagccgaggacacggccgtatattactgtgcgagag\t.........................................................................cctct\tggattcaccttc............aacaactatgcc\tatgagttgggtccgccaggctccagggaaggggctggaatgggtctcaact\tattactagtggt......ggtggtagtaca\tttgtacgcagactccgtgaag...ggccggttcaccatctccagagacaatttcaaggacacgctgtatctgcaaatgaacagcctgagagccgaggacacggccgtatattactgt\tgcgagagggcctcgatcgcgcggctacggtatggacgtc\ttgtgcgagagggcctcgatcgcgcggctacggtatggacgtctgg\tctacggtatggacgtctggggccaagggaccacggtcaccgtctcctca\ttggggccaagggaccacggtcaccgtctcctca\t\n' |
| b |
| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/3_Nt-sequences.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/3_Nt-sequences.txt Mon Feb 03 13:37:26 2025 +0000 |
| b |
| b"@@ -0,0 +1,22434 @@\n+Sequence number\tSequence ID\tFunctionality\tV-GENE and allele\tJ-GENE and allele\tD-GENE and allele\tV-D-J-REGION\tV-J-REGION\tV-REGION\tFR1-IMGT\tCDR1-IMGT\tFR2-IMGT\tCDR2-IMGT\tFR3-IMGT\tCDR3-IMGT\tJUNCTION\t3'V-REGION\t(N-D)-J-REGION\t(N-D)-REGION\tP3'V\tN-REGION\tN1-REGION\tP5'D\tD-REGION\tP3'D\tP5'D1\tD1-REGION\tP3'D1\tN2-REGION\tP5'D2\tD2-REGION\tP3'D2\tN3-REGION\tP5'D3\tD3-REGION\tP3'D3\tN4-REGION\tP5'J\t5'J-REGION\tD-J-REGION\tJ-REGION\tFR4-IMGT\tV-D-J-REGION start\tV-D-J-REGION end\tV-J-REGION start\tV-J-REGION end\tV-REGION start\tV-REGION end\tFR1-IMGT start\tFR1-IMGT end\tCDR1-IMGT start\tCDR1-IMGT end\tFR2-IMGT start\tFR2-IMGT end\tCDR2-IMGT start\tCDR2-IMGT end\tFR3-IMGT start\tFR3-IMGT end\tCDR3-IMGT start\tCDR3-IMGT end\tJUNCTION start\tJUNCTION end\t3'V-REGION start\t3'V-REGION end\t(N-D)-J-REGION start\t(N-D)-J-REGION end\t(N-D)-REGION start\t(N-D)-REGION end\tP3'V start\tP3'V end\tN-REGION start\tN-REGION end\tN1-REGION start\tN1-REGION end\tP5'D start\tP5'D end\tD-REGION start\tD-REGION end\tP3'D start\tP3'D end\tP5'D1 start\tP5'D1 end\tD1-REGION start\tD1-REGION end\tP3'D1 start\tP3'D1 end\tN2-REGION start\tN2-REGION end\tP5'D2 start\tP5'D2 end\tD2-REGION start\tD2-REGION end\tP3'D2 start\tP3'D2 end\tN3-REGION start\tN3-REGION end\tP5'D3 start\tP5'D3 end\tD3-REGION start\tD3-REGION end\tP3'D3 start\tP3'D3 end\tN4-REGION start\tN4-REGION end\tP5'J start\tP5'J end\t5'J-REGION start\t5'J-REGION end\tD-J-REGION start\tD-J-REGION end\tJ-REGION start\tJ-REGION end\tFR4-IMGT start\tFR4-IMGT end\t\n+1\tJY8QFUQ01DD1I8\tNo results\t\n+2\tJY8QFUQ01BR14W\tunknown\tHomsap IGHV3-16*01 ORF, or Homsap IGHV3-16*02 ORF or Homsap IGHV3-19*01 P or Homsap IGHV3-21*01 F or Homsap IGHV3-21*02 F or Homsap IGHV3-21*03 F or Homsap IGHV3-21*04 F or Homsap IGHV3-35*01 ORF or Homsap IGHV3-48*01 F or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t\t\t\t\ttctggattcaccttcagcaaccataacatgaact\ttct\tggattcaccttcagcaaccataac\tatgaac\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t34\t1\t3\t4\t27\t28\t33\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+3\tJY8QFUQ01DI33C\tNo results\t\n+4\tJY8QFUQ01AHA5U\tNo results\t\n+5\tJY8QFUQ01C6E2Q\tNo results\t\n+6\tJY8QFUQ01DTOF7\tNo results\t\n+7\tJY8QFUQ01DTQZ4\tNo results\t\n+8\tJY8QFUQ01CH7HW\tNo results\t\n+9\tJY8QFUQ01DRIUN\tNo results\t\n+10\tJY8QFUQ01DMFB3\tNo results\t\n+11\tJY8QFUQ01DBKZ5\tNo results\t\n+12\tJY8QFUQ01ALILW\tNo results\t\n+13\tJY8QFUQ01DQT5M\tNo results\t\n+14\tJY8QFUQ01CU1U5\tNo results\t\n+15\tJY8QFUQ01AZ7M4\tNo results\t\n+16\tJY8QFUQ01BJI4T\tNo results\t\n+17\tJY8QFUQ01A8WKP\tNo results\t\n+18\tJY8QFUQ01CDRAH\tNo results\t\n+19\tJY8QFUQ01BSZTH\tNo results\t\n+20\tJY8QFUQ01COV1I\tNo results\t\n+21\tJY8QFUQ01BYN3R\tNo results\t\n+22\tJY8QFUQ01BB6L9\tunknown\tHomsap IGHV3-74*01 F, or Homsap IGHV3-74*02 F or Homsap IGHV3-74*03 F\t\t\t\t\ttccggattcacctttagtagttactggatgcactgggtccagggcttcttccc\ttcc\tggattcacctttagtagttactgg\tatgcactgggtccagggcttcttc\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t53\t1\t3\t4\t27\t28\t51\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+23\tJY8QFUQ01AK5S0\tNo results\t\n+24\tJY8QFUQ01A3U3N\tNo results\t\n+25\tJY8QFUQ01DMJ3V\tNo results\t\n+26\tJY8QFUQ01DULTP\tNo results\t\n+27\tJY8QFUQ01DXFUU\tNo results\t\n+28\tJY8QFUQ01BDHX9\tNo results\t\n+29\tJY8QFUQ01BFXXE\tNo results\t\n+30\tJY8QFUQ01DA0S9\tNo results\t\n+31\tJY8QFUQ01A8RD7\tNo results\t\n+32\tJY8QFUQ01DUD3G\tunknown\tHomsap IGHV3-20*01 F, or Homsap IGHV3-20*02 ORF\t\t\t\t\tctctggattcacctttggttattatggcatgagctgg\tctct\tggattcacctttggttattatggc\tatgagctgg\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t37\t1\t4\t5\t28\t29\t37\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+33\tJY8QFUQ01BAEVW\tunknown\tHomsap IGHV3-48*01 F, or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t\t\t\t\tctctggatttgccctcagtgactatgccatgcactgggtccgccaggctccagggaaggggctggagtggattgcatacattagtgtttctacttacaccattttctacgcagagtctgtta\tctct\tggatttgccctcagtgactatgcc\tatgcactgggtccgccaggctccagggaaggggctggagtggattgcatac\tattagtgtttctacttacaccatt\tttctacgcagagtctgtt\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t122\t1\t4\t5\t28\t29\t79\t80\t103\t104\t121\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+34\tJY8QFUQ01C5VTQ\tNo results\t\n+35\tJY8QFUQ01DV0LO\tunknown\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*02 F or Ho"..b'cagcatttggacgtctggggtcaagggaccacggtcatcgtctcatcag\t\tcgtctggattcaacttcaatagttttggcatgcactgggtccgccaggctccgggcaagggactggagtgggtggcaaacatatggtatgatggaggtagtcaacactatgcagacctcgtgaagggccgattcaccatctctagagacaattccaagaacatcttgttcctgcaaatgagcgacctgagagccgaggacacggctgtttattattgtgtgagcga\tcgtct\tggattcaacttcaatagttttggc\tatgcactgggtccgccaggctccgggcaagggactggagtgggtggcaaac\tatatggtatgatggaggtagtcaa\tcactatgcagacctcgtgaagggccgattcaccatctctagagacaattccaagaacatcttgttcctgcaaatgagcgacctgagagccgaggacacggctgtttattattgt\tgtgagcgatagagaactccattaccagcatttggacgtc\ttgtgtgagcgatagagaactccattaccagcatttggacgtctgg\ttgtgtgagcga\ttagagaactccattaccagcatttggacgtctggggtcaagggaccacggtcatcgtctcatcag\ttagagaactccattaccagcatt\tt\t\tagagaactccat\t\ttaccagc\t\t\t\t\tatt\t\t\t\t\t\t\t\t\t\ttggacgtctgg\ttaccagcatttggacgtctggggtcaagggaccacggtcatcgtctcatcag\ttggacgtctggggtcaagggaccacggtcatcgtctcatcag\ttggggtcaagggaccacggtcatcgtctcatcag\t1\t291\t\t\t1\t226\t1\t5\t6\t29\t30\t80\t81\t104\t105\t218\t219\t257\t216\t260\t216\t226\t227\t291\t227\t249\t227\t227\t\t\t228\t239\t\t\t240\t246\t\t\t\t\t\t\t\t\t247\t249\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t250\t260\t240\t291\t250\t291\t258\t291\t\n+22432\tJY8QFUQ01ARNFI\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ4*02 F\tHomsap IGHD2-15*01 F\tcctctggattcacctttaccacctccgccatggcctgggtccgccaggttccagggaaggggctggagtgggtctcaactattagacctagtggtgagagaacctactacgcagagtccgtgaggggccgcttcaccatctccagagacaattccgagaacacgttgtatctacaactgaacaacctgagagtcgaggacacggccatatattactgtgcgaaggaggaaggtgctactggagtctattatgttgaccactggggccagggaacccgggtcaccgtctcctcat\t\tcctctggattcacctttaccacctccgccatggcctgggtccgccaggttccagggaaggggctggagtgggtctcaactattagacctagtggtgagagaacctactacgcagagtccgtgaggggccgcttcaccatctccagagacaattccgagaacacgttgtatctacaactgaacaacctgagagtcgaggacacggccatatattactgtgcgaagga\tcctct\tggattcacctttaccacctccgcc\tatggcctgggtccgccaggttccagggaaggggctggagtgggtctcaact\tattagacctagtggtgagagaacc\ttactacgcagagtccgtgaggggccgcttcaccatctccagagacaattccgagaacacgttgtatctacaactgaacaacctgagagtcgaggacacggccatatattactgt\tgcgaaggaggaaggtgctactggagtctattatgttgaccac\ttgtgcgaaggaggaaggtgctactggagtctattatgttgaccactgg\ttgtgcgaagga\tggaaggtgctactggagtctattatgttgaccactggggccagggaacccgggtcaccgtctcctcat\tggaaggtgctactggagtctattatg\t\t\t\t\tggaaggtgctact\t\t\t\t\tggagtctattatg\t\t\t\t\t\t\t\t\t\tttgaccactgg\tggaaggtgctactggagtctattatgttgaccactggggccagggaacccgggtcaccgtctcctcat\tttgaccactggggccagggaacccgggtcaccgtctcctcat\ttggggccagggaacccgggtcaccgtctcctcat\t1\t294\t\t\t1\t226\t1\t5\t6\t29\t30\t80\t81\t104\t105\t218\t219\t260\t216\t263\t216\t226\t227\t294\t227\t252\t\t\t\t\t\t\t\t\t227\t239\t\t\t\t\t\t\t\t\t240\t252\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t253\t263\t227\t294\t253\t294\t261\t294\t\n+22433\tJY8QFUQ01CDTOM\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ6*02 F\tHomsap IGHD5-12*01 F\tcctctggattcaccttcaacaactatgccatgagttgggtccgccaggctccagggaaggggctggaatgggtctcaactattactagtggtggtggtagtacattgtacgcagactccgtgaagggccggttcaccatctccagagacaatttcaaggacacgctgtatctgcaaatgaacagcctgagagccgaggacacggccgtatattactgtgcgagagggcctcgatcgcgcggctacggtatggacgtctggggccaagggaccacggtcaccgtctcctca\t\tcctctggattcaccttcaacaactatgccatgagttgggtccgccaggctccagggaaggggctggaatgggtctcaactattactagtggtggtggtagtacattgtacgcagactccgtgaagggccggttcaccatctccagagacaatttcaaggacacgctgtatctgcaaatgaacagcctgagagccgaggacacggccgtatattactgtgcgagag\tcctct\tggattcaccttcaacaactatgcc\tatgagttgggtccgccaggctccagggaaggggctggaatgggtctcaact\tattactagtggtggtggtagtaca\tttgtacgcagactccgtgaagggccggttcaccatctccagagacaatttcaaggacacgctgtatctgcaaatgaacagcctgagagccgaggacacggccgtatattactgt\tgcgagagggcctcgatcgcgcggctacggtatggacgtc\ttgtgcgagagggcctcgatcgcgcggctacggtatggacgtctgg\ttgtgcgagag\tggcctcgatcgcgcggctacggtatggacgtctggggccaagggaccacggtcaccgtctcctca\tggcctcgatcgcgcgg\t\t\t\t\tggcctcgat\t\t\t\t\tcgcgcgg\t\t\t\t\t\t\t\t\t\tctacggtatggacgtctgg\tggcctcgatcgcgcggctacggtatggacgtctggggccaagggaccacggtcaccgtctcctca\tctacggtatggacgtctggggccaagggaccacggtcaccgtctcctca\ttggggccaagggaccacggtcaccgtctcctca\t1\t290\t\t\t1\t225\t1\t5\t6\t29\t30\t80\t81\t104\t105\t218\t219\t257\t216\t260\t216\t225\t226\t290\t226\t241\t\t\t\t\t\t\t\t\t226\t234\t\t\t\t\t\t\t\t\t235\t241\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t242\t260\t226\t290\t242\t290\t258\t290\t\n' |
| b |
| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/4_IMGT-gapped-AA-sequences.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/4_IMGT-gapped-AA-sequences.txt Mon Feb 03 13:37:26 2025 +0000 |
| b |
| b'@@ -0,0 +1,22434 @@\n+Sequence number\tSequence ID\tFunctionality\tV-GENE and allele\tJ-GENE and allele\tD-GENE and allele\tV-D-J-REGION\tV-J-REGION\tV-REGION\tFR1-IMGT\tCDR1-IMGT\tFR2-IMGT\tCDR2-IMGT\tFR3-IMGT\tCDR3-IMGT\tJUNCTION\tJ-REGION\tFR4-IMGT\t\n+1\tJY8QFUQ01DD1I8\tNo results\t\n+2\tJY8QFUQ01BR14W\tunknown\tHomsap IGHV3-16*01 ORF, or Homsap IGHV3-16*02 ORF or Homsap IGHV3-19*01 P or Homsap IGHV3-21*01 F or Homsap IGHV3-21*02 F or Homsap IGHV3-21*03 F or Homsap IGHV3-21*04 F or Homsap IGHV3-35*01 ORF or Homsap IGHV3-48*01 F or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t\t\t\t\t.........................SGFTF....SNHNMN\t.........................S\tGFTF....SNHN\tMN\t\t\t\t\t\t\t\n+3\tJY8QFUQ01DI33C\tNo results\t\n+4\tJY8QFUQ01AHA5U\tNo results\t\n+5\tJY8QFUQ01C6E2Q\tNo results\t\n+6\tJY8QFUQ01DTOF7\tNo results\t\n+7\tJY8QFUQ01DTQZ4\tNo results\t\n+8\tJY8QFUQ01CH7HW\tNo results\t\n+9\tJY8QFUQ01DRIUN\tNo results\t\n+10\tJY8QFUQ01DMFB3\tNo results\t\n+11\tJY8QFUQ01DBKZ5\tNo results\t\n+12\tJY8QFUQ01ALILW\tNo results\t\n+13\tJY8QFUQ01DQT5M\tNo results\t\n+14\tJY8QFUQ01CU1U5\tNo results\t\n+15\tJY8QFUQ01AZ7M4\tNo results\t\n+16\tJY8QFUQ01BJI4T\tNo results\t\n+17\tJY8QFUQ01A8WKP\tNo results\t\n+18\tJY8QFUQ01CDRAH\tNo results\t\n+19\tJY8QFUQ01BSZTH\tNo results\t\n+20\tJY8QFUQ01COV1I\tNo results\t\n+21\tJY8QFUQ01BYN3R\tNo results\t\n+22\tJY8QFUQ01BB6L9\tunknown\tHomsap IGHV3-74*01 F, or Homsap IGHV3-74*02 F or Homsap IGHV3-74*03 F\t\t\t\t\t.........................SGFTF....SSYWMHWVQGFF\t.........................S\tGFTF....SSYW\tMHWVQGFF\t\t\t\t\t\t\t\n+23\tJY8QFUQ01AK5S0\tNo results\t\n+24\tJY8QFUQ01A3U3N\tNo results\t\n+25\tJY8QFUQ01DMJ3V\tNo results\t\n+26\tJY8QFUQ01DULTP\tNo results\t\n+27\tJY8QFUQ01DXFUU\tNo results\t\n+28\tJY8QFUQ01BDHX9\tNo results\t\n+29\tJY8QFUQ01BFXXE\tNo results\t\n+30\tJY8QFUQ01DA0S9\tNo results\t\n+31\tJY8QFUQ01A8RD7\tNo results\t\n+32\tJY8QFUQ01DUD3G\tunknown\tHomsap IGHV3-20*01 F, or Homsap IGHV3-20*02 ORF\t\t\t\t\t.........................SGFTF....GYYGMSW\t.........................S\tGFTF....GYYG\tMSW\t\t\t\t\t\t\t\n+33\tJY8QFUQ01BAEVW\tunknown\tHomsap IGHV3-48*01 F, or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t\t\t\t\t.........................SGFAL....SDYAMHWVRQAPGKGLEWIAYISVS..TYTIFYAESV\t.........................S\tGFAL....SDYA\tMHWVRQAPGKGLEWIAY\tISVS..TYTI\tFYAESV\t\t\t\t\t\n+34\tJY8QFUQ01C5VTQ\tNo results\t\n+35\tJY8QFUQ01DV0LO\tunknown\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*02 F or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t\t\t\t\t.........................SGFTF....GSYIMSWVRQAPGKGLEWVSAISGR..GVD\t.........................S\tGFTF....GSYI\tMSWVRQAPGKGLEWVSA\tISGR..GVD\t\t\t\t\t\t\n+36\tJY8QFUQ01BQV49\tNo results\t\n+37\tJY8QFUQ01BG2BI\tNo results\t\n+38\tJY8QFUQ01DDCUU\tunknown\tHomsap IGHV3-15*01 F, or Homsap IGHV3-15*02 F\tHomsap IGHJ4*03 F\t\t.........................SGFTV....NNAWMTWVRQAPGKGLEWVGRIRSKTDGGTADYAPFVD.DRFTISTDDSKITLYLLSIPDQPKVFPLSLCSTQPDGNVVIACLVQGFFP\t\t.........................SGFTV....NNAWMTWVRQAPGKGLEWVGRIRSKTDGGTADYAPFVD.DRFTISTDDSKITLYLLSIPDQPKVFPLSLCS\t.........................S\tGFTV....NNAW\tMTWVRQAPGKGLEWVGR\tIRSKTDGGTA\tDYAPFVD.DRFTISTDDSKITLYLLSIPDQPKVFPLSLC\tSTQPDGNVVIACL\t\tASSP\t\t\n+39\tJY8QFUQ01DTYS9\tunknown\tHomsap IGHV3-7*01 F, or Homsap IGHV3-7*02 F or Homsap IGHV3-7*03 F\t\t\t\t\t.........................SGFTF....SNHWMNWVQGFFP\t.........................S\tGFTF....SNHW\tMNWVQGFFP\t\t\t\t\t\t\t\n+40\tJY8QFUQ01DWUUL\tNo results\t\n+41\tJY8QFUQ01BDC06\tNo results\t\n+42\tJY8QFUQ01DQ6VG\tunknown\tHomsap IGHV1-NL1*01 P\t\t\t\t\tPEVLLEEGA.RGKTDGPLVEATDEATR\tPEVLLEEGA.RGKTDGPLVEATDEAT\tR\t\t\t\t\t\t\t\t\n+43\tJY8QFUQ01C3GCP\tNo results\t\n+44\tJY8QFUQ01A1UV9\tNo results\t\n+45\tJY8QFUQ01CVLJY\tNo results\t\n+46\tJY8QFUQ01BAK18\tNo results\t\n+47\tJY8QFUQ01CEPBG\tNo results\t\n+48\tJY8QFUQ01ART19\tNo results\t\n+49\tJY8QFUQ01CA0L6\tunknown\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*02 F or Homsap IGHV3-23*03 F or Homsap IGHV3-23*04 F or Homsap IGHV3-23*05 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F or Homsap IGHV3-7*01 F or Homsap IGHV3-7*02 F or Homsap IGHV3-7*03 F\t\t\t\t\t.........................SGFTF....SSYAMSWVKDYFPHQSTVSWNS\t.........................S\tGFTF....SSYA\tMSWVKDYFPHQSTVSWN\tS\t\t\t\t\t\t\n+50\tJY8QFUQ01BLYKI\tNo results\t\n+51\tJY8QFUQ01CMHH0\tNo resu'..b'YYS...GST\tYYNPSLK.SRVTISVDTSKNQFSLKLSSVTAADTAVYYC\tARSRTFYGSANY\tCARSRTFYGSANYW\tGPGNPGHRLL\tGGQGTLVTVSS\t\n+22425\tJY8QFUQ01AV4SA\tNo results\t\n+22426\tJY8QFUQ01BC2PX\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ4*02 F\tHomsap IGHD1-26*01 F\t.........................SGFTF....NDYAMSWVRQAPDKGLEWVSTVSSR..GDTTHYADFVK.GRLTISRDNSRNTLYLQMNSLTAEDTAIYYCAKVMWGVTGPIDPFDYWGQGTLVTVSS\t\t.........................SGFTF....NDYAMSWVRQAPDKGLEWVSTVSSR..GDTTHYADFVK.GRLTISRDNSRNTLYLQMNSLTAEDTAIYYCAK\t.........................S\tGFTF....NDYA\tMSWVRQAPDKGLEWVST\tVSSR..GDTT\tHYADFVK.GRLTISRDNSRNTLYLQMNSLTAEDTAIYYC\tAKVMWGVTGPIDPFDY\tCAKVMWGVTGPIDPFDYW\tFDYWGQGTLVTVSS\tWGQGTLVTVSS\t\n+22427\tJY8QFUQ01CA2ZU\tNo results\t\n+22428\tJY8QFUQ01BLYJ4\tunproductive\tHomsap IGHV4-59*01 F, or Homsap IGHV4-59*07 F\tHomsap IGHJ3*02 F\tHomsap IGHD6-6*01 F\t.........................SGGSM....SSHYWSWIRQSSGKGLEWLGYIHYS...GSTRFNPSLN.SRVTISVDTSKSQFFLLLNSVTAADTATYYCARDSSNWSDAF*YLEPRDNGHRLF\t\t.........................SGGSM....SSHYWSWIRQSSGKGLEWLGYIHYS...GSTRFNPSLN.SRVTISVDTSKSQFFLLLNSVTAADTATYYCAR\t.........................S\tGGSM....SSHY\tWSWIRQSSGKGLEWLGY\tIHYS...GST\tRFNPSLN.SRVTISVDTSKSQFFLLLNSVTAADTATYYC\tARDSSNWSDAF*Y\tCARDSSNWSDAF*YL\tF*YLEPRDNGHRLF\tWSQGTMVTVSS\t\n+22429\tJY8QFUQ01C1IBJ\tunproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ4*02 F\tHomsap IGHD4-17*01 F\t.........................SGFTF....TNYGMSWVRQAPGRGLEWVSGISGS..GDTTYHADSVQ.GRFTISRDNSKNTLYLQMNSLRVEDTAVYYCARFGPLTRPDYWGPGNFGHRLL\t\t.........................SGFTF....TNYGMSWVRQAPGRGLEWVSGISGS..GDTTYHADSVQ.GRFTISRDNSKNTLYLQMNSLRVEDTAVYYCA\t.........................S\tGFTF....TNYG\tMSWVRQAPGRGLEWVSG\tISGS..GDTT\tYHADSVQ.GRFTISRDNSKNTLYLQMNSLRVEDTAVYYC\tARFGPLTRPDY\tCARFGPLTRPDYW\tGPGNFGHRLL\tGGQGTLVTVSS\t\n+22430\tJY8QFUQ01B48C0\tproductive\tHomsap IGHV3-33*05 F\tHomsap IGHJ4*02 F\tHomsap IGHD5-12*01 F\t........................RLGFSF....SNYAIHWVRQAPGKGLEWVATISYD..INKRYYAESVR.GRFTLSRDNSKNTLDLLMDTLRFDDTAVYYCVKGRGYNDYGLDYWGPGTLLTVSS\t\t........................RLGFSF....SNYAIHWVRQAPGKGLEWVATISYD..INKRYYAESVR.GRFTLSRDNSKNTLDLLMDTLRFDDTAVYYC\t........................RL\tGFSF....SNYA\tIHWVRQAPGKGLEWVAT\tISYD..INKR\tYYAESVR.GRFTLSRDNSKNTLDLLMDTLRFDDTAVYYC\tVKGRGYNDYGLDY\tCVKGRGYNDYGLDYW\tDYWGPGTLLTVSS\tWGPGTLLTVSS\t\n+22431\tJY8QFUQ01BLN4B\tproductive\tHomsap IGHV3-33*01 F, or Homsap IGHV3-33*06 F\tHomsap IGHJ6*01 F\tHomsap IGHD2-2*01 F\t.........................SGFNF....NSFGMHWVRQAPGKGLEWVANIWYD..GGSQHYADLVK.GRFTISRDNSKNILFLQMSDLRAEDTAVYYCVSDRELHYQHLDVWGQGTTVIVSS\t\t.........................SGFNF....NSFGMHWVRQAPGKGLEWVANIWYD..GGSQHYADLVK.GRFTISRDNSKNILFLQMSDLRAEDTAVYYCVS\t.........................S\tGFNF....NSFG\tMHWVRQAPGKGLEWVAN\tIWYD..GGSQ\tHYADLVK.GRFTISRDNSKNILFLQMSDLRAEDTAVYYC\tVSDRELHYQHLDV\tCVSDRELHYQHLDVW\tDVWGQGTTVIVSS\tWGQGTTVIVSS\t\n+22432\tJY8QFUQ01ARNFI\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ4*02 F\tHomsap IGHD2-15*01 F\t.........................SGFTF....TTSAMAWVRQVPGKGLEWVSTIRPS..GERTYYAESVR.GRFTISRDNSENTLYLQLNNLRVEDTAIYYCAKEEGATGVYYVDHWGQGTRVTVSS\t\t.........................SGFTF....TTSAMAWVRQVPGKGLEWVSTIRPS..GERTYYAESVR.GRFTISRDNSENTLYLQLNNLRVEDTAIYYCAK\t.........................S\tGFTF....TTSA\tMAWVRQVPGKGLEWVST\tIRPS..GERT\tYYAESVR.GRFTISRDNSENTLYLQLNNLRVEDTAIYYC\tAKEEGATGVYYVDH\tCAKEEGATGVYYVDHW\tDHWGQGTRVTVSS\tWGQGTRVTVSS\t\n+22433\tJY8QFUQ01CDTOM\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ6*02 F\tHomsap IGHD5-12*01 F\t.........................SGFTF....NNYAMSWVRQAPGKGLEWVSTITSG..GGSTLYADSVK.GRFTISRDNFKDTLYLQMNSLRAEDTAVYYCARGPRSRGYGMDVWGQGTTVTVSS\t\t.........................SGFTF....NNYAMSWVRQAPGKGLEWVSTITSG..GGSTLYADSVK.GRFTISRDNFKDTLYLQMNSLRAEDTAVYYCAR\t.........................S\tGFTF....NNYA\tMSWVRQAPGKGLEWVST\tITSG..GGST\tLYADSVK.GRFTISRDNFKDTLYLQMNSLRAEDTAVYYC\tARGPRSRGYGMDV\tCARGPRSRGYGMDVW\tYGMDVWGQGTTVTVSS\tWGQGTTVTVSS\t\n' |
| b |
| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/5_AA-sequences.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/5_AA-sequences.txt Mon Feb 03 13:37:26 2025 +0000 |
| b |
| b'@@ -0,0 +1,22434 @@\n+Sequence number\tSequence ID\tFunctionality\tV-GENE and allele\tJ-GENE and allele\tD-GENE and allele\tV-D-J-REGION\tV-J-REGION\tV-REGION\tFR1-IMGT\tCDR1-IMGT\tFR2-IMGT\tCDR2-IMGT\tFR3-IMGT\tCDR3-IMGT\tJUNCTION\tJ-REGION\tFR4-IMGT\t\n+1\tJY8QFUQ01DD1I8\tNo results\t\n+2\tJY8QFUQ01BR14W\tunknown\tHomsap IGHV3-16*01 ORF, or Homsap IGHV3-16*02 ORF or Homsap IGHV3-19*01 P or Homsap IGHV3-21*01 F or Homsap IGHV3-21*02 F or Homsap IGHV3-21*03 F or Homsap IGHV3-21*04 F or Homsap IGHV3-35*01 ORF or Homsap IGHV3-48*01 F or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t\t\t\t\tSGFTFSNHNMN\tS\tGFTFSNHN\tMN\t\t\t\t\t\t\t\n+3\tJY8QFUQ01DI33C\tNo results\t\n+4\tJY8QFUQ01AHA5U\tNo results\t\n+5\tJY8QFUQ01C6E2Q\tNo results\t\n+6\tJY8QFUQ01DTOF7\tNo results\t\n+7\tJY8QFUQ01DTQZ4\tNo results\t\n+8\tJY8QFUQ01CH7HW\tNo results\t\n+9\tJY8QFUQ01DRIUN\tNo results\t\n+10\tJY8QFUQ01DMFB3\tNo results\t\n+11\tJY8QFUQ01DBKZ5\tNo results\t\n+12\tJY8QFUQ01ALILW\tNo results\t\n+13\tJY8QFUQ01DQT5M\tNo results\t\n+14\tJY8QFUQ01CU1U5\tNo results\t\n+15\tJY8QFUQ01AZ7M4\tNo results\t\n+16\tJY8QFUQ01BJI4T\tNo results\t\n+17\tJY8QFUQ01A8WKP\tNo results\t\n+18\tJY8QFUQ01CDRAH\tNo results\t\n+19\tJY8QFUQ01BSZTH\tNo results\t\n+20\tJY8QFUQ01COV1I\tNo results\t\n+21\tJY8QFUQ01BYN3R\tNo results\t\n+22\tJY8QFUQ01BB6L9\tunknown\tHomsap IGHV3-74*01 F, or Homsap IGHV3-74*02 F or Homsap IGHV3-74*03 F\t\t\t\t\tSGFTFSSYWMHWVQGFF\tS\tGFTFSSYW\tMHWVQGFF\t\t\t\t\t\t\t\n+23\tJY8QFUQ01AK5S0\tNo results\t\n+24\tJY8QFUQ01A3U3N\tNo results\t\n+25\tJY8QFUQ01DMJ3V\tNo results\t\n+26\tJY8QFUQ01DULTP\tNo results\t\n+27\tJY8QFUQ01DXFUU\tNo results\t\n+28\tJY8QFUQ01BDHX9\tNo results\t\n+29\tJY8QFUQ01BFXXE\tNo results\t\n+30\tJY8QFUQ01DA0S9\tNo results\t\n+31\tJY8QFUQ01A8RD7\tNo results\t\n+32\tJY8QFUQ01DUD3G\tunknown\tHomsap IGHV3-20*01 F, or Homsap IGHV3-20*02 ORF\t\t\t\t\tSGFTFGYYGMSW\tS\tGFTFGYYG\tMSW\t\t\t\t\t\t\t\n+33\tJY8QFUQ01BAEVW\tunknown\tHomsap IGHV3-48*01 F, or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t\t\t\t\tSGFALSDYAMHWVRQAPGKGLEWIAYISVSTYTIFYAESV\tS\tGFALSDYA\tMHWVRQAPGKGLEWIAY\tISVSTYTI\tFYAESV\t\t\t\t\t\n+34\tJY8QFUQ01C5VTQ\tNo results\t\n+35\tJY8QFUQ01DV0LO\tunknown\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*02 F or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t\t\t\t\tSGFTFGSYIMSWVRQAPGKGLEWVSAISGRGVD\tS\tGFTFGSYI\tMSWVRQAPGKGLEWVSA\tISGRGVD\t\t\t\t\t\t\n+36\tJY8QFUQ01BQV49\tNo results\t\n+37\tJY8QFUQ01BG2BI\tNo results\t\n+38\tJY8QFUQ01DDCUU\tunknown\tHomsap IGHV3-15*01 F, or Homsap IGHV3-15*02 F\tHomsap IGHJ4*03 F\t\tSGFTVNNAWMTWVRQAPGKGLEWVGRIRSKTDGGTADYAPFVDDRFTISTDDSKITLYLLSIPDQPKVFPLSLCSTQPDGNVVIACLVQGFFP\t\tSGFTVNNAWMTWVRQAPGKGLEWVGRIRSKTDGGTADYAPFVDDRFTISTDDSKITLYLLSIPDQPKVFPLSLCS\tS\tGFTVNNAW\tMTWVRQAPGKGLEWVGR\tIRSKTDGGTA\tDYAPFVDDRFTISTDDSKITLYLLSIPDQPKVFPLSLC\tSTQPDGNVVIACL\t\tASSP\t\t\n+39\tJY8QFUQ01DTYS9\tunknown\tHomsap IGHV3-7*01 F, or Homsap IGHV3-7*02 F or Homsap IGHV3-7*03 F\t\t\t\t\tSGFTFSNHWMNWVQGFFP\tS\tGFTFSNHW\tMNWVQGFFP\t\t\t\t\t\t\t\n+40\tJY8QFUQ01DWUUL\tNo results\t\n+41\tJY8QFUQ01BDC06\tNo results\t\n+42\tJY8QFUQ01DQ6VG\tunknown\tHomsap IGHV1-NL1*01 P\t\t\t\t\tPEVLLEEGARGKTDGPLVEATDEATR\tPEVLLEEGARGKTDGPLVEATDEAT\tR\t\t\t\t\t\t\t\t\n+43\tJY8QFUQ01C3GCP\tNo results\t\n+44\tJY8QFUQ01A1UV9\tNo results\t\n+45\tJY8QFUQ01CVLJY\tNo results\t\n+46\tJY8QFUQ01BAK18\tNo results\t\n+47\tJY8QFUQ01CEPBG\tNo results\t\n+48\tJY8QFUQ01ART19\tNo results\t\n+49\tJY8QFUQ01CA0L6\tunknown\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*02 F or Homsap IGHV3-23*03 F or Homsap IGHV3-23*04 F or Homsap IGHV3-23*05 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F or Homsap IGHV3-7*01 F or Homsap IGHV3-7*02 F or Homsap IGHV3-7*03 F\t\t\t\t\tSGFTFSSYAMSWVKDYFPHQSTVSWNS\tS\tGFTFSSYA\tMSWVKDYFPHQSTVSWN\tS\t\t\t\t\t\t\n+50\tJY8QFUQ01BLYKI\tNo results\t\n+51\tJY8QFUQ01CMHH0\tNo results\t\n+52\tJY8QFUQ01DTU6H\tNo results\t\n+53\tJY8QFUQ01AFK93\tNo results\t\n+54\tJY8QFUQ01CAQ1G\tNo results\t\n+55\tJY8QFUQ01DGVKY\tNo results\t\n+56\tJY8QFUQ01DTVWR\tNo results\t\n+57\tJY8QFUQ01DHF6P\tNo results\t\n+58\tJY8QFUQ01DW0GO\tunknown\tHomsap IGHV1-NL1*01 P\t\t\t\t\tPEVLLEEGARGKTDGPLVEATDEATR\tPEVLLEEGARGKTDGPLVEATDEAT\tR\t\t\t\t\t\t\t\t\n+59\tJY8QFUQ01B3H3U\tNo results\t\n+60\tJY8QFUQ01BG2D6\tNo results\t\n+61\tJY8QFUQ01CU2N8\tunknown\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t\t\t\t\tSAASGFTFNS'..b'0*01 F\tHomsap IGHJ3*01 F\tHomsap IGHD1-14*01 ORF\tSGFTFSAFTMHWVXQAPGEGLEWVAAISYDGSKKYYADFVKGRFTISRDNPKSTLYLQMNGLGGDDTALYYCACGPYAGWL*CLGPRDKGHRLF\t\tSGFTFSAFTMHWVXQAPGEGLEWVAAISYDGSKKYYADFVKGRFTISRDNPKSTLYLQMNGLGGDDTALYYCA\tS\tGFTFSAFT\tMHWVXQAPGEGLEWVAA\tISYDGSKK\tYYADFVKGRFTISRDNPKSTLYLQMNGLGGDDTALYYC\tACGPYAGWL*C\tCACGPYAGWL*CL\tWL*CLGPRDKGHRLF\tWGQGTKVTVSS\t\n+22424\tJY8QFUQ01BK9ED\tunproductive\tHomsap IGHV4-39*01 F, or Homsap IGHV4-39*05 F\tHomsap IGHJ5*02 F\tHomsap IGHD5-18*01 F\tSGGSISSSSYYWGWIRQPPGKGLEWIGSIYYSGSTYYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARSRTFYGSANYWGPGNPGHRLL\t\tSGGSISSSSYYWGWIRQPPGKGLEWIGSIYYSGSTYYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCAR\tS\tGGSISSSSYY\tWGWIRQPPGKGLEWIGS\tIYYSGST\tYYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYC\tARSRTFYGSANY\tCARSRTFYGSANYW\tGPGNPGHRLL\tGGQGTLVTVSS\t\n+22425\tJY8QFUQ01AV4SA\tNo results\t\n+22426\tJY8QFUQ01BC2PX\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ4*02 F\tHomsap IGHD1-26*01 F\tSGFTFNDYAMSWVRQAPDKGLEWVSTVSSRGDTTHYADFVKGRLTISRDNSRNTLYLQMNSLTAEDTAIYYCAKVMWGVTGPIDPFDYWGQGTLVTVSS\t\tSGFTFNDYAMSWVRQAPDKGLEWVSTVSSRGDTTHYADFVKGRLTISRDNSRNTLYLQMNSLTAEDTAIYYCAK\tS\tGFTFNDYA\tMSWVRQAPDKGLEWVST\tVSSRGDTT\tHYADFVKGRLTISRDNSRNTLYLQMNSLTAEDTAIYYC\tAKVMWGVTGPIDPFDY\tCAKVMWGVTGPIDPFDYW\tFDYWGQGTLVTVSS\tWGQGTLVTVSS\t\n+22427\tJY8QFUQ01CA2ZU\tNo results\t\n+22428\tJY8QFUQ01BLYJ4\tunproductive\tHomsap IGHV4-59*01 F, or Homsap IGHV4-59*07 F\tHomsap IGHJ3*02 F\tHomsap IGHD6-6*01 F\tSGGSMSSHYWSWIRQSSGKGLEWLGYIHYSGSTRFNPSLNSRVTISVDTSKSQFFLLLNSVTAADTATYYCARDSSNWSDAF*YLEPRDNGHRLF\t\tSGGSMSSHYWSWIRQSSGKGLEWLGYIHYSGSTRFNPSLNSRVTISVDTSKSQFFLLLNSVTAADTATYYCAR\tS\tGGSMSSHY\tWSWIRQSSGKGLEWLGY\tIHYSGST\tRFNPSLNSRVTISVDTSKSQFFLLLNSVTAADTATYYC\tARDSSNWSDAF*Y\tCARDSSNWSDAF*YL\tF*YLEPRDNGHRLF\tWSQGTMVTVSS\t\n+22429\tJY8QFUQ01C1IBJ\tunproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ4*02 F\tHomsap IGHD4-17*01 F\tSGFTFTNYGMSWVRQAPGRGLEWVSGISGSGDTTYHADSVQGRFTISRDNSKNTLYLQMNSLRVEDTAVYYCARFGPLTRPDYWGPGNFGHRLL\t\tSGFTFTNYGMSWVRQAPGRGLEWVSGISGSGDTTYHADSVQGRFTISRDNSKNTLYLQMNSLRVEDTAVYYCA\tS\tGFTFTNYG\tMSWVRQAPGRGLEWVSG\tISGSGDTT\tYHADSVQGRFTISRDNSKNTLYLQMNSLRVEDTAVYYC\tARFGPLTRPDY\tCARFGPLTRPDYW\tGPGNFGHRLL\tGGQGTLVTVSS\t\n+22430\tJY8QFUQ01B48C0\tproductive\tHomsap IGHV3-33*05 F\tHomsap IGHJ4*02 F\tHomsap IGHD5-12*01 F\tRLGFSFSNYAIHWVRQAPGKGLEWVATISYDINKRYYAESVRGRFTLSRDNSKNTLDLLMDTLRFDDTAVYYCVKGRGYNDYGLDYWGPGTLLTVSS\t\tRLGFSFSNYAIHWVRQAPGKGLEWVATISYDINKRYYAESVRGRFTLSRDNSKNTLDLLMDTLRFDDTAVYYC\tRL\tGFSFSNYA\tIHWVRQAPGKGLEWVAT\tISYDINKR\tYYAESVRGRFTLSRDNSKNTLDLLMDTLRFDDTAVYYC\tVKGRGYNDYGLDY\tCVKGRGYNDYGLDYW\tDYWGPGTLLTVSS\tWGPGTLLTVSS\t\n+22431\tJY8QFUQ01BLN4B\tproductive\tHomsap IGHV3-33*01 F, or Homsap IGHV3-33*06 F\tHomsap IGHJ6*01 F\tHomsap IGHD2-2*01 F\tSGFNFNSFGMHWVRQAPGKGLEWVANIWYDGGSQHYADLVKGRFTISRDNSKNILFLQMSDLRAEDTAVYYCVSDRELHYQHLDVWGQGTTVIVSS\t\tSGFNFNSFGMHWVRQAPGKGLEWVANIWYDGGSQHYADLVKGRFTISRDNSKNILFLQMSDLRAEDTAVYYCVS\tS\tGFNFNSFG\tMHWVRQAPGKGLEWVAN\tIWYDGGSQ\tHYADLVKGRFTISRDNSKNILFLQMSDLRAEDTAVYYC\tVSDRELHYQHLDV\tCVSDRELHYQHLDVW\tDVWGQGTTVIVSS\tWGQGTTVIVSS\t\n+22432\tJY8QFUQ01ARNFI\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ4*02 F\tHomsap IGHD2-15*01 F\tSGFTFTTSAMAWVRQVPGKGLEWVSTIRPSGERTYYAESVRGRFTISRDNSENTLYLQLNNLRVEDTAIYYCAKEEGATGVYYVDHWGQGTRVTVSS\t\tSGFTFTTSAMAWVRQVPGKGLEWVSTIRPSGERTYYAESVRGRFTISRDNSENTLYLQLNNLRVEDTAIYYCAK\tS\tGFTFTTSA\tMAWVRQVPGKGLEWVST\tIRPSGERT\tYYAESVRGRFTISRDNSENTLYLQLNNLRVEDTAIYYC\tAKEEGATGVYYVDH\tCAKEEGATGVYYVDHW\tDHWGQGTRVTVSS\tWGQGTRVTVSS\t\n+22433\tJY8QFUQ01CDTOM\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ6*02 F\tHomsap IGHD5-12*01 F\tSGFTFNNYAMSWVRQAPGKGLEWVSTITSGGGSTLYADSVKGRFTISRDNFKDTLYLQMNSLRAEDTAVYYCARGPRSRGYGMDVWGQGTTVTVSS\t\tSGFTFNNYAMSWVRQAPGKGLEWVSTITSGGGSTLYADSVKGRFTISRDNFKDTLYLQMNSLRAEDTAVYYCAR\tS\tGFTFNNYA\tMSWVRQAPGKGLEWVST\tITSGGGST\tLYADSVKGRFTISRDNFKDTLYLQMNSLRAEDTAVYYC\tARGPRSRGYGMDV\tCARGPRSRGYGMDVW\tYGMDVWGQGTTVTVSS\tWGQGTTVTVSS\t\n' |
| b |
| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/6_Junction.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/6_Junction.txt Mon Feb 03 13:37:26 2025 +0000 |
| b |
| b"@@ -0,0 +1,22434 @@\n+Sequence number\tSequence ID\tFunctionality\tV-GENE and allele\tJ-GENE and allele\tD-GENE and allele\tJUNCTION frame\tJUNCTION\tJUNCTION (with frameshift)\t3'V-REGION\tP3'V\tN-REGION\tN1-REGION\tP5'D\tD-REGION\tP3'D\tP5'D1\tD1-REGION\tP3'D1\tN2-REGION\tP5'D2\tD2-REGION\tP3'D2\tN3-REGION\tP5'D3\tD3-REGION\tP3'D3\tN4-REGION\tP5'J\t5'J-REGION\tJUNCTION-nt nb\t3'V-REGION-nt nb\tP3'V-nt nb\tN-REGION-nt nb\tN1-REGION-nt nb\tP5'D-nt nb\tD-REGION-nt nb\tP3'D-nt nb\tP5'D1-nt nb\tD1-REGION-nt nb\tP3'D1-nt nb\tN2-REGION-nt nb\tP5'D2-nt nb\tD2-REGION-nt nb\tP3'D2-nt nb\tN3-REGION-nt nb\tP5'D3-nt nb\tD3-REGION-nt nb\tP3'D2-nt nb\tN4-REGION-nt nb\tP5'J-nt nb\t5'J-REGION-nt nb\t3'V-REGION trimmed-nt nb\t5'D-REGION trimmed-nt nb\t3'D-REGION trimmed-nt nb\t5'D1-REGION trimmed-nt nb\t3'D1-REGION trimmed-nt nb\t5'D2-REGION trimmed-nt nb\t3'D2-REGION trimmed-nt nb\t5'D3-REGION trimmed-nt nb\t3'D3-REGION trimmed-nt nb\t5'J-REGION trimmed-nt nb\t3'V-REGION mut-nt nb\tD-REGION mut-nt nb\tD1-REGION mut-nt nb\tD2-REGION mut-nt nb\tD3-REGION mut-nt nb\t5'J-REGION mut-nt nb\tD-REGION reading frame\tNgc\tCDR3-IMGT length\tMolecular mass\tpI\t3'V-REGION accepted mut nb\tD-REGION accepted mut nb\t5'J-REGION accepted mut nb\tAccepted D-GENE nb\tCDR3-IMGT\tCDR3-IMGT-nt nb\tCDR3-IMGT (with frameshift)\tCDR3-IMGT (AA)\tCDR3-IMGT (AA) (with frameshift)\tJUNCTION (AA)\tJUNCTION (AA) (with frameshift)\t\n+1\tJY8QFUQ01DD1I8\tNo results\t\n+2\tJY8QFUQ01BR14W\tunknown\tHomsap IGHV3-16*01 ORF, or Homsap IGHV3-16*02 ORF or Homsap IGHV3-19*01 P or Homsap IGHV3-21*01 F or Homsap IGHV3-21*02 F or Homsap IGHV3-21*03 F or Homsap IGHV3-21*04 F or Homsap IGHV3-35*01 ORF or Homsap IGHV3-48*01 F or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t\n+3\tJY8QFUQ01DI33C\tNo results\t\n+4\tJY8QFUQ01AHA5U\tNo results\t\n+5\tJY8QFUQ01C6E2Q\tNo results\t\n+6\tJY8QFUQ01DTOF7\tNo results\t\n+7\tJY8QFUQ01DTQZ4\tNo results\t\n+8\tJY8QFUQ01CH7HW\tNo results\t\n+9\tJY8QFUQ01DRIUN\tNo results\t\n+10\tJY8QFUQ01DMFB3\tNo results\t\n+11\tJY8QFUQ01DBKZ5\tNo results\t\n+12\tJY8QFUQ01ALILW\tNo results\t\n+13\tJY8QFUQ01DQT5M\tNo results\t\n+14\tJY8QFUQ01CU1U5\tNo results\t\n+15\tJY8QFUQ01AZ7M4\tNo results\t\n+16\tJY8QFUQ01BJI4T\tNo results\t\n+17\tJY8QFUQ01A8WKP\tNo results\t\n+18\tJY8QFUQ01CDRAH\tNo results\t\n+19\tJY8QFUQ01BSZTH\tNo results\t\n+20\tJY8QFUQ01COV1I\tNo results\t\n+21\tJY8QFUQ01BYN3R\tNo results\t\n+22\tJY8QFUQ01BB6L9\tunknown\tHomsap IGHV3-74*01 F, or Homsap IGHV3-74*02 F or Homsap IGHV3-74*03 F\t\n+23\tJY8QFUQ01AK5S0\tNo results\t\n+24\tJY8QFUQ01A3U3N\tNo results\t\n+25\tJY8QFUQ01DMJ3V\tNo results\t\n+26\tJY8QFUQ01DULTP\tNo results\t\n+27\tJY8QFUQ01DXFUU\tNo results\t\n+28\tJY8QFUQ01BDHX9\tNo results\t\n+29\tJY8QFUQ01BFXXE\tNo results\t\n+30\tJY8QFUQ01DA0S9\tNo results\t\n+31\tJY8QFUQ01A8RD7\tNo results\t\n+32\tJY8QFUQ01DUD3G\tunknown\tHomsap IGHV3-20*01 F, or Homsap IGHV3-20*02 ORF\t\n+33\tJY8QFUQ01BAEVW\tunknown\tHomsap IGHV3-48*01 F, or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t\n+34\tJY8QFUQ01C5VTQ\tNo results\t\n+35\tJY8QFUQ01DV0LO\tunknown\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*02 F or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t\n+36\tJY8QFUQ01BQV49\tNo results\t\n+37\tJY8QFUQ01BG2BI\tNo results\t\n+38\tJY8QFUQ01DDCUU\tunknown\tHomsap IGHV3-15*01 F, or Homsap IGHV3-15*02 F\tHomsap IGHJ4*03 F\t\n+39\tJY8QFUQ01DTYS9\tunknown\tHomsap IGHV3-7*01 F, or Homsap IGHV3-7*02 F or Homsap IGHV3-7*03 F\t\n+40\tJY8QFUQ01DWUUL\tNo results\t\n+41\tJY8QFUQ01BDC06\tNo results\t\n+42\tJY8QFUQ01DQ6VG\tunknown\tHomsap IGHV1-NL1*01 P\t\n+43\tJY8QFUQ01C3GCP\tNo results\t\n+44\tJY8QFUQ01A1UV9\tNo results\t\n+45\tJY8QFUQ01CVLJY\tNo results\t\n+46\tJY8QFUQ01BAK18\tNo results\t\n+47\tJY8QFUQ01CEPBG\tNo results\t\n+48\tJY8QFUQ01ART19\tNo results\t\n+49\tJY8QFUQ01CA0L6\tunknown\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*02 F or Homsap IGHV3-23*03 F or Homsap IGHV3-23*04 F or Homsap IGHV3-23*05 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F or Homsap IGHV3-7*01 F or Homsap IGHV3-7*02 F or Homsap IGHV3-7*03 F\t\n+50\tJY8QFUQ01BLYKI\tNo results\t\n+51\tJY8QFUQ01CMHH0\tNo results\t\n+52\tJY8QFUQ01DTU6H\tNo results\t\n+53\tJY8QFUQ01AFK93\tNo results\t\n+54\tJY8QFUQ01CAQ1G\tNo results\t\n+55\tJY8QFUQ01DGVKY\tNo results\t\n+56\tJY8QFUQ01DTVWR\tNo results\t\n+57\tJY"..b'p IGHD5-18*01 F\tout-of-frame\ttgtgcgagaagtagaaccttctatggttcggccaactactggg\ttgtgcgagaagtagaaccttctatggttcggccaactactg..gg\ttgtgcgaga\t\t\tagtagaacctt\t\tctatggtt\t\t\t\t\tcggccaactactg\t\t\t\t\t\t\t\t\t\tgg\t43\t9\t0\t0\t11\t0\t8\t0\t0\t0\t0\t13\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t2\t10\t2\t0\t0\t0\t0\t0\t0\t18\t0\t0\t0\t0\t0\t0\t1\t12/24\tNR\tNR\tNR\t0\t2\t0\t1\tgcgagaagtagaaccttctatggttcggccaactact\t37\tgcgagaagtagaaccttctatggttcggccaactactg..\tARSRTFYGSANY\tSRTFYGSANY\tCARSRTFYGSANYW\tCARSRTFYGSANY##\t\n+22425\tJY8QFUQ01AV4SA\tNo results\t\n+22426\tJY8QFUQ01BC2PX\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ4*02 F\tHomsap IGHD1-26*01 F\tin-frame\ttgtgcgaaagttatgtggggagttacaggtccaattgatccctttgactactgg\t\ttgtgcgaaag\t\t\tt\t\ttatgtggggagttac\t\t\t\t\taggtccaattgatcc\t\t\t\t\t\t\t\t\t\tctttgactactgg\t54\t10\t0\t0\t1\t0\t15\t0\t0\t0\t0\t15\t0\t0\t0\t0\t0\t0\t0\t0\t0\t13\t1\t2\t3\t0\t0\t0\t0\t0\t0\t4\t0\t4\t0\t0\t0\t0\t1\t7/16\t16\t2085.43528\t4.4376220703125\t2\t4\t2\t1\tgcgaaagttatgtggggagttacaggtccaattgatccctttgactac\t48\t\tAKVMWGVTGPIDPFDY\t\tCAKVMWGVTGPIDPFDYW\t\t\n+22427\tJY8QFUQ01CA2ZU\tNo results\t\n+22428\tJY8QFUQ01BLYJ4\tunproductive\tHomsap IGHV4-59*01 F, or Homsap IGHV4-59*07 F\tHomsap IGHJ3*02 F\tHomsap IGHD6-6*01 F\tout-of-frame\ttgtgcgagagactctagcaattggtcagacgcattttgatatctgg\ttgtgcgagagactctagcaattggtcagacgca..ttttgatatctgg\ttgtgcgagaga\t\t\tctc\t\ttagcaattggtc\t\t\t\t\tagacgca\t\t\t\t\t\t\t\t\t\tttttgatatctgg\t46\t11\t0\t0\t3\t0\t12\t0\t0\t0\t0\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t13\t0\t5\t1\t0\t0\t0\t0\t0\t0\t6\t0\t3\t0\t0\t0\t0\t2\t6/10\tNR\tNR\tNR\t2\t4\t2\t1\tgcgagagactctagcaattggtcagacgcattttgatatc\t40\tgcgagagactctagcaattggtcagacgca..ttttgatatct\tARDSSNWSDAF*Y\tDSSNWSDA#FD\tCARDSSNWSDAF*YL\tCARDSSNWSDA#FDIW\t\n+22429\tJY8QFUQ01C1IBJ\tunproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ4*02 F\tHomsap IGHD4-17*01 F\tout-of-frame\ttgtgcgagattcggcccacttactcgacctgactactggg\ttgtgcgagattcggcccacttactcgacctgactactg..gg\ttgtgcga\t\t\tgattcggcccacttactcgacc\t\ttgactac\t\t\t\t\ttg\t\t\t\t\t\t\t\t\t\tgg\t40\t7\t0\t0\t22\t0\t7\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t4\t9\t0\t0\t0\t0\t0\t0\t0\t15\t0\t0\t0\t0\t0\t0\t3\t14/24\tNR\tNR\tNR\t2\t4\t2\t1\tgcgagattcggcccacttactcgacctgactact\t34\tgcgagattcggcccacttactcgacctgactactg..\tARFGPLTRPDY\tFGPLTRPDY\tCARFGPLTRPDYW\tCARFGPLTRPDY##\t\n+22430\tJY8QFUQ01B48C0\tproductive\tHomsap IGHV3-33*05 F\tHomsap IGHJ4*02 F\tHomsap IGHD5-12*01 F\tin-frame\ttgtgttaaaggacgtggatacaatgactacggcctcgactactgg\t\ttgtg\t\t\tttaaagg\tac\tgtggatacaatgactacg\t\t\t\t\tgcctc\t\t\t\t\t\t\t\t\t\tgactactgg\t45\t4\t0\t0\t7\t2\t18\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t9\t7\t0\t5\t0\t0\t0\t0\t0\t0\t8\t0\t3\t0\t0\t0\t0\t3\t6/12\t13\t1808.9923800000001\t6.2906494140625\t2\t4\t2\t1\tgttaaaggacgtggatacaatgactacggcctcgactac\t39\t\tVKGRGYNDYGLDY\t\tCVKGRGYNDYGLDYW\t\t\n+22431\tJY8QFUQ01BLN4B\tproductive\tHomsap IGHV3-33*01 F, or Homsap IGHV3-33*06 F\tHomsap IGHJ6*01 F\tHomsap IGHD2-2*01 F\tin-frame\ttgtgtgagcgatagagaactccattaccagcatttggacgtctgg\t\ttgtgtgagcga\tt\t\tagagaactccat\t\ttaccagc\t\t\t\t\tatt\t\t\t\t\t\t\t\t\t\ttggacgtctgg\t45\t11\t1\t0\t12\t0\t7\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t11\t0\t15\t9\t0\t0\t0\t0\t0\t0\t21\t2\t0\t0\t0\t0\t0\t1\t5/15\t13\t1900.1052799999998\t5.5450439453125\t2\t4\t2\t1\tgtgagcgatagagaactccattaccagcatttggacgtc\t39\t\tVSDRELHYQHLDV\t\tCVSDRELHYQHLDVW\t\t\n+22432\tJY8QFUQ01ARNFI\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ4*02 F\tHomsap IGHD2-15*01 F\tin-frame\ttgtgcgaaggaggaaggtgctactggagtctattatgttgaccactgg\t\ttgtgcgaagga\t\t\t\t\tggaaggtgctact\t\t\t\t\tggagtctattatg\t\t\t\t\t\t\t\t\t\tttgaccactgg\t48\t11\t0\t0\t0\t0\t13\t0\t0\t0\t0\t13\t0\t0\t0\t0\t0\t0\t0\t0\t0\t11\t0\t16\t2\t0\t0\t0\t0\t0\t0\t6\t1\t2\t0\t0\t0\t1\t3\t5/13\t14\t1827.99228\t4.7056884765625\t2\t4\t2\t1\tgcgaaggaggaaggtgctactggagtctattatgttgaccac\t42\t\tAKEEGATGVYYVDH\t\tCAKEEGATGVYYVDHW\t\t\n+22433\tJY8QFUQ01CDTOM\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tHomsap IGHJ6*02 F\tHomsap IGHD5-12*01 F\tin-frame\ttgtgcgagagggcctcgatcgcgcggctacggtatggacgtctgg\t\ttgtgcgagag\t\t\t\t\tggcctcgat\t\t\t\t\tcgcgcgg\t\t\t\t\t\t\t\t\t\tctacggtatggacgtctgg\t45\t10\t0\t0\t0\t0\t9\t0\t0\t0\t0\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t19\t1\t11\t3\t0\t0\t0\t0\t0\t0\t13\t1\t2\t0\t0\t0\t0\t2\t7/7\t13\t1710.96168\t9.3170166015625\t2\t4\t2\t1\tgcgagagggcctcgatcgcgcggctacggtatggacgtc\t39\t\tARGPRSRGYGMDV\t\tCARGPRSRGYGMDVW\t\t\n' |
| b |
| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/7_V-REGION-mutation-and-AA-change-table.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/7_V-REGION-mutation-and-AA-change-table.txt Mon Feb 03 13:37:26 2025 +0000 |
| b |
| b'@@ -0,0 +1,22434 @@\n+Sequence number\tSequence ID\tFunctionality\tV-GENE and allele\tV-REGION\tFR1-IMGT\tCDR1-IMGT\tFR2-IMGT\tCDR2-IMGT\tFR3-IMGT\tCDR3-IMGT\t\n+1\tJY8QFUQ01DD1I8\tNo results\t\n+2\tJY8QFUQ01BR14W\tunknown\tHomsap IGHV3-16*01 ORF, or Homsap IGHV3-16*02 ORF or Homsap IGHV3-19*01 P or Homsap IGHV3-21*01 F or Homsap IGHV3-21*02 F or Homsap IGHV3-21*03 F or Homsap IGHV3-21*04 F or Homsap IGHV3-35*01 ORF or Homsap IGHV3-48*01 F or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\tt105>c|a109>c,S37>H(+ - -)|g110>a,S37>H(+ - -)|g112>a,D38>N(+ + -)|\t\tt105>c|a109>c,S37>H(+ - -)|g110>a,S37>H(+ - -)|g112>a,D38>N(+ + -)|\t\t\t\t\t\n+3\tJY8QFUQ01DI33C\tNo results\t\n+4\tJY8QFUQ01AHA5U\tNo results\t\n+5\tJY8QFUQ01C6E2Q\tNo results\t\n+6\tJY8QFUQ01DTOF7\tNo results\t\n+7\tJY8QFUQ01DTQZ4\tNo results\t\n+8\tJY8QFUQ01CH7HW\tNo results\t\n+9\tJY8QFUQ01DRIUN\tNo results\t\n+10\tJY8QFUQ01DMFB3\tNo results\t\n+11\tJY8QFUQ01DBKZ5\tNo results\t\n+12\tJY8QFUQ01ALILW\tNo results\t\n+13\tJY8QFUQ01DQT5M\tNo results\t\n+14\tJY8QFUQ01CU1U5\tNo results\t\n+15\tJY8QFUQ01AZ7M4\tNo results\t\n+16\tJY8QFUQ01BJI4T\tNo results\t\n+17\tJY8QFUQ01A8WKP\tNo results\t\n+18\tJY8QFUQ01CDRAH\tNo results\t\n+19\tJY8QFUQ01BSZTH\tNo results\t\n+20\tJY8QFUQ01COV1I\tNo results\t\n+21\tJY8QFUQ01BYN3R\tNo results\t\n+22\tJY8QFUQ01BB6L9\tunknown\tHomsap IGHV3-74*01 F, or Homsap IGHV3-74*02 F or Homsap IGHV3-74*03 F\tt78>c|c90>t|c108>t|g128>a,R43>Q(+ - -)|c129>g,R43>Q(+ - -)|c130>g,Q44>G(- - -)|a131>g,Q44>G(- - -)|a132>c,Q44>G(- - -)|g133>t,A45>F(+ - -)|c134>t,A45>F(+ - -)|t135>c,A45>F(+ - -)|c136>t,P46>F(- - -)|c137>t,P46>F(- - -)|a138>c,P46>F(- - -)|g139>c|g140>c|\tt78>c|\tc90>t|c108>t|\tg128>a,R43>Q(+ - -)|c129>g,R43>Q(+ - -)|c130>g,Q44>G(- - -)|a131>g,Q44>G(- - -)|a132>c,Q44>G(- - -)|g133>t,A45>F(+ - -)|c134>t,A45>F(+ - -)|t135>c,A45>F(+ - -)|c136>t,P46>F(- - -)|c137>t,P46>F(- - -)|a138>c,P46>F(- - -)|\t\t\t\t\n+23\tJY8QFUQ01AK5S0\tNo results\t\n+24\tJY8QFUQ01A3U3N\tNo results\t\n+25\tJY8QFUQ01DMJ3V\tNo results\t\n+26\tJY8QFUQ01DULTP\tNo results\t\n+27\tJY8QFUQ01DXFUU\tNo results\t\n+28\tJY8QFUQ01BDHX9\tNo results\t\n+29\tJY8QFUQ01BFXXE\tNo results\t\n+30\tJY8QFUQ01DA0S9\tNo results\t\n+31\tJY8QFUQ01A8RD7\tNo results\t\n+32\tJY8QFUQ01DUD3G\tunknown\tHomsap IGHV3-20*01 F, or Homsap IGHV3-20*02 ORF\ta104>g,D35>G(- - -)|g106>t,D36>Y(- - -)|\t\ta104>g,D35>G(- - -)|g106>t,D36>Y(- - -)|\t\t\t\t\t\n+33\tJY8QFUQ01BAEVW\tunknown\tHomsap IGHV3-48*01 F, or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\tc84>t|a85>g,T29>A(- - -)|t88>c,F30>L(+ - -)|a106>g,S36>D(- - -)|g107>a,S36>D(- - -)|a112>g,S38>A(- + -)|g113>c,S38>A(- + -)|a118>c,N40>H(- - -)|g157>a,V53>I(+ - +)|t160>g,S54>A(- + -)|a172>g,S58>V(- - -)|g173>t,S58>V(- - -)|a175>t|g176>c|g185>c,S62>T(+ - +)|a187>t,S63>Y(+ - -)|g188>a,S63>Y(+ - -)|t189>c,S63>Y(+ - -)|a195>t|a197>t,Y66>F(- + -)|c207>g,D69>E(+ - +)|g213>t|\t\tc84>t|a85>g,T29>A(- - -)|t88>c,F30>L(+ - -)|a106>g,S36>D(- - -)|g107>a,S36>D(- - -)|a112>g,S38>A(- + -)|g113>c,S38>A(- + -)|\ta118>c,N40>H(- - -)|g157>a,V53>I(+ - +)|t160>g,S54>A(- + -)|\ta172>g,S58>V(- - -)|g173>t,S58>V(- - -)|a175>t|g176>c|g185>c,S62>T(+ - +)|a187>t,S63>Y(+ - -)|g188>a,S63>Y(+ - -)|t189>c,S63>Y(+ - -)|a195>t|\ta197>t,Y66>F(- + -)|c207>g,D69>E(+ - +)|g213>t|\t\t\n+34\tJY8QFUQ01C5VTQ\tNo results\t\n+35\tJY8QFUQ01DV0LO\tunknown\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*02 F or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\ta103>g,S35>G(+ + -)|g112>a,A38>I(+ - +)|c113>t,A38>I(+ - +)|t177>g,S59>R(- - -)|g188>t,G63>V(- - -)|a190>g,S64>D(- - -)|g191>a,S64>D(- - -)|\t\ta103>g,S35>G(+ + -)|g112>a,A38>I(+ - +)|c113>t,A38>I(+ - +)|\t\tt177>g,S59>R(- - -)|g188>t,G63>V(- - -)|a190>g,S64>D(- - -)|g191>a,S64>D(- - -)|\t\t\t\n+36\tJY8QFUQ01BQV49\tNo results\t\n+37\tJY8QFUQ01BG2BI\tNo results\t\n+38\tJY8QFUQ01DDCUU\tunknown\tHomsap IGHV3-15*01 F, or Homsap IGHV3-15*02 F\tt88>g,F30>V(+ - -)|g104>a,S35>N(- - -)|g119>c,S40>T(+ - +)|a170>g,K57>R(+ + +)|t186>c|a193>g,T65>A(- - -)|g205>c,A69>P(- - -)|c208>t,P70>F(- - -)|c209>t,P70>F(- - -)|c210>t,P70>F(- - -)|a214>g,K72>D(+ - -)|a216>c,K72>D(+ - -)|g221>a,G74>D(- - -)|c234>t|g239>c,R80>T(- - -)|a254>t,N85>I(- - -)|c259>t|g267>c|a269>t,'..b'162>g|g163>a,V55>T(- - -)|t164>c,V55>T(- - -)|t165>c,V55>T(- - -)|a168>t|g184>a,G62>I(- - -)|g185>t,G62>I(- - -)|a186>t,G62>I(- - -)|g188>a,S63>N(- - -)|t192>a,N64>K(+ - -)|a194>g,K65>R(+ + +)|c198>t|c207>g,D69>E(+ - +)|a215>g,K72>R(+ + +)|a232>c,I78>L(+ + +)|g258>t|g261>c|t262>g,Y88>D(- - -)|a269>t,Q90>L(- - -)|a270>c,Q90>L(- - -)|a274>g,N92>D(+ + -)|c276>t,N92>D(+ + -)|g278>c,S93>T(+ - +)|g282>t|a283>c|a285>g|g286>t,A96>F(+ - -)|c287>t,A96>F(+ - -)|g291>c,E97>D(+ - +)|g303>c|c309>t|\ta72>g|g73>c,A25>R(- - -)|c74>g,A25>R(- - -)|g75>t,A25>R(- - -)|t76>c,S26>L(- - -)|c77>t,S26>L(- - -)|t78>g,S26>L(- - -)|\ta85>t,T29>S(+ - +)|t105>c|g107>a,S36>N(- - -)|c108>t,S36>N(- - -)|g113>c,G38>A(- + -)|\tg117>c,M39>I(+ + -)|a162>g|g163>a,V55>T(- - -)|t164>c,V55>T(- - -)|t165>c,V55>T(- - -)|\ta168>t|g184>a,G62>I(- - -)|g185>t,G62>I(- - -)|a186>t,G62>I(- - -)|g188>a,S63>N(- - -)|t192>a,N64>K(+ - -)|a194>g,K65>R(+ + +)|\tc198>t|c207>g,D69>E(+ - +)|a215>g,K72>R(+ + +)|a232>c,I78>L(+ + +)|g258>t|g261>c|t262>g,Y88>D(- - -)|a269>t,Q90>L(- - -)|a270>c,Q90>L(- - -)|a274>g,N92>D(+ + -)|c276>t,N92>D(+ + -)|g278>c,S93>T(+ - +)|g282>t|a283>c|a285>g|g286>t,A96>F(+ - -)|c287>t,A96>F(+ - -)|g291>c,E97>D(+ - +)|g303>c|c309>t|\tc314>t,A105>V(+ - +)|g315>t,A105>V(+ - +)|g317>a,R106>K(+ + +)|a320>g|\t\n+22431\tJY8QFUQ01BLN4B\tproductive\tHomsap IGHV3-33*01 F, or Homsap IGHV3-33*06 F\tc86>a,T29>N(- + -)|g104>a,S35>N(- - -)|c108>t|a110>t,Y37>F(- + -)|a138>g|g147>a|g163>a,V55>N(- - -)|t164>a,V55>N(- - -)|t165>c,V55>N(- - -)|a187>g,S63>G(+ + -)|a191>g,N64>S(- - -)|a193>c,K65>Q(+ - -)|t196>c,Y66>H(+ - -)|t208>c,S70>L(- - -)|c209>t,S70>L(- - -)|c237>t|c257>t,T86>I(- - -)|g258>c,T86>I(- - -)|c259>t|a263>t,Y88>F(- + -)|t264>c,Y88>F(- + -)|a275>g,N92>S(- - -)|a277>g,S93>D(- - -)|g278>a,S93>D(- - -)|g303>t|c309>t|c314>t,A105>V(+ - +)|a318>c,R106>S(- - -)|\t\tc86>a,T29>N(- + -)|g104>a,S35>N(- - -)|c108>t|a110>t,Y37>F(- + -)|\ta138>g|g147>a|g163>a,V55>N(- - -)|t164>a,V55>N(- - -)|t165>c,V55>N(- - -)|\ta187>g,S63>G(+ + -)|a191>g,N64>S(- - -)|a193>c,K65>Q(+ - -)|\tt196>c,Y66>H(+ - -)|t208>c,S70>L(- - -)|c209>t,S70>L(- - -)|c237>t|c257>t,T86>I(- - -)|g258>c,T86>I(- - -)|c259>t|a263>t,Y88>F(- + -)|t264>c,Y88>F(- + -)|a275>g,N92>S(- - -)|a277>g,S93>D(- - -)|g278>a,S93>D(- - -)|g303>t|c309>t|\tc314>t,A105>V(+ - +)|a318>c,R106>S(- - -)|\t\n+22432\tJY8QFUQ01ARNFI\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tg104>c,S35>T(+ - +)|g107>c,S36>T(+ - +)|a110>c,Y37>S(+ - -)|t111>c,Y37>S(+ - -)|a118>g,S40>A(- + -)|g119>c,S40>A(- + -)|c134>t,A45>V(+ - +)|g163>a,A55>T(- - -)|t171>a,S57>R(- - -)|g172>c,G58>P(+ - -)|g173>c,G58>P(+ - -)|g188>a,G63>E(- - -)|t189>g,G63>E(- - -)|c192>a,S64>R(- - -)|a195>c|c207>g,D69>E(+ - +)|a215>g,K72>R(+ + +)|g225>c|a250>g,K84>E(+ - -)|c259>t|g267>a|a271>c,M91>L(+ + -)|g278>a,S93>N(- - -)|c287>t,A96>V(+ - +)|g301>a,V101>I(+ - +)|a318>g|\t\tg104>c,S35>T(+ - +)|g107>c,S36>T(+ - +)|a110>c,Y37>S(+ - -)|t111>c,Y37>S(+ - -)|\ta118>g,S40>A(- + -)|g119>c,S40>A(- + -)|c134>t,A45>V(+ - +)|g163>a,A55>T(- - -)|\tt171>a,S57>R(- - -)|g172>c,G58>P(+ - -)|g173>c,G58>P(+ - -)|g188>a,G63>E(- - -)|t189>g,G63>E(- - -)|c192>a,S64>R(- - -)|a195>c|\tc207>g,D69>E(+ - +)|a215>g,K72>R(+ + +)|g225>c|a250>g,K84>E(+ - -)|c259>t|g267>a|a271>c,M91>L(+ + -)|g278>a,S93>N(- - -)|c287>t,A96>V(+ - +)|g301>a,V101>I(+ - +)|\ta318>g|\t\n+22433\tJY8QFUQ01CDTOM\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\tt90>c|g104>a,S35>N(- - -)|g107>a,S36>N(- - -)|c120>t|g153>a|g163>a,A55>T(- - -)|g170>c,S57>T(+ - +)|g172>a,G58>S(+ + -)|a175>g,S59>G(+ + -)|c192>t|a197>t,Y66>L(- - -)|c198>g,Y66>L(- - -)|c248>t,S83>F(- - -)|a253>g,N85>D(+ + -)|a317>g,K106>R(+ + +)|\t\tt90>c|g104>a,S35>N(- - -)|g107>a,S36>N(- - -)|\tc120>t|g153>a|g163>a,A55>T(- - -)|\tg170>c,S57>T(+ - +)|g172>a,G58>S(+ + -)|a175>g,S59>G(+ + -)|c192>t|\ta197>t,Y66>L(- - -)|c198>g,Y66>L(- - -)|c248>t,S83>F(- - -)|a253>g,N85>D(+ + -)|\ta317>g,K106>R(+ + +)|a320>g|\t\n' |
| b |
| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/8_V-REGION-nt-mutation-statistics.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/8_V-REGION-nt-mutation-statistics.txt Mon Feb 03 13:37:26 2025 +0000 |
| b |
| b'@@ -0,0 +1,22434 @@\n+Sequence number\tSequence ID\tFunctionality\tV-GENE and allele\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\t\n+1\tJY8QFUQ01DD1I8\tNo results\t\n+2\tJY8QFUQ01BR14W\tunknown\tHomsap IGHV3-16*01 ORF, or Homsap IGHV3-16*02 ORF or Homsap IGHV3-19*01 P or Homsap IGHV3-21*01 F or Homsap IGHV3-21*02 F or Homsap IGHV3-21*03 F or Homsap IGHV3-21*04 F or Homsap IGHV3-35*01 ORF or Homsap IGHV3-48*01 F or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t121\t34\t30\t4\t1\t3\t0\t2\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t78\t3\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t36\t24\t20\t4\t1\t3\t0\t2\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t6\t6\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+3\tJY8QFUQ01DI33C\tNo results\t\n+4\tJY8QFUQ01AHA5U\tNo results\t\n+5\tJY8QFUQ01C6E2Q\tNo results\t\n+6\tJY8QFUQ01DTOF7\tNo results\t\n+7\tJY8QFUQ01DTQZ4\tNo results\t\n+8\tJY8QFUQ01CH7HW\tNo results\t\n+9\tJY8QFUQ01DRIUN\tNo results\t\n+10\tJY8QFUQ01DMFB3\tNo results\t\n+11\tJY8QFUQ01DBKZ5\tNo results\t\n+12\tJY8QFUQ01ALILW\tNo results\t\n+13\tJY8QFUQ01DQT5M\tNo results\t\n+14\tJY8QFUQ01CU1U5\tNo results\t\n+15\tJY8QFUQ01AZ7M4\tNo results\t\n+16\tJY8QFUQ01BJI4T\tNo results\t\n+17\tJY8QFUQ01A8WKP\tNo results\t\n+18\tJY8QFUQ01CDRAH\tNo results\t\n+19\tJY8QFUQ01BSZTH\tNo results\t\n+20\tJY8QFUQ01COV1I\tNo results\t\n+21\tJY8QFUQ01BYN3R\tNo results\t\n+22\tJY8QFUQ01BB6L9\tunknown\tHomsap IGHV3-74*01 F, or Homsap IGHV3-74*02 F or Homsap IGHV3-74*03 F\t140\t53\t37\t16\t5\t11\t1\t1\t5\t2\t2\t0\t0\t0\t2\t2\t1\t0\t78\t3\t2\t1\t1\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t36\t24\t22\t2\t2\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2'..b'\t30\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t51\t51\t51\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t30\t21\t21\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t117\t114\t114\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t6 (8)\t6 (8)\t6\t0 (2)\t0 (2)\t0\t0 (1)\t0\t0\t0\t0\t0 (1)\t0\t0\t0\t0\t0\t0\t\n+22423\tJY8QFUQ01CBRT1\tunproductive\tHomsap IGHV3-30*01 F\t315 (320)\t220 (225)\t196 (198)\t24 (27)\t6 (7)\t18 (20)\t6 (7)\t4\t4\t2\t1 (2)\t0\t1 (2)\t1\t1\t1\t2\t0\t78\t4\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t36\t24\t20\t4\t0\t4\t1\t1\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t51\t51\t47\t4\t1\t3\t1\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t30\t24\t22\t2\t1\t1\t0\t0\t0\t0\t1\t0\t0\t1\t0\t0\t0\t0\t117\t114\t100\t14\t4\t10\t4\t2\t4\t1\t0\t0\t0\t0\t0\t1\t2\t0\t3 (8)\t3 (8)\t3 (5)\t0 (3)\t0 (1)\t0 (2)\t0 (1)\t0\t0\t0\t0 (1)\t0\t0 (1)\t0\t0\t0\t0\t0\t\n+22424\tJY8QFUQ01BK9ED\tunproductive\tHomsap IGHV4-39*01 F, or Homsap IGHV4-39*05 F\t318 (320)\t227 (229)\t227\t0 (2)\t0 (2)\t0\t0 (1)\t0\t0\t0\t0\t0 (1)\t0\t0\t0\t0\t0\t0\t78\t5\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t36\t30\t30\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t51\t51\t51\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t30\t21\t21\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t117\t114\t114\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t6 (8)\t6 (8)\t6\t0 (2)\t0 (2)\t0\t0 (1)\t0\t0\t0\t0\t0 (1)\t0\t0\t0\t0\t0\t0\t\n+22425\tJY8QFUQ01AV4SA\tNo results\t\n+22426\tJY8QFUQ01BC2PX\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t319 (320)\t224 (225)\t200\t24 (25)\t5 (6)\t19\t4\t8\t2\t3\t0\t0\t0 (1)\t0\t2\t1\t1\t3\t78\t4\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t36\t24\t18\t6\t2\t4\t1\t2\t1\t1\t0\t0\t0\t0\t0\t1\t0\t0\t51\t51\t46\t5\t2\t3\t1\t2\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t30\t24\t18\t6\t0\t6\t1\t2\t0\t0\t0\t0\t0\t0\t1\t0\t0\t2\t117\t114\t107\t7\t1\t6\t1\t2\t1\t2\t0\t0\t0\t0\t1\t0\t0\t0\t7 (8)\t7 (8)\t7\t0 (1)\t0 (1)\t0\t0\t0\t0\t0\t0\t0\t0 (1)\t0\t0\t0\t0\t0\t\n+22427\tJY8QFUQ01CA2ZU\tNo results\t\n+22428\tJY8QFUQ01BLYJ4\tunproductive\tHomsap IGHV4-59*01 F, or Homsap IGHV4-59*07 F\t320\t223\t194\t29\t8\t21\t4\t5\t7\t4\t2\t1\t2\t0\t2\t2\t0\t0\t78\t5\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t36\t24\t21\t3\t1\t2\t0\t0\t1\t1\t0\t0\t0\t0\t0\t1\t0\t0\t51\t51\t43\t8\t4\t4\t0\t1\t4\t1\t1\t0\t0\t0\t1\t0\t0\t0\t30\t21\t19\t2\t1\t1\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t117\t114\t98\t16\t2\t14\t4\t4\t2\t1\t1\t0\t2\t0\t1\t1\t0\t0\t8\t8\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\n+22429\tJY8QFUQ01C1IBJ\tunproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t316 (320)\t222 (226)\t207 (208)\t15 (18)\t5 (7)\t10 (11)\t1 (2)\t3\t2\t2\t1\t0\t1 (2)\t0\t2\t2\t1 (2)\t0\t78\t5\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t36\t24\t21\t3\t0\t3\t0\t1\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t51\t51\t49\t2\t0\t2\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t30\t24\t22\t2\t0\t2\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t117\t114\t106\t8\t5\t3\t0\t1\t2\t2\t1\t0\t1\t0\t0\t0\t1\t0\t4 (8)\t4 (8)\t4 (5)\t0 (3)\t0 (2)\t0 (1)\t0 (1)\t0\t0\t0\t0\t0\t0 (1)\t0\t0\t0\t0 (1)\t0\t\n+22430\tJY8QFUQ01B48C0\tproductive\tHomsap IGHV3-33*05 F\t319 (320)\t227 (228)\t180\t47 (48)\t12 (13)\t35\t6 (7)\t5\t7\t4\t3\t0\t4\t1\t7\t2\t6\t2\t78\t7\t0\t7\t1\t6\t1\t0\t1\t1\t0\t0\t0\t0\t1\t1\t1\t1\t36\t24\t19\t5\t1\t4\t0\t1\t1\t1\t0\t0\t1\t0\t1\t0\t0\t0\t51\t51\t46\t5\t1\t4\t1\t1\t0\t2\t0\t0\t0\t0\t1\t0\t0\t0\t30\t24\t17\t7\t1\t6\t1\t2\t0\t0\t0\t0\t2\t1\t0\t0\t1\t0\t117\t114\t94\t20\t8\t12\t3\t0\t4\t0\t3\t0\t1\t0\t4\t1\t3\t1\t7 (8)\t7 (8)\t4\t3 (4)\t0 (1)\t3\t0 (1)\t1\t1\t0\t0\t0\t0\t0\t0\t0\t1\t0\t\n+22431\tJY8QFUQ01BLN4B\tproductive\tHomsap IGHV3-33*01 F, or Homsap IGHV3-33*06 F\t320\t226\t198\t28\t7\t21\t5\t4\t7\t4\t2\t1\t2\t1\t1\t0\t1\t0\t78\t5\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t36\t24\t20\t4\t1\t3\t0\t1\t1\t0\t0\t1\t1\t0\t0\t0\t0\t0\t51\t51\t46\t5\t2\t3\t1\t2\t0\t1\t0\t0\t0\t1\t0\t0\t0\t0\t30\t24\t21\t3\t0\t3\t2\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t117\t114\t100\t14\t4\t10\t2\t1\t5\t3\t0\t0\t1\t0\t1\t0\t1\t0\t8\t8\t6\t2\t0\t2\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t\n+22432\tJY8QFUQ01ARNFI\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t320\t226\t200\t26\t5\t21\t4\t5\t3\t1\t3\t1\t0\t1\t6\t1\t0\t1\t78\t5\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t36\t24\t20\t4\t0\t4\t0\t0\t0\t1\t1\t0\t0\t0\t2\t0\t0\t0\t51\t51\t47\t4\t0\t4\t1\t1\t1\t0\t0\t0\t0\t0\t1\t0\t0\t0\t30\t24\t17\t7\t1\t6\t0\t1\t0\t0\t1\t1\t0\t1\t2\t0\t0\t1\t117\t114\t104\t10\t3\t7\t2\t3\t2\t0\t1\t0\t0\t0\t1\t1\t0\t0\t8\t8\t7\t1\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\n+22433\tJY8QFUQ01CDTOM\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t319 (320)\t225 (226)\t210\t15 (16)\t4 (5)\t11\t3 (4)\t5\t3\t1\t0\t0\t1\t0\t1\t1\t0\t0\t78\t5\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t36\t24\t21\t3\t1\t2\t0\t2\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t51\t51\t48\t3\t2\t1\t0\t2\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t30\t24\t20\t4\t1\t3\t1\t1\t1\t0\t0\t0\t0\t0\t1\t0\t0\t0\t117\t114\t110\t4\t0\t4\t1\t0\t1\t0\t0\t0\t1\t0\t0\t1\t0\t0\t7 (8)\t7 (8)\t6\t1 (2)\t0 (1)\t1\t1 (2)\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\n' |
| b |
| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/9_V-REGION-AA-change-statistics.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/9_V-REGION-AA-change-statistics.txt Mon Feb 03 13:37:26 2025 +0000 |
| b |
| b'@@ -0,0 +1,22434 @@\n+Sequence number\tSequence ID\tFunctionality\tV-GENE and allele\tV-REGION Nb of positions including IMGT gaps (AA)\tV-REGION Nb of AA\tV-REGION Nb of identical AA\tV-REGION Nb of AA changes\tV-REGION +++\tV-REGION ++-\tV-REGION +-+\tV-REGION +--\tV-REGION -+-\tV-REGION --+\tV-REGION ---\tV-REGION Very similar\tV-REGION Similar\tV-REGION Dissimilar\tV-REGION Very dissimilar\tFR1-IMGT Nb of positions including IMGT gaps (AA)\tFR1-IMGT Nb of AA\tFR1-IMGT Nb of identical AA\tFR1-IMGT Nb of AA changes\tFR1-IMGT +++\tFR1-IMGT ++-\tFR1-IMGT +-+\tFR1-IMGT +--\tFR1-IMGT -+-\tFR1-IMGT --+\tFR1-IMGT ---\tFR1-IMGT Very similar\tFR1-IMGT Similar\tFR1-IMGT Dissimilar\tFR1-IMGT Very dissimilar\tCDR1-IMGT Nb of positions including IMGT gaps (AA)\tCDR1-IMGT Nb of AA\tCDR1-IMGT Nb of identical AA\tCDR1-IMGT Nb of AA changes\tCDR1-IMGT +++\tCDR1-IMGT ++-\tCDR1-IMGT +-+\tCDR1-IMGT +--\tCDR1-IMGT -+-\tCDR1-IMGT --+\tCDR1-IMGT ---\tCDR1-IMGT Very similar\tCDR1-IMGT Similar\tCDR1-IMGT Dissimilar\tCDR1-IMGT Very dissimilar\tFR2-IMGT Nb of positions including IMGT gaps (AA)\tFR2-IMGT Nb of AA\tFR2-IMGT Nb of identical AA\tFR2-IMGT Nb of AA changes\tFR2-IMGT +++\tFR2-IMGT ++-\tFR2-IMGT +-+\tFR2-IMGT +--\tFR2-IMGT -+-\tFR2-IMGT --+\tFR2-IMGT ---\tFR2-IMGT Very similar\tFR2-IMGT Similar\tFR2-IMGT Dissimilar\tFR2-IMGT Very dissimilar\tCDR2-IMGT Nb of positions including IMGT gaps (AA)\tCDR2-IMGT Nb of AA\tCDR2-IMGT Nb of identical AA\tCDR2-IMGT Nb of AA changes\tCDR2-IMGT +++\tCDR2-IMGT ++-\tCDR2-IMGT +-+\tCDR2-IMGT +--\tCDR2-IMGT -+-\tCDR2-IMGT --+\tCDR2-IMGT ---\tCDR2-IMGT Very similar\tCDR2-IMGT Similar\tCDR2-IMGT Dissimilar\tCDR2-IMGT Very dissimilar\tFR3-IMGT Nb of positions including IMGT gaps (AA)\tFR3-IMGT Nb of AA\tFR3-IMGT Nb of identical AA\tFR3-IMGT Nb of AA changes\tFR3-IMGT +++\tFR3-IMGT ++-\tFR3-IMGT +-+\tFR3-IMGT +--\tFR3-IMGT -+-\tFR3-IMGT --+\tFR3-IMGT ---\tFR3-IMGT Very similar\tFR3-IMGT Similar\tFR3-IMGT Dissimilar\tFR3-IMGT Very dissimilar\tCDR3-IMGT Nb of positions including IMGT gaps (AA)\tCDR3-IMGT Nb of AA\tCDR3-IMGT Nb of identical AA\tCDR3-IMGT Nb of AA changes\tCDR3-IMGT +++\tCDR3-IMGT ++-\tCDR3-IMGT +-+\tCDR3-IMGT +--\tCDR3-IMGT -+-\tCDR3-IMGT --+\tCDR3-IMGT ---\tCDR3-IMGT Very similar\tCDR3-IMGT Similar\tCDR3-IMGT Dissimilar\tCDR3-IMGT Very dissimilar\t\n+1\tJY8QFUQ01DD1I8\tNo results\t\n+2\tJY8QFUQ01BR14W\tunknown\tHomsap IGHV3-16*01 ORF, or Homsap IGHV3-16*02 ORF or Homsap IGHV3-19*01 P or Homsap IGHV3-21*01 F or Homsap IGHV3-21*02 F or Homsap IGHV3-21*03 F or Homsap IGHV3-21*04 F or Homsap IGHV3-35*01 ORF or Homsap IGHV3-48*01 F or Homsap IGHV3-48*02 F or Homsap IGHV3-48*04 F\t40\t11\t9\t2\t0\t1\t0\t1\t0\t0\t0\t0\t1\t1\t0\t26\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\t8\t6\t2\t0\t1\t0\t1\t0\t0\t0\t0\t1\t1\t0\t2\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t\t\t\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t\t\t\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t\t\t\t\n+3\tJY8QFUQ01DI33C\tNo results\t\n+4\tJY8QFUQ01AHA5U\tNo results\t\n+5\tJY8QFUQ01C6E2Q\tNo results\t\n+6\tJY8QFUQ01DTOF7\tNo results\t\n+7\tJY8QFUQ01DTQZ4\tNo results\t\n+8\tJY8QFUQ01CH7HW\tNo results\t\n+9\tJY8QFUQ01DRIUN\tNo results\t\n+10\tJY8QFUQ01DMFB3\tNo results\t\n+11\tJY8QFUQ01DBKZ5\tNo results\t\n+12\tJY8QFUQ01ALILW\tNo results\t\n+13\tJY8QFUQ01DQT5M\tNo results\t\n+14\tJY8QFUQ01CU1U5\tNo results\t\n+15\tJY8QFUQ01AZ7M4\tNo results\t\n+16\tJY8QFUQ01BJI4T\tNo results\t\n+17\tJY8QFUQ01A8WKP\tNo results\t\n+18\tJY8QFUQ01CDRAH\tNo results\t\n+19\tJY8QFUQ01BSZTH\tNo results\t\n+20\tJY8QFUQ01COV1I\tNo results\t\n+21\tJY8QFUQ01BYN3R\tNo results\t\n+22\tJY8QFUQ01BB6L9\tunknown\tHomsap IGHV3-74*01 F, or Homsap IGHV3-74*02 F or Homsap IGHV3-74*03 F\t46\t17\t13\t4\t0\t0\t0\t2\t0\t0\t2\t0\t0\t2\t2\t26\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\t8\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t8\t4\t4\t0\t0\t0\t2\t0\t0\t2\t0\t0\t2\t2\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t\t\t\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t\t\t\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t\t\t\t\n+23\tJY8QFUQ01AK5S0\tNo results\t\n+24\tJY8QFUQ01A3U3N\tNo results\t\n+25\tJY8QFUQ01DMJ3V\tNo results\t\n+26\tJY8QFUQ01DULTP\tNo results\t\n+27\tJY8QFUQ01DXFUU\tNo results\t\n+28\tJY8QFUQ01BDHX9\tNo results\t\n+29\tJY8QFUQ01BFXXE\tNo results\t\n+30\tJY8QFUQ01DA0S9\tNo results\t\n+31\tJY8QFUQ01A8RD7\tNo results\t\n+32\tJY8QFUQ01DUD3G\tunknown\tHomsap IGHV3-20*01 F, or Homsap IGHV3-20*02 ORF\t41\t12\t10\t2\t0\t0\t0\t0\t0\t0\t'..b'(1)+0+0\t0 (1)\t\n+22420\tJY8QFUQ01AARY1\tunknown\tHomsap IGHV1-18*01 F, or Homsap IGHV1-18*02 (F) or Homsap IGHV1-18*03 F or Homsap IGHV7-81*01 ORF\t67\t35\t15\t20\t0\t0\t2\t5\t1\t0\t12\t0\t2\t6\t12\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t\t\t\t12\t8\t4\t4\t0\t0\t1\t2\t0\t0\t1\t0\t1\t2\t1\t17\t17\t10\t7\t0\t0\t0\t1\t0\t0\t6\t0\t0\t1\t6\t10\t8\t1\t7\t0\t0\t1\t1\t1\t0\t4\t0\t1\t2\t4\t2\t2\t0\t2\t0\t0\t0\t1\t0\t0\t1\t0\t0\t1\t1\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t\t\t\t\n+22421\tJY8QFUQ01BHRCO\tunproductive\tHomsap IGHV4-61*02 F\t106\t75\t57\t18\t2\t0\t5\t3\t0\t0\t8\t2\t5\t3\t8\t26\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\t10\t7\t3\t0\t0\t1\t0\t0\t0\t2\t0\t1\t0\t2\t17\t17\t15\t2\t1\t0\t0\t0\t0\t0\t1\t1\t0\t0\t1\t10\t7\t3\t4\t0\t0\t2\t0\t0\t0\t2\t0\t2\t0\t2\t39\t38\t29\t9\t1\t0\t2\t3\t0\t0\t3\t1\t2\t3\t3\t2\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\n+22422\tJY8QFUQ01CEIUR\tunproductive\tHomsap IGHV4-39*01 F, or Homsap IGHV4-39*05 F\t106\t76\t76\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t26\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\t10\t10\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t17\t17\t17\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t10\t7\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t39\t38\t38\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\n+22423\tJY8QFUQ01CBRT1\tunproductive\tHomsap IGHV3-30*01 F\t105 (106)\t73 (74)\t58\t15 (16)\t0\t1\t3\t3\t3\t0\t5 (6)\t0\t4\t6\t5 (6)\t26\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\t8\t5\t3\t0\t0\t0\t0\t2\t0\t1\t0\t0\t2\t1\t17\t17\t14\t3\t0\t0\t1\t1\t0\t0\t1\t0\t1\t1\t1\t10\t8\t7\t1\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t0\t39\t38\t30\t8\t0\t1\t2\t1\t1\t0\t3\t0\t3\t2\t3\t1 (2)\t1 (2)\t1\t0 (1)\t0\t0\t0\t0\t0\t0\t0 (1)\t0\t0\t0\t0 (1)\t\n+22424\tJY8QFUQ01BK9ED\tunproductive\tHomsap IGHV4-39*01 F, or Homsap IGHV4-39*05 F\t106\t75\t75\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t26\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\t10\t10\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t17\t17\t17\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t10\t7\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t39\t38\t38\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\n+22425\tJY8QFUQ01AV4SA\tNo results\t\n+22426\tJY8QFUQ01BC2PX\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t106\t74\t59\t15\t1\t1\t3\t2\t0\t0\t8\t1\t4\t2\t8\t26\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\t8\t6\t2\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t2\t17\t17\t15\t2\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t2\t10\t8\t3\t5\t0\t1\t2\t0\t0\t0\t2\t0\t3\t0\t2\t39\t38\t32\t6\t1\t0\t1\t2\t0\t0\t2\t1\t1\t2\t2\t2\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\n+22427\tJY8QFUQ01CA2ZU\tNo results\t\n+22428\tJY8QFUQ01BLYJ4\tunproductive\tHomsap IGHV4-59*01 F, or Homsap IGHV4-59*07 F\t106\t73\t59\t14\t1\t1\t0\t6\t2\t0\t4\t1\t1\t8\t4\t26\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\t8\t6\t2\t0\t1\t0\t1\t0\t0\t0\t0\t1\t1\t0\t17\t17\t14\t3\t1\t0\t0\t2\t0\t0\t0\t1\t0\t2\t0\t10\t7\t6\t1\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t0\t39\t38\t30\t8\t0\t0\t0\t2\t2\t0\t4\t0\t0\t4\t4\t2\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\n+22429\tJY8QFUQ01C1IBJ\tunproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t105 (106)\t73 (74)\t63\t10 (11)\t1 (2)\t0\t3\t2\t2\t0\t2\t1 (2)\t3\t4\t2\t26\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\t8\t5\t3\t0\t0\t1\t0\t1\t0\t1\t0\t1\t1\t1\t17\t17\t15\t2\t1\t0\t0\t0\t1\t0\t0\t1\t0\t1\t0\t10\t8\t6\t2\t0\t0\t1\t0\t0\t0\t1\t0\t1\t0\t1\t39\t38\t35\t3\t0\t0\t1\t2\t0\t0\t0\t0\t1\t2\t0\t1 (2)\t1 (2)\t1\t0 (1)\t0 (1)\t0\t0\t0\t0\t0\t0\t0 (1)\t0\t0\t0\t\n+22430\tJY8QFUQ01B48C0\tproductive\tHomsap IGHV3-33*05 F\t106\t75\t53\t22\t4\t2\t5\t2\t1\t0\t8\t4\t7\t3\t8\t26\t2\t0\t2\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t2\t12\t8\t5\t3\t0\t0\t1\t0\t1\t0\t1\t0\t1\t1\t1\t17\t17\t15\t2\t0\t1\t0\t0\t0\t0\t1\t0\t1\t0\t1\t10\t8\t4\t4\t1\t0\t0\t1\t0\t0\t2\t1\t0\t1\t2\t39\t38\t29\t9\t2\t1\t3\t1\t0\t0\t2\t2\t4\t1\t2\t2\t2\t0\t2\t1\t0\t1\t0\t0\t0\t0\t1\t1\t0\t0\t\n+22431\tJY8QFUQ01BLN4B\tproductive\tHomsap IGHV3-33*01 F, or Homsap IGHV3-33*06 F\t106\t74\t59\t15\t0\t1\t1\t2\t3\t0\t8\t0\t2\t5\t8\t26\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\t8\t5\t3\t0\t0\t0\t0\t2\t0\t1\t0\t0\t2\t1\t17\t17\t16\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t1\t10\t8\t5\t3\t0\t1\t0\t1\t0\t0\t1\t0\t1\t1\t1\t39\t38\t32\t6\t0\t0\t0\t1\t1\t0\t4\t0\t0\t2\t4\t2\t2\t0\t2\t0\t0\t1\t0\t0\t0\t1\t0\t1\t0\t1\t\n+22432\tJY8QFUQ01ARNFI\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t106\t74\t57\t17\t1\t1\t6\t3\t1\t0\t5\t1\t7\t4\t5\t26\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\t8\t5\t3\t0\t0\t2\t1\t0\t0\t0\t0\t2\t1\t0\t17\t17\t14\t3\t0\t0\t1\t0\t1\t0\t1\t0\t1\t1\t1\t10\t8\t4\t4\t0\t0\t0\t1\t0\t0\t3\t0\t0\t1\t3\t39\t38\t31\t7\t1\t1\t3\t1\t0\t0\t1\t1\t4\t1\t1\t2\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t\n+22433\tJY8QFUQ01CDTOM\tproductive\tHomsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F\t106\t74\t64\t10\t1\t3\t1\t0\t0\t0\t5\t1\t4\t0\t5\t26\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\t8\t6\t2\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t2\t17\t17\t16\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t1\t10\t8\t5\t3\t0\t2\t1\t0\t0\t0\t0\t0\t3\t0\t0\t39\t38\t35\t3\t0\t1\t0\t0\t0\t0\t2\t0\t1\t0\t2\t2\t2\t1\t1\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t\n' |
| b |
| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/CONTROL_NWK377_PB_IGHC_MID1_40nt_2.tar.gz |
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| Binary file tests/data/CONTROL_NWK377_PB_IGHC_MID1_40nt_2.tar.gz has changed |
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| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/CONTROL_NWK377_PB_IGHC_MID1_40nt_2.tar.xz |
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| Binary file tests/data/CONTROL_NWK377_PB_IGHC_MID1_40nt_2.tar.xz has changed |
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| diff -r d714f5ea83d7 -r 5b79485234e1 tests/data/README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/README.txt Mon Feb 03 13:37:26 2025 +0000 |
| b |
| @@ -0,0 +1,16 @@ +This archive should contain 6 following files in CSV format: + +1_Summary.txt: the synthesis of the analysis +3_Nt-sequences.txt: includes the ungapped nt sequences of all described labels +4_IMGT-gapped-AA-sequences.txt: includes the AA sequences of labels that have been gapped according to the IMGT unique numbering +5_AA-sequences.txt: includes the ungapped AA sequences of labels +8_V-REGION-nt-mutation-statistics.txt: includes the number (nb) of nt positions including IMGT gaps, the nb of nt, the nb of identical nt, ... +11_Parameters.txt: includes the date of the analysis, the IMGT/V-QUEST version, and the parameters used for the analysis + +For more information on these files, please visit the IMGT/HighV-QUEST Documentation page. + + +Acknowledgements: this work was granted access to the HPC resources of CINES under the allocation 2013-036029 made by GENCI (Grand Equipement National de Calcul Int +ensif). +Please quote: Alamyar E., Giudicelli V., Li S., Duroux P., Lefranc M.-P. Immunome Research, 2012. + |
| b |
| diff -r d714f5ea83d7 -r 5b79485234e1 wrapper.sh --- a/wrapper.sh Wed Jan 10 12:32:47 2024 +0000 +++ b/wrapper.sh Mon Feb 03 13:37:26 2025 +0000 |
| b |
| @@ -837,7 +837,7 @@ echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $log echo "<table border = 1>" >> $log echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log -tIFS="$TMP" +tIFS="$IFS" IFS=$'\t' while read step seq perc do |