oxpig / anarci Goto Github PK
View Code? Open in Web Editor NEWAntibody Numbering and Antigen Receptor ClassIfication
License: BSD 3-Clause "New" or "Revised" License
anarci's People
Contributors
Stargazers
Watchers
Forkers
hugecadd hwang-happy menchant sdvillal ancientor kottmast mrsouthern lafemmemarie owenustc pdeszynski r-krishna grigoryang priyojitr yancylau andreaskdk gvrocha heiidii mukhyala fanxuezhe proteinqure addgene bighat-biosciences martinleach quzhihu jones-gareth mabsilico kongwf5813 yq625 pequode kkhatri99 bnemoz alchemab tmsincomb prihoda hunter-leo lydiaanzures nicexai sonnybrilliant sw32-seo biochunan fraternalilab merkys joshualin24 superxiang dweb0 adlerpriit jpburckert erichardson97 dstcr otienoanyango rtmatrix abc0202k tgfheisenber boland jxshi sunyj28 yanmc vsboijlfkh8566 tommy-spfv zyh0608 yangluom sanavia-oncology dudzicp joethequant sschmeier cmalherbe benjamin-kroeger yujijun indupro ideayuye kokrah lwrainbow emlbrg ddiem-ri-4d seok0801 ywilke baverso evqlv-tech yoochanmyung scala-biodesign maxshay biocoder007 calmdownkarmanarci's Issues
wrong number id of imgt
When I run an antibody sequence , it gives the domains number id like ths: ((111, ' '), 'N'), ((112, 'A'), 'N'), ((112, ' '), 'S'), ((113, ' '), 'D'). But I think 112 should in front of 112A , not 112A in front of 112.
Issue with alignment using kabat numbering
README is inconsistent.
ANARCI -i Example_sequence_files/sequences.fasta -o Numbered_sequences.anarci -ht hit_tables.txt -s chothia -r ig
Line 18 in the README-file.
Please update this line since 'sequences.fasta' is not in the 'Example_sequence_files'-folder.
Maybe just write:
ANARCI -i Example_sequence_files/12e8.fasta -o Numbered_sequences.anarci -ht hit_tables.txt -s chothia -r ig
because the 12e8.fasta-file is existing in this folder.
Adding convenience API functions
Hi all,
I would welcome a few more convenience functions in terms of the Python API. For example, an object-oriented representation of an antibody chain that would provide methods for getting CDR regions, printing, aligning with other chains, etc.
If I implement these, should I create and publish my own utility package wrapping ANARCI (as a bioconda dependency), or would you consider adding these directly to ANARCI?
def Chain:
@classmethod
def from_str(cls, seq_str, scheme='imgt', allowed_species=None):
# Allowed species: ['human', 'mouse','rat','rabbit','rhesus','pig','alpaca']
all_numbered, all_ali, all_hits = anarci([('id', seq_str)], scheme=scheme, allowed_species=allowed_species)
# We only have one sequence
numbered = all_numbered[0]
ali = all_ali[0]
hits = all_hits[0]
if numbered is None:
raise ValueError(f'No alignment found for sequence: "{seq_str}"')
if len(numbered) != 1:
raise NotImplementedError(f'Unsupported: Multiple ANARCI domains found in sequence: "{seq_str}"')
positions, start, end = numbered[0]
position_dict = {f'{num}{letter}'.strip(): aa for (num, letter), aa in positions if aa != '-'}
return cls(position_dict)
...And then the usage:
chain = Chain.from_str('ELVMTQSPSSLSASVGDRVNIACRASQGISSALAWYQQKPGKAPRLLIYDASNLESGVPSRFSGSGSGTDFTLTISSLQPEDFAIYYCQQFNSYPLTFGGGTKVEIKRTV')
print(chain)
# ELVMTQSPSSLSASVGDRVNIACRASQGISSALAWYQQKPGKAPRLLIYDASNLESGVPSRFSGSGSGTDFTLTISSLQPEDFAIYYCQQFNSYPLTFGGGTKVEIK
# ^^^^^^ ^^^ ^^^^^^^^^
chain.cdr3
# OrderedDict([('105', 'Q'), ('106', 'Q'), ('107', 'F'), ('108', 'N'), ('109', 'S'), ('114', 'Y'), ('115', 'P'), ('116', 'L'), ('117', 'T')])
chain.cdr3_seq
# QQFNSYPLTCheers,
David
germlines
Hello everyone,
I was wondering why the germlines.py file was deleted?
But I saw in the anarci.py file we still import from .germlines ?
Could anyone give me some insight?
Best regards
allowed_species parameter having cryptic and unexpected behaviour
The allowed_species parameter has a cryptic and unexpected behaviour. If you run the code snippet below, you will notice ANARCI internally fixes uppercase letters when specifying allowed species without brackets, but when using brackets it doesn't.
import anarci
raw_query = 'DIVMTQSPLSLPVTPGEPASISCRSSQSIVHSNGNTYLQWYLQKPGQSPQLLIYKVSNRLYGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPWTFGQGTKVEIK'
anarci_no_brackets_lower = anarci.run_anarci(raw_query, allowed_species='human')[1][0][0][0]
anarci_no_brackets_upper = anarci.run_anarci(raw_query, allowed_species='Human')[1][0][0][0]
anarci_brackets_lower = anarci.run_anarci(raw_query, allowed_species=['human'])[1][0][0][0]
anarci_brackets_upper = anarci.run_anarci(raw_query, allowed_species=['Human'])[1][0][0][0]
for anbl, anbu, abl, abu in zip(anarci_no_brackets_lower, anarci_no_brackets_upper, anarci_brackets_lower, anarci_brackets_upper):
if anbu != abu:
print(anbl, anbu, abl, abu)
# anarci_brackets_upper (abu) fails to use specified species, while the rest works fine
breakI guess the bug here is two-fold.
- There should be consistency between using and not using brackets
- The error messages should inform that the given species doesn't exist, instead of saying "hits did not achieve a high enough bitscore", making you believe the specified species is not the problem. In this case, the species doesn't exists and therefore no hits were generated meaning none of them (because they don't exist) achieved a high enough bitscore.
can not use in win10, need help
the error is below:
running install
C:\Users\qiuqingpo\AppData\Local\Programs\Python\Python310\lib\site-packages\setuptools\command\install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
running egg_info
writing anarci.egg-info\PKG-INFO
writing dependency_links to anarci.egg-info\dependency_links.txt
writing top-level names to anarci.egg-info\top_level.txt
reading manifest file 'anarci.egg-info\SOURCES.txt'
adding license file 'LICENCE'
adding license file 'LICENCE_MUSCLE'
writing manifest file 'anarci.egg-info\SOURCES.txt'
running build_scripts
running install_lib
running install_data
running install_egg_info
removing 'C:\Users\qiuqingpo\AppData\Local\Programs\Python\Python310\Lib\site-packages\anarci-1.3-py3.10.egg-info' (and everything under it)
Copying anarci.egg-info to C:\Users\qiuqingpo\AppData\Local\Programs\Python\Python310\Lib\site-packages\anarci-1.3-py3.10.egg-info
running install_scripts
INFO: ANARCI lives in: C:\Users\qiuqingpo\AppData\Local\Programs\Python\Python310\anarci
INFO: Downloading germlines from IMGT and building HMMs...
INFO: running 'RUN_pipeline.sh', this will take a couple a minutes.
??? Linux ? Windows ?????????????
?????? Microsoft Store ??????:
https://aka.ms/wslstoreerror: [Errno 2] No such file or directory: 'curated_alignments/germlines.py'
some one who tell me need to install HMMER3 version 3.1 higher,
but i see my localhost, my version is v0.2.3, the most important thing is that: i can not install the hmmer 3.1 or higher, please help!
can I use it to do "cdr annotation"? how to do it, tell me some suggestions
can I use it to do "cdr annotation"? how to do it, tell me some suggestions, thank you!
Install Error
I am trying to install on OSX Monterey V 12.
hmmer 3.3.2 installed
python 3.8
I tried this in a conda env both with and without biopython installed.
sudo python setup.py install
Errors (2)
Traceback (most recent call last):
File "./FormatAlignments.py", line 480, in <module>
main()
File "./FormatAlignments.py", line 454, in main
jalignments = format_j_genes(jalignments)
File "./FormatAlignments.py", line 179, in format_j_genes
pr = Popen( [ "muscle_macOS", "-in", ffile, "-gapopen", "-10", "-out", al_filename, ], stdout=PIPE, stderr=PIPE )
File "/usr/local/Caskroom/miniconda/base/envs/ANARCI_PY38/lib/python3.8/subprocess.py", line 858, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/local/Caskroom/miniconda/base/envs/ANARCI_PY38/lib/python3.8/subprocess.py", line 1704, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'muscle_macOS'
Alignment input open failed.
couldn't open ./curated_alignments/ALL.stockholm for reading
Error: File existence/permissions problem in trying to open HMM file ./HMMs/ALL.hmm.
HMM file ./HMMs/ALL.hmm not found (nor an .h3m binary of it)
Traceback (most recent call last):
File "setup.py", line 73, in <module>
shutil.copy( "curated_alignments/germlines.py", ANARCI_LOC )
File "/usr/local/Caskroom/miniconda/base/envs/ANARCI_PY38/lib/python3.8/shutil.py", line 418, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/usr/local/Caskroom/miniconda/base/envs/ANARCI_PY38/lib/python3.8/shutil.py", line 264, in copyfile
with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: 'curated_alignments/germlines.py'Warnings
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLKESGP.GLVQPSQTLSLTCTVSGFSL.....TSYNVHWVRQPPGKGLEWMGVIWSG...GNTDYNSALK.PRLSISRDTSKSQVFLTMNSLQTEDTGIY.YCNR,('Rattus_norvegicus', 'H'),('Rattus norvegicus_BN/SsNHsdMCW', 'IGHV2S13*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLKESGP.GLVQPSETLSLTCTVSGFSL.....TSYSVHWVRQHSGKSLEWMGRMWSD...GDTSYNSAFT.SRLSISRDTSKSQVFLKMNSLQTEDTGTY.YCAR,('Rattus_norvegicus', 'H'),('Rattus norvegicus_BN/SsNHsdMCW', 'IGHV2S18*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLKESGP.GLVQPSQTLSLTCTVSGFSL.....SSYGVIWVRQPPGKGLEWMGVIWGN...GNTNYNSALK.SRLSISRDTSKSQVFLKMNNLQTEDTAMY.FCA.,('Rattus_norvegicus', 'H'),('Rattus norvegicus_BN/SsNHsdMCW', 'IGHV2S61*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLKESGP.GLVQPSQTLSLTCTVSGFSL.....TDYSVHWVRQPPGKGLEWMGVMWSG...GSTAYNSALK.SRLSISRDTSKSQVFLKMNSLQTEDTAIY.YCTR,('Rattus_norvegicus', 'H'),('Rattus norvegicus_BN/SsNHsdMCW', 'IGHV2S63*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQPGSSLKVSCVASGFTF.....SSYVMHWFRQAPENGIEWLAYINTD..SSSTHYAETVK.GRFTISRDNAKNTVDMQLSSLRSEDTAMY.FCAR,('Rattus_norvegicus', 'H'),('Rattus norvegicus_BN; Sprague-Dawley', 'IGHV5-43*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQPGRSLKLSCAASGFTF.....SDYNMAWVRQAPKKGLEWVATIIYD..GSRTYYRDSVK.GRFTISRDNAKSTLYLQMDSLRSEDTATY.YCAT,('Rattus_norvegicus', 'H'),('Rattus norvegicus_BN/SsNHsdMCW', 'IGHV5S10*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQPGRSMKLSCAASGFTF.....SNYYMAWVRQAPTKGLEWVASISTG..GGNTYYRDSVK.GRFTISRDNAKSTLYLQMDSLRSEETATY.YCAR,('Rattus_norvegicus', 'H'),('Rattus norvegicus_BN/SsNHsdMCW', 'IGHV5S11*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQPGRSLKLSCAASGFTF.....SNYGMAWVRQAPTKGLEWVASISTG..GGNTYYRDSVK.GRFTISRDNAKNTQYLQMDSLRSEDTATY.YCAR,('Rattus_norvegicus', 'H'),('Rattus norvegicus_BN/SsNHsdMCW', 'IGHV5S13*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVKLVESGG.GLVQPGRPLKLSCAASGFTF.....SSNWLNWIRQAPGKGLEWVASINPD..GSSTLYPDTVK.GRFVVSKDNAKNTRYLQMNNLRSEDTAMY.YCAR,('Rattus_norvegicus', 'H'),('Rattus norvegicus_BN/SsNHsdMCW', 'IGHV5S8*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVQSGA.EVKKP.GASVKISCKAS.GYTF....TDYYLHWVRQAPGKGLEWMGRVDPE..DGEAIHAQKFQ.DRVTITRDTSTDTAYMELSSLRSEDTAVYYCAT,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV1-111*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLVQSGA.EVKKP.GSSVKVSCKAS.GYIF....TDYYMHWVRQAPGQGLEWMGEINPK..TGGTNYAQKFQ.GRVTTTRDTSTSTAYMELSSLRSEDTAVYYCER,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV1-138*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLVQSGA.EVKKP.GASVKLSCKAS.GYTF....SIYAISWVRQAPGQGLEWMGGIIPL..VGITNYAQKFQ.GRVTITADTSTSTAYMELSSLRSEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV1-151*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVQSGA.EVKKP.GASVKVSCKVS.GYTF....TELSMHWVRQAPGKGLEWMGGVDPV..YGEIIHAEKFQ.GRVTMTEDTSTDTAYMELSSLRSEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV1-156*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVQSGA.EVKKP.GASVKVSCKVS.GYTF....TELSMHWVRQAPGKGLEWMGGVDPV..YGEIIHAEKFQ.GRVTMTEDTSTDTAYMELSSLRSEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV1-156D*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLVQSGA.EIKQP.GASVKLSCKAS.GYTF....TSYYMHWVRQAPGQGLEWIGLISPY..NGNKGYAQNFQ.GRVTITTDTSTSTGYMELSSLRSEDTAVYYCTR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV1-180*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLVQSGA.EVKKP.GASVKVSCKAS.GFTF....GSYAISWVRQAPGQGLEWMGVIIPL..VGVTNYAEKFQ.GRVTITADTSTSTAYMELSSLRSEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV1-198*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLVQSGA.EVKKP.GASVKLSCKAS.GYTF....TSYYINWVRQAPGQGLDWMGWINPS..NGNTGYAQKFQ.GRVTMTRDTSTSTAYMELNSLRSEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV1-200*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EMQLVQSEA.EVKKP.GASVKISCKAS.GYTF....TYRYLHWLRQTPGQGLEWMGWITPY..NGNTNYAQKFQ.DRATITRDRSMSTAYMELSSLRSEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV1-69*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QEQLVQSGA.EVKKP.GASVKVSCKAS.GYIF....TSYVISWLRQAPGQGFEWMGGIHPG..YGSTSYAQKFQ.GRVTITADMSTSTVYMELSSLRSEDMAVYYCAA,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV1-70*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLVQSGA.EVKKP.GSSVKVSCKAS.GYTF....TDYYMHWVRQAPRQGLEWMGWINPY..NGNTKYAQKFQ.GRVTMTRDTSTSTAYMELSSLRSEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_17573', 'IGHV1S2*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVTLKESGP.ALVKP.TQTLTLTCTFS.GFSLT..TSGMGVGWIRQPPGKALEWLALIYWD...DDKRYSTSLK.SRLTISKDTSKNQVVLTMTNMDPMDTATYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV2-152*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVTLKESGP.ALVKP.TQTLTLTCTFS.GFSIS..TTGTGVSWIRQPPGKALEWLASIYWD...DDKYYSTSLK.SRLTISKDTSKNQVVLTMTNMDPVDTATYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV2-161*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVTLKESGP.ALVKP.TQTLTLTCTFS.GFSLT..TSGMGVGWIRQPPGKALEWLALIYWD...DDKRYSTSLK.SRLTISKDTSKNQVVLTMTNMDPVDTATYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV2-174*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVTLKESGP.ALVKP.TQTLTLTCTFS.GFSIS..TTGTGVGWIRQPPGKALEWLASIYWN...DSKYYSTSLK.SRLTISKDTSKNQVVLTMTNMDPVDTATYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV2-95*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVTLKESGP.ALVKP.TQTLTLTCTFS.GFSLS..TSGMGVGWIRQPPGKALEWLASIYWD...DDKYYSTSLK.SRLTISKDTSKNQVVLTMTNMDPVDTATYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_17573', 'IGHV2S1*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVKP.GGSLRLSCVAS.GFTF....SSYVMHWVRQAPGKGLEWVSVISES..GGTTYYADSVK.GRFTISRDNAKNSLFLQMNSLRAEDTAVYYCTR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-100*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLAKP.GGSLRLSCAAS.GFTF....SSYAMHWVRQAPGKGLEWVSAINSG...GSTYYADSVK.GRFTISRDNSKNTLSLQMNSLRAEDTAVYYCAK,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-103*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGR.GLVQP.GGSLRLSCAVS.GFTF....SDHYMSWVRQAPGKGPEWVGFMRNKANGGRTEYAASGK.GRFTISRDDSKSIASLQMSSLKTEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-108*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCVAS.GFSF....SDHYMDWVRQAPGKGLEWVSSISSGS.GSTTLYPDSVK.GRFTISRDNAKNTVYLQMNSLRAEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-110*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLAESGG.GLVQP.GGSLRLSCAAS.GFTF....SGYEMHWVRQAPGKGLESVSVIGGD..SSYTHYADSVK.GRFTISRDNAKNSLSLQMNSLRAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-115*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRVSCAAS.GFTF....SDYYMQWVRQAPGKGPEWVGFIRNKANGGTAEYAASVK.GRFTISRDDSKSIASLQMNSLKTEDTAVYYCTR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-116*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAS.GFTF....SSSAMHWVRQASGKGLEWVGRIRSKSNNYETGYAASVK.GRFTISRDDSKNTAYLQMNSLKTEDTAVYYCTT,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-118*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLAESGG.GLVQP.GGSLRLSCAAS.GFTF....SSYWMYWVRQAPGKGLEWVSRISSD..GSSTSYADSVK.GRFTISRENAKNSLYLQMNSLRAEDTAVYYCAK,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-119*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GRSLRPSCAAS.GFTF....SSYGMHWVRQAPEEGLVWVSYIGS....STMYYADSVK.GRFTISRDNAKNSLYLQMNSLRAEDTAVYYCVR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-12*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLAKP.GGSLRLSCAAS.GFTF....SDYYMDWVRQAPGKGLEWVSRIKWW...GSTYYADSVK.GRFTISRENAKNTLYLQMDSLRAEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-124*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAS.GFTF....SNYYMHWVRQAQGKGLEWVGLIRNKANSYTTEYAAAVK.GRFTISRDDSKNTLYLQMSSLKTEDTALYYCTK,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-13*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
VEQLVESGG.GLVQP.GASLRLSCAAS.EFTF....SSYDMHWVRQAPGKGLEWVSGISIG...GGTYYPDSVK.GRFTISRDNAKNSLYLQMNSLRAEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-132*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVKP.GGSLRLSCAAS.GFTF....DDYAMSWVRQAPGKGLEWVSRISWD..GGSTYYADSVK.GRFTISRDNAKNTLYLQMDRLRAEDTALYYCSR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-134*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAS.GFTF....SSYDMSWVRQAPGKGLEWVSYISYT..GKTIYYADSVK.GRFTISRDNAKNSLSLQMSSLRAEDTAVYYCTR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-136*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAS.GFTF....SDYAMDWVRQAPGKGPEWVGFIRSKAYGGTAEYAASVK.GRFTISRDDSKNTAYLQMSSLKTEDTAVYYCTR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-153*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAS.GFTF....SDYAMDWVRQAPGKGLEWVGFIRSKAYGGTAEYAASVK.GRFTISRDDSKNTAYLQMSSLKTEDTAVYYCTR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-153D*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAS.GFTF....SNYWMNWVRQAPGKGLEWVGFIKNKADGGTAAYAESVK.GRFTISRDDSKNTLYLQMNSLKTEDTAVYYCTR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-16*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLAESGG.GLVQP.GGSLRLSCAAS.GFTI....SSYWMSWVCQAPGKGLEWLSDIYG....STMYYGDSVK.GLFTVSRDNAKNSLYLQMNSLRAEDTAVYYCTR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-175*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQPGGGSLRLSCAAS.GFTF....SDDYMEWVRQAPGKGLEWVGQINPN..GGTTFLMDSVK.GRFTISRDNAKNTLYLQINSLKIEDTAVYYCTR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-176*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLAKP.GGSLRLSCAAS.GFTF....SDYYMDWVRQAPGKGLEWVSRISNG..GGSTWYADSVK.GRFTISRENAKNTLYLQMNSLRAEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-178*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAS.GFTF....GDYGMHWVRQAPGKGLEWVSSISNT..GKTVYYADSVK.GRFTISRDNAKNSLSLQMSSLRAEDTAVYYCTR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-183*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAS.GFTF....SDYYMYWVRQAPGKGLEWVGFIRSKAYGGTAEYAASVK.GRFTISRDDSKSIAYLQMSSLKTEDTAVYYCTR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-184*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GVVQP.GGSLRLSCAAS.GFTF....DDYAMHWVRQAPGKGLEWVSGISWS..GGSTYYADSVK.GRFTISRDNAKNSLYLQMGSLRAEDTALYYCAK,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-201*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLAKP.GGSLRLSCAAS.GFTF....SSYWMHWVRQAPGKGLEWISAINSA..GSSTYYADSVK.GRFTISRENAKNTLYLQMDSLRAEDTALYYCAG,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-28*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAS.GFTF....SNVWMNWVRQAPGKGLEWVARIKRKADGETADYAASVK.GRFTISRDDSKNTLYLQMNSLKTEDTAVYYCTT,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-30*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAP.GFTS....GNSDLIWIRQAPGKGLEWVSYISSG...GSIYYSDSVK.GRFTISRDNAKNTLYLQMSSLRVEDTAVYYCAK,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-32*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVKLVESGG.GLVQP.GGSLRLSCAAS.GFTF....SNYWMFWVRQAPGKGLEWVSSISGS..SSSTYYPDSVK.GRFTISRDNAKNTLYLQMNSLRAEDTAVHYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-34*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVEYGG.GLVQP.GGSLRLSC....GFTF....SVHFMSWVRQAPGKGPEWVGFMRNKANGGTAEYATSVK.GRFTISRDDSKSIAYLQMSSLNTEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-35*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCVAS.GFTF....SDYCMDWVRQASGKGLEWVSSISGS..SSNTYYPDSVK.GRFTISRDNAKNTLYLQMNSLRAEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-37*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLAQP.GGSLRLSCAAS.GFTF....SDHYMDWVRQAPGKGLEWVGRIRNKANSYTTEYAASVK.GRFTISRDDSKNTLYLQMSSLKTEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-38*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAS.GFTF....SSYGMSWVRQTPGKGLEWVAVIWYD..GSKKYYADSVK.DRFTISRDNSKNMLYLQMNNLKLEDTAVYYCGR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-54*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EAQLMETGG.GLVQP.GGSLRLSCAAS.GFTF....SDHYMQWVRQAPGKGLEWVGLIRNKADGETTDYALSVK.GRFTISRDDSKSITYLQMNNLKTEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-58*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLAKP.GGSLRLSCAAS.GFTF....SDYYMHWVRQASGKGLEWVSRISNG..GGSTWYADSVK.GRFTISRENAKNTLYLQMDSLRAEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-59*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAS.GFTF....SSYAMQWVHQAPGKGLEWVSAIGPG...GDTYYADAVK.GRFTISRDNAKNSLYLQMNSLRAEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-72*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GVVQP.GGSLRLSCAAS.GFTF....DDYAMGWVRQAPGKGLEWVSAISWN..GDSTYYADSVK.GRFTISRENAKNSLYLQINRLRAEDTALYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-78*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCTGS.GFTF....SSYYMYWVRQAPGKGLEWVSAINTG..GGSTWYTDSVK.GRFTISKENAKNTLYLQMDSLRAEDTAVYYCAK,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV3-8*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAS.GFTF....SSYDMSWVRQALGKGLEWVSSISNT..GKTIYYADSVK.GRFTISRDNAKNSLSLQMNSLKTEDTAVYYCTR,('Macaca_mulatta', 'H'),('Macaca mulatta_17573', 'IGHV3S4*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQRVESGG.GLVQP.GGSLRLSCAAS.GFTI....SSSWMNWDFQAPGKGLECVSHISSG...VSTDYPDSIK.GQFTISRDNTETMLYVQMNSLRAEDMAVNYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_17573', 'IGHV3S40*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCATS.GFTF....SNYWMYWFRQAPGKGLEWVSSISGS..SSNTYYPDSVK.GRFTISRDNAKNTLYLQMNSLRAEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_17573', 'IGHV3S41*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLAKP.GGSLRLSCAAS.GFTF....SSYWMNWVRQTPGKGLEWISAINSG..GGSTYYADSVK.GRFTISRDNSKNTLSLQMNSLRAEDTAVYYCAK,('Macaca_mulatta', 'H'),('Macaca mulatta_17573', 'IGHV3S42*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVESGG.GLVQP.GGSLRLSCAAP.GFTS....GNSDLIWIRQAPGKGLEWVSYISSG...GSIYYSDSVK.GRFTISRDNAKNTLYLQMSSLRVEDTAVYYCAK,('Macaca_mulatta', 'H'),('Macaca mulatta_17573', 'IGHV3S43*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCAVS.GGSIS...DDYYWSWIRQPPGKGLEWIGYIYGS..GGGTNYNPSLK.NRVTISIDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-106*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCAVS.GGSIS..SSYYYWSWIRQAPGKGLEWIGYIYGG..SGSTSYNPSLK.SRVTISRDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-122*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCAVS.GYSIS...SGYGWSWIRQPPGKGLEWIGYIGGS..SGSTNYNPSLK.SRVTISKDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-127*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCTVS.GGSIS...GYYYWSWIRQPPGKGLEWIGGIYGN..SASTYYNPSLK.SRVTISKDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-143*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCAVS.GGSI....SSNYWSWIRQPPGKGLEWIGRIYGS..SGSTSYNPSLT.SRVTISTDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-147*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCAVS.GGSI....SSNYWSWIRQPPGKGLEWIGRIYGS..GGSTDYNPSLK.SRVTISTDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-160*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCAVS.GGSI....SGYYWSWIRQPPGKGLEWIGYIGGS..SGSTYYNPSLK.SRVTISTDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-165*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QLQLQESGP.GLVKP.SETLSVTCAVS.GGSI....SSSYWSWIRQAPGKGLEWIGYIYGS..GSSTNYNPSLK.SRVTLSVDTSKNQLSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-169*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QLQLQESGP.GLVKP.SETLSLTCAVS.GGSI....SSNYWSWIRQPPGKGLEWIGRISGS..GGSTDYNPSLK.SRVTISTDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-173*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCAVS.GGSIS...SSNWWSWIRQPPGKGLEWIGYISGS..SGSTYYNPSLK.SRVTISTDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-65*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVKLQQWGE.GLVKP.SETLSLTCAVY.GGSIS...GYYYWSWIRQPPGKGLEWIGYIYGN..SASTNYNPSLK.NRVTISKDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-73*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCAVS.GGSIS...GGYDWSWIRQPPGKGLEWIGYIYGS..SGSTNYNPSLK.NRVTISKDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-76*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCAVS.GASI....SSYWWSWIRQPPGKGLEWIGEINGN..SGSTYYNPSLK.SRVTISKDASKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-80*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QLQLQESGP.GLVKP.SETLSLTCAVS.GGSI....SGYYWSWIRQPPGKGLEWIGNIDGN..IAGTNYNPSLK.SRVTISKDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-81*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCAVS.GGSIS...SSNWWSWIRQPPGKGLEWIGRISGS..GGSTSDNPSLK.SRVTISKDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-92*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.AVVKP.SETLSLTCAVS.GGSIS...SSNWWSWIRQSPGKGLEWIGGIYGS..GGSTEYNPSLK.SRVTISKDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-93*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCAVS.GYSIS...SGYYWGWIRQPPGKGLEYIGYISGS..SGSTYYNPSLK.SRVTISKDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV4-99*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GVVKP.SETLSLTCAVS.GGSIS...DSYWWSWIRQPPGKGLEWIGYIYGS..STSTNYNPSLK.SRVTISKDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_17573', 'IGHV4S10*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GVVKP.SETLSLTCAVS.GGSIS..SGYYYWSWIRQPPGKGLEWIGGIYSN..SESTNYNPSLK.SRVTISKDTSKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_17573', 'IGHV4S13*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLPLTCAVS.GASI....SSNYWSWIRQAPGKGLEWIGRIYGS..GGSTDYNPSLK.SRVTISIDTCKNQFSLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_17573', 'IGHV4S2*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SETLSLTCAVS.GGSIS...DYYYWNWIRQPPGKGLEWIGNIYGN..SASTYYNPSLK.SRVTISKDTSKNQFFLKLSSVTAADTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_17573', 'IGHV4S9*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVQSGA.EVKRP.GESLKISCKTS.GYSF....TSYWISWVRQMPGKGLEWMGAIDPS..DSDTRYNPSFQ.GQVTISADKSISTAYLQWSRLKASDTATYYCAK,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV5-20*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EVQLVQSGA.EVKRP.GESLRISCKTS.GYSF....TSSWISWVRQMPGKGLEWMGSIYPG..DSDTRYNPSFQ.GHVTISADKSISTTYLQWSSLKASDTATYYCAK,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV5-43*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLQESGP.GLVKP.SQTLSLTCAIS.GDSVS..SNSATWNWIRQSPSRGLEWLGRTYYRS.KWYNDYAQSVQ.NRISINPDTSKNQFSLQLNSVTPEDMAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV6-1*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLVQSGA.EVKQP.GASVKVSCKAS.GYTF....TSYGMNWVRQAHGQRLEWMGWINTD..TGNPTYAQGFK.ERFTFSMDTSISTAYLQISSLKAEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV7-114*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVQLVQSGP.EVKQP.GASVKVSCKAS.GYSS....TTYGMNWVRQAPGQGLEWMGWMNTY..TGNPTYAQGFT.ERFVFSMDTSVSTVYLQISSLKAEDTAVYYCAR,('Macaca_mulatta', 'H'),('Macaca mulatta_AG07107', 'IGHV7-193*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDKVT.ITCQASQSI......SSWLAWYQQKPGKAPKPLIYKA.......SSLESGVP.SRFSGSG..SGTDFTLTISSLQPEDFATYYCQQY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-16*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDKVT.ITCRASQGI......SSWLAWYQQKPGKAPKLLIYAA.......SSLQSGVP.SRFSGSG..SGTDYTLTISSLQPEDFATYYCQQG,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-18*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDKVT.ITCHASQGI......SSWLAWYQQKPGKAPKPLIYAA.......SSLQSGVP.SRFSGSG..SGTDYTLTISSLQPEDFATYYCQQY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-19*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQGI......SSWLAWYQQKPGKAPKLLIYKA.......SSLQSGVP.SRFSGSG..SGTDFTLTISSLQPEDFATYYCQQY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-21*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDTVT.ITCRASQSI......SSWLAWYQQKPGKAPKLLIYKA.......SSLQSGVP.SRFSGSG..SGTDFTLTISSLQPEDFATYYCLQY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-22*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQGI......SSYLAWYQQKPGKAPKLLIYKA.......STLQSGVP.SRFSGSG..SGTDFTLTISSLQPEDFATYYCQQH,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-25*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCQASQGI......SSWLAWYQQKPGKAPKLLLYKA.......PGLQSGVP.SMFSGSG..SGTDFTLTISSLQPEYFATYYCQQF,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-27*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDTVT.ITCRASQGI......SSYLNWFQQKPGKAPKLLIYAA.......TTLQSGVP.SRFSGSG..SGTEFTLTISSLQPEDFAAYYCLQH,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-28*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQGI......SSYLNWYQQKPGKAPKLLIYYA.......NRLESGVP.SRFSGSG..SGTEFTLTISSLQPEDFATYYCQQY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-32*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDKVT.ITCRASQGI......SNALAWYQQKPGKAPKLLIYAA.......SNLQSGVP.SRFSGSG..SGTDFTLTISSLQPEDFAVYYCQQR,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-33*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQGI......SNYLSWYQQKPGKAPKLLIYAA.......SSLESGVP.SRFSGSG..SGTEFTLTISSLQPEDFAAYYCLQY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-36*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQGI......SSYLAWYQQKPGKAPKPLIYYA.......SNLESGVP.SRFSGSG..SGTEFTLTISSLQPEDFAIYYCQQY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-37*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQLTQSPSSLSASVGDRVT.ITCRASQGI......SSYLAWYQQKPGKAPKLLIYDA.......SNLQSGVP.SRFSGSG..SGTDFTLTISSLQPEDFAVYYCQQR,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-38*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQGI......SNYLNWYQQEPGKAPKLLIYAA.......SSLESGVP.SRFSGSG..SGTEFTLTISSLQPEDFATYYCQPF,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-41*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASAGDRVT.ITCRASQGI......STYLNWYQQKPGKAPKRLIYAA.......SSLESGVP.SRFSGSG..SGTDFTLTISSLQPEDFATYYCLQY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-43*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQTI......SSYLAWYQQKPGKVPKLLIYAA.......SSLESGVP.SRFSGSG..SGTEFTLTISSLQPEDFATYYCQQH,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-44*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDSVT.ITCRASQSF......SSSLAWYQQKPGKAPKLLIYSA.......SSLQSGVP.SRFSGSK..SGTDFTLTISSLQPEDIASYYCQQY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-46*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
AIQMTQSPSSLSASVGDKVT.ITCRASQSI......GSNLAWYQQKPGKVPKLLIYAA.......STLQSEVP.SRFSGSG..SGTDFTLTISSLQPEEVATYYCQKC,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-59*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQGI......NNYLSWYQQKPGKAPKPLIYYA.......SSLERGVP.SRFSGSR..SGTDYTLTISSLQPEDIATYYCQQY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-66*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQGI......SNWLAWYQQKPGKAPKLLIYRA.......SNLETGVP.SRFSGSG..SGTDFTLTISSLQPEDIATYYCQQH,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-69*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASENV......NNYLNWYQQKPGKAPKLLIYKA.......STLQSGVP.SRFSGSG..SGTDYTFTISSLQPEDVATYYCQHG,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-74*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDTVT.ITCRASQGI......NNELAWYQQKPGKAPTLLLYSG.......SSLHTGVP.SQFSGSG..SGTDFTLTISSLQPEDVATYYCRQD,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-80*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQPPSSLSASVGDRVN.ITCQASQSI......SNYLNWYPQKTWKAPKFLTYRA.......SGLQRGVP.SQFSGSG..YGRDFTLTISSLRPEDFAIYYCQQE,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-84*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.VTCRASQGI......NKELSWYQQKPGKAPTLLIYAA.......SSLQTGVS.SRFSGSG..SGTDFTLTISSLQPEDVATYYCQQD,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV1-94*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDTVT.ITCRASQGI......SSWLAWYQQKPGKAPKLLIYAA.......SSLQSGVP.SRFSGSG..SGTDFTLTISSLQPEDFAVYYCQQR,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S11*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQTI......SSYLAWYQQKPGKVPKLLIYAA.......STLQSGVP.SRFSGSG..SGTEFTLTISSLQPEDFATYYCLQY,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S12*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDTVT.ITCRASQGI......SNYLAWYQQKPGKAPKLLIYAA.......SSLESGVP.SRFSGSG..SGTDFTLTISSLQPEDFAAYYCLQH,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S13*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDTVT.ITCRASQGI......SNYLAWYQQKPGKAPKPLIYYA.......SNLESGVP.SRFSGSG..SGTDFTLTISSLQPEDFATYYCQQH,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S14*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDTVT.ITCRASQGI......SNYLAWYQQKPGKAPKPLIYYA.......SSLESGVP.SRFSGSG..SGTDFTLTISSLQPEDFATYYCQQG,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S15*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDTVT.ITCRASQGI......SNYLAWYQQKPGKAPKPLIYYA.......SSLESGVP.SRFSGSG..YGTDFTLTISSLQPEDFATYYCQQH,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S16*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQGI......SNNLAWYQQKPGKAPKLLIYAA.......SSLESGVP.SRFSGSG..SGTDFTLTISSLQPEDFATYYCLQY,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S17*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDTVT.ITCRASQGI......SNYLNWYQQKPGKAPKLLIYAA.......SSLESGVP.SRFSGSG..SGTDFTLTISSLQPEDFAAYYCLQH,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S19*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQGI......SNYLNWYQQKPGKAPKRLIYDA.......SSLQSGVP.SRFSGSG..SGTDFTLTISSLQPEDFAAYYCLQY,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S21*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQGI......SSWLAWYQQKPGKVPKLLIYAA.......STLQSGVP.SRFSGSG..SGTEFTLTISSLQPEDFATYYCQQH,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S25*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDTVT.ITCRASQGI......SNYLAWYQQKPGKAPKPLIYYA.......SSLESGVP.SRFSGSG..SGTDFTLTISSLQPEDFATYYCQQH,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S3*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCQASQGI......SSWLAWYQQKPGKAPKLLLYKA.......PGLQSGVP.SMFSGSG..SGTEFTLTISSLQPEDFATYYCQQH,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S4*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQTI......SSYLAWYQQKPGKAPKRLIYAA.......SSLESGVP.SRFSGSG..SGTEFTLTISSLQPEDFATYYCQQH,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S5*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDKVT.ITCRASQGI......SSWLAWYQQKPGKAPKLLIYKA.......SSLASGVP.SRFSGSG..SGTEFTLTISSLQPEDFATYYCQQH,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S6*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMTQSPSSLSASVGDRVT.ITCRASQTI......SSYLAWYQQKPGKVPKLLIYAA.......STLQSGVP.SRFSGSG..SGTDFTLTISSLQPEDFATYYCQQY,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S8*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIQMSQSPSSLSASVGDTVT.ITCRASQGI......SNYLNWFQQKPGKAPKLLIYAA.......TTLQSGVP.SRFSGSG..SGTDFTLTISSLQPEDFATYYCQQH,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV1S9*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DVAMTQSPLSLPVTLGQPAS.ISCRSSQSLLHS.NGNTYLSWFQQKPGQSPRRLIYKV.......SNRDSGVP.DRFSGSG..AGTDFTLKISRVEAEDVGVYYCMEG,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-58*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPVTLGEPAS.ISCRSSQSLLSS.NGYNYLNWYLQKPGQSPQLLIYYG.......SNRASGVP.DRFSGSG..SGTDFTLKISRVEAEDVGVYYCMQA,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-60*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPVTPGEPAS.ISCRSSQSLLHT.DGYTYLDWYLQKPGQSPQLLIYGG.......SNRASGVP.DRFSGSG..SGTDFTLKISKVEAEDVGVYYCMQH,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-61*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DVVMTQSPLSLPITPGQPAS.ISCRSSQSLVHS.DGNTYLSWYQQKPGQPPRLLIYKV.......SNRDSGVP.DRFSGSG..AGTDFTLKISRVEAEDVGVYYCGQG,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-64*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DVVMTQSPLSLPITPGQPAS.ISCRSSQSLVHS.NGNTYLSWYQQKPGQPPRRLIYEV.......SNRDSGVP.DRFSGSG..AGTDFTLKISRVEAEDVGVYYCGQG,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-65*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTLLSLPVTPGEPAS.ISCRSSQSLLHS.NGNTYLDWYLQKPGQSPRFLIYKV.......TNREPGVP.DRFSGSG..SGTDFTLKISRVEPEDVGVCYCMQS,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-68*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLSVTPREPAS.ISCRSSQSLLHT.DGRTYLYWYLQKPGQPPRLLIYRV.......SNRFSGVP.DRFSGSG..SGTDFTLKISRVEAEDVGVYYCMQA,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-70*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPITPGEPAS.ISCRSSQSLLHS.NGNTYLHWYLQKPGQSPQLLIYGG.......SNRASGVP.DRFSGSG..SGTDFTLKISKVEAEDVGVYYCVQA,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-72*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPVTPGEPAS.ISCRSSQSLLHS.DGNTYLYWYLQKPGQPPRLLIYRV.......SNRFSGVP.DRFSGSG..SGTDFTLKISRVKAEDVGVYYCMQA,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-73*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPITPGEPAS.ISCRSSQSFLDSDDGYTYLDWYLQKPGQPPQPLIYFV.......SSRASGVP.DRFNGSG..SGSDFTLKISGVEADDVGVYYCMQC,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-76*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPVTPGEPAS.ISCRSSQSLLDS.DGYTHLHWYLQKPGQSPQLLIYLG.......SNRASGVP.DRFSGSG..SGTDFTLKISRVEAEDVGVYYCMQT,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-78*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPVTLGEPAS.ISCRSSQSLVYS.DGKTYLDWYLQKPGQSPQLLMYLV.......SKRASGVP.DKFSGSG..SGTDFTLKISRVEAEDVGVYYCMQA,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-82*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPVTPGEPAS.ISCRSSQSLLDSEDGNTYLDWYLQKPGQSPQPLIYEV.......SNRASGVP.DRFSGSG..SDTDFTLKISRVEAEDVGVYYCMQY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-86*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPVTPGEPAS.ISCRSSQSLLDS.DGYTCLDWYLQKPGQSPQLLIYEV.......SNRVSGVP.DRFSGSG..SGTDFTLKISRVEAEDVGVYYCMQS,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-90*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPVTPGEPAS.ISCRSSQSLLHS.NGYTYLYWYLQKPGQSPQLLMYFA.......SYRASGVP.DRFSGSG..SGTDFTLGISRVEAEDIGVYYCMQG,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-91*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPVTPGEPAS.ISCRSSQSLFDSDYANTYLDWCLQKPGQSPQLLIYML.......FNRVSGVP.DRFSGSG..SGTDFTLKISRVEAEDVGVYYCMQS,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV2-99*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLSVTPGQPAS.ISCKSSQSLLHS.DGKTYLYWYLQKPGQSPQLLIYEV.......SSRFSGVP.DRFSGSG..SGTDFTLKISRVEAEDVGVYYCMQG,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV2S15*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPVTPGEPAS.ISCRSSQSLLHS.NGNTYLDWYLQKPGQSPRLLIYKV.......TNRESGVP.DRFSGSG..SGTDFTLKISRVEPEDVGVYYCMQS,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV2S2*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPVTPGEPAS.ISCRSSQSLLDSEDGNTYLEWYLQKPGQSPQPLIYEV.......SNRASGVP.DRFSGSG..SDTDFTLKISRVEAEDVGVYYCMQG,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV2S20*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQTPLSLPVTPGEPAS.ISCRSSQSLLHS.NGNTYLHWYLQKPGQSPRLLIYKV.......TNRESGVP.DRFSGSG..SGTDFTLKISRVEPEDVGVYYCMQS,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV2S3*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DVVMTQSPLSLPVTPGQPAS.ISCRSSQSLVHS.DGKTYLNWLQQKPGQPPRRLIYQV.......SNRDSGVP.DRFSGSG..AGTDFTLKISRVEAEDVGVYYCGQG,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV2S8*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DVVMTQSPLSLPVTPGQPAS.ISCRSSQSLVHS.DGKTYLNWLQQKPGQPPRRLIYQV.......SNRDSGVP.DRFSGSG..AGTDFTLKISRVEAEDVGVYYCVQG,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV2S9*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EIVMTQSPATLSLSPGERAT.LSCRASQSV......SSSLAWYQQKPGQAPRLLIYDA.......SSRVTGIP.DRFSGSG..SGTDFTLTISSLEPEDVGVYFCQQE,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV3-17*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EIVMTQSPATLSLSPGERAT.LSCRASQSV......SSSLAWYQQKPGQAPRLLIYGA.......SSRATGIP.DRFSGSG..SGTDFTLTISSLEPEDVAVYYCLQR,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV3-24*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EIVMTQSPATLSLSPGETAT.ISCRTSQSV......SSYLAWYQQKPGQAPRLLIYGA.......SSRATGIP.DRFSGSG..SGTDFTLTISSLEPEYFAVYYCQET,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV3-31*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EIVMTQSPATLSLSPGERAT.LSCRASQSV......SSNLAWYQQKPGQAPRLLIYDA.......SNRATGIP.DRFSGSG..SGTDFTLTISSLEPEDVGVYYCQQE,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV3-35*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EIVMTQSPATLSLSPGETAT.LSCRASESV......GSYLAWYQQKPGQAPKLLVRSA.......YFRATGIP.DRFSGSG..SRTDFTLTISSLEPEDVGVYHCQQY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV3-40*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EIVMTQSPATLSLSPGERAT.LSCRASQSV......SSSLAWYQQKPGQAPRLLIYGA.......SSRATGIP.DRFSGSG..SGTEFTLTISSLEPEDVAVYYCQQN,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV3-42*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVILTQSPATLSLSPGERAT.LSCRASQSV......SSSLAWYQQKPGQAPRLLIYGA.......SSRATGIP.DRFSGSG..SGTEFTLTISSLEPEDFAVYYCQKY,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV3-53*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
QVILTQSPATLSLSPGERAT.LSCRASQSV......GSNLAWYQQKPGQAPRLLIYGA.......SSRATGIP.DRFSGSG..SGTDFTLTISSLEPEDVAVYYCLQR,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV3S11*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EIVMTQSPATLSLSPGERAT.LSCRASQSV......SSRLAWYKQKPGQAPRLLIYDA.......SSRATGIP.DRFSGSG..SGTEFTLTISSLEPEDVAVYLCQQE,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV3S5*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EIVMTQSPATLSLSPGERAT.LSCRASQSV......SSYVAWYQQKPGQAPRLLIYGA.......SSRATGIP.DRFSGSG..SGTEFTLTISSLEPEDFAVYYCQQY,('Macaca_mulatta', 'K'),('Macaca mulatta', 'IGKV3S9*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
DIVMTQSPAFVSVTPGEKVT.ITCQVSEGI......SNYLHWYQQKPDQAPKLFIQYA.......SQSISGVP.SRFTGSG..SGTDFTFTISSLEVEDAATYYCQQG,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV6-47*01')
Warning - this sequence alignment looks odd. Probably want to handle. Find where I am printing
EIVLTQSPAFRSVTLKEKVT.ITCQASQSI......GSSLHWYQQKPDQSPKLLIKYA.......SQSISGVP.SRFSGSG..SGTDFTLTINSLEAEDAATYYCQQS,('Macaca_mulatta', 'K'),('Macaca mulatta_AG07107', 'IGKV6-55*01')
conda list
# packages in environment at /usr/local/Caskroom/miniconda/base/envs/ANARCI_PY38:
#
# Name Version Build Channel
anarci 1.3 pypi_0 pypi
biopython 1.78 py38h9ed2024_0
blas 1.0 mkl
ca-certificates 2021.10.26 hecd8cb5_2
certifi 2021.10.8 py38hecd8cb5_2
intel-openmp 2021.4.0 hecd8cb5_3538
libcxx 12.0.0 h2f01273_0
libffi 3.3 hb1e8313_2
mkl 2021.4.0 hecd8cb5_637
mkl-service 2.4.0 py38h9ed2024_0
mkl_fft 1.3.1 py38h4ab4a9b_0
mkl_random 1.2.2 py38hb2f4e1b_0
ncurses 6.3 hca72f7f_2
numpy 1.21.2 py38h4b4dc7a_0
numpy-base 1.21.2 py38he0bd621_0
openssl 1.1.1m hca72f7f_0
pip 22.0.3 pypi_0 pypi
python 3.8.12 h88f2d9e_0
readline 8.1.2 hca72f7f_1
setuptools 60.9.0 pypi_0 pypi
six 1.16.0 pyhd3eb1b0_1
sqlite 3.37.2 h707629a_0
tk 8.6.11 h7bc2e8c_0
wheel 0.37.1 pyhd3eb1b0_0
xz 5.2.5 h1de35cc_0
zlib 1.2.11 h4dc903c_4 This logic won't be triggered
This assertion won't ever be triggered since it's called after this return check
Maybe consider asserting within each numbering function and alert the user they have chosen a numbering scheme that can't handle their long HCDR3.
Wrong CYS id of IMGT
When I tried to number the light chain 'SDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL' in IMGT scheme, it gives me the 1-st CYS at (24, ' '). However, according to the IMGT official website, the 1-st CYS should be at (23, ' '). I'm wondering why this would happen. Also, the conserved TRP and 2-nd CYS are also shifted to (42, ' ') and (105, ' ') which should be (41, ' ') and (104, ' ').
Here is my code:
>> from anarci import number
>> seq = 'SDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL'
>> numbering, chain_type = number(seq, scheme='imgt')
>> numbering
Different species webapp vs python
Wrong species value when using Anarci python library (pip install anarci) compared to the webapp version,but CDRs are exactly the same. Please see below.
For this sequence:
IVFLLKGVQSEVKLEESGGGLVQPGGSMKLSCAASGFTFSDAWMDWVRQSPEKGLEWVAEIRNKANNHATYYDESVKGRFTISRDDSKSRVYLQMISLRAEDTGLYYCTGEFANWGQGTLVTVSA
Output from Webapp shows that species is "mouse".
Output from command line version shows that species is "human".
ANARCI -i IVFLLKGVQSEVKLEESGGGLVQPGGSMKLSCAASGFTFSDAWMDWVRQSPEKGLEWVAEIRNKANNHATYYDESVKGRFTISRDDSKSRVYLQMISLRAEDTGLYYCTGEFANWGQGTLVTVSA --scheme imgt
Input sequence
ANARCI numbered
Domain 1 of 1
Most significant HMM hit
|species|chain_type|e-value|score|seqstart_index|seqend_index|
|human|H|1.5e-52|168.2|10|124|
Scheme = imgt
Output from the python library shows that species is "human".
aaseq = "IVFLLKGVQSEVKLEESGGGLVQPGGSMKLSCAASGFTFSDAWMDWVRQSPEKGLEWVAEIRNKANNHATYYDESVKGRFTISRDDSKSRVYLQMISLRAEDTGLYYCTGEFANWGQGTLVTVSA"
scheme = "imgt"
from anarci import anarci
n, x, _ = anarci(
sequences=[("id0", aaseq)],
scheme=scheme,
)
print(x)
[[{'id': 'human_H', 'description': '', 'evalue': 1.5e-52, 'bitscore': 168.2, 'bias': 0.2, 'query_start': 10, 'query_end': 124, 'species': 'human', 'chain_type': 'H', 'scheme': 'imgt', 'query_name': 'id0'}]]
Tested with python library version 1.3
pip list | grep anarci
anarci 1.3
and hmmscan version 3.3
hmmscan :: search sequence(s) against a profile database
HMMER 3.3 (Nov 2019); http://hmmer.org/
Copyright (C) 2019 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.
README awfully difficult to read
Hi Authors,
Is there any reason the README is written in this particular format? I found it awfully painful to read this. I am attaching a screenshot as well.
Cannot build germlines [sent to [email protected]]
Hi,
I am trying to install ANARCI on ubuntu system with Python 2.7 and HMMER installed.
I ran the command: python2.7 setup.py install
Please see below the output, at the end it gives the error ( i have highligh:
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/anarci
copying lib/python/anarci/schemes.py -> build/lib.linux-x86_64-2.7/anarci
copying lib/python/anarci/__init__.py -> build/lib.linux-x86_64-2.7/anarci
copying lib/python/anarci/anarci.py -> build/lib.linux-x86_64-2.7/anarci
creating build/lib.linux-x86_64-2.7/anarci/Bio
copying lib/python/anarci/Bio/SeqRecord.py -> build/lib.linux-x86_64-2.7/anarci/Bio
copying lib/python/anarci/Bio/__init__.py -> build/lib.linux-x86_64-2.7/anarci/Bio
copying lib/python/anarci/Bio/File.py -> build/lib.linux-x86_64-2.7/anarci/Bio
copying lib/python/anarci/Bio/bgzf.py -> build/lib.linux-x86_64-2.7/anarci/Bio
copying lib/python/anarci/Bio/Seq.py -> build/lib.linux-x86_64-2.7/anarci/Bio
copying lib/python/anarci/Bio/_utils.py -> build/lib.linux-x86_64-2.7/anarci/Bio
creating build/lib.linux-x86_64-2.7/anarci/Bio/Align
copying lib/python/anarci/Bio/Align/AlignInfo.py -> build/lib.linux-x86_64-2.7/anarci/Bio/Align
copying lib/python/anarci/Bio/Align/Generic.py -> build/lib.linux-x86_64-2.7/anarci/Bio/Align
copying lib/python/anarci/Bio/Align/__init__.py -> build/lib.linux-x86_64-2.7/anarci/Bio/Align
creating build/lib.linux-x86_64-2.7/anarci/Bio/Alphabet
copying lib/python/anarci/Bio/Alphabet/IUPAC.py -> build/lib.linux-x86_64-2.7/anarci/Bio/Alphabet
copying lib/python/anarci/Bio/Alphabet/__init__.py -> build/lib.linux-x86_64-2.7/anarci/Bio/Alphabet
copying lib/python/anarci/Bio/Alphabet/Reduced.py -> build/lib.linux-x86_64-2.7/anarci/Bio/Alphabet
creating build/lib.linux-x86_64-2.7/anarci/Bio/Data
copying lib/python/anarci/Bio/Data/SCOPData.py -> build/lib.linux-x86_64-2.7/anarci/Bio/Data
copying lib/python/anarci/Bio/Data/__init__.py -> build/lib.linux-x86_64-2.7/anarci/Bio/Data
copying lib/python/anarci/Bio/Data/IUPACData.py -> build/lib.linux-x86_64-2.7/anarci/Bio/Data
copying lib/python/anarci/Bio/Data/CodonTable.py -> build/lib.linux-x86_64-2.7/anarci/Bio/Data
creating build/lib.linux-x86_64-2.7/anarci/Bio/_py3k
copying lib/python/anarci/Bio/_py3k/__init__.py -> build/lib.linux-x86_64-2.7/anarci/Bio/_py3k
copying lib/python/anarci/Bio/_py3k/_ordereddict.py -> build/lib.linux-x86_64-2.7/anarci/Bio/_py3k
creating build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO
copying lib/python/anarci/Bio/SearchIO/FastaIO.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO
copying lib/python/anarci/Bio/SearchIO/__init__.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO
copying lib/python/anarci/Bio/SearchIO/_index.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO
copying lib/python/anarci/Bio/SearchIO/BlatIO.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO
copying lib/python/anarci/Bio/SearchIO/_utils.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO
creating build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/_model
copying lib/python/anarci/Bio/SearchIO/_model/hit.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/_model
copying lib/python/anarci/Bio/SearchIO/_model/__init__.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/_model
copying lib/python/anarci/Bio/SearchIO/_model/_base.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/_model
copying lib/python/anarci/Bio/SearchIO/_model/hsp.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/_model
copying lib/python/anarci/Bio/SearchIO/_model/query.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/_model
creating build/lib.linux-x86_64-2.7/anarci/Bio/SeqIO
copying lib/python/anarci/Bio/SeqIO/FastaIO.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SeqIO
copying lib/python/anarci/Bio/SeqIO/_convert.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SeqIO
copying lib/python/anarci/Bio/SeqIO/__init__.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SeqIO
copying lib/python/anarci/Bio/SeqIO/Interfaces.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SeqIO
copying lib/python/anarci/Bio/SeqIO/_index.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SeqIO
creating build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/HmmerIO
copying lib/python/anarci/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/HmmerIO
copying lib/python/anarci/Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/HmmerIO
copying lib/python/anarci/Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/HmmerIO
copying lib/python/anarci/Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/HmmerIO
copying lib/python/anarci/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/HmmerIO
copying lib/python/anarci/Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-x86_64-2.7/anarci/Bio/SearchIO/HmmerIO
creating build/lib.linux-x86_64-2.7/anarci/Bio/AlignIO
copying lib/python/anarci/Bio/AlignIO/FastaIO.py -> build/lib.linux-x86_64-2.7/anarci/Bio/AlignIO
copying lib/python/anarci/Bio/AlignIO/ClustalIO.py -> build/lib.linux-x86_64-2.7/anarci/Bio/AlignIO
copying lib/python/anarci/Bio/AlignIO/NexusIO.py -> build/lib.linux-x86_64-2.7/anarci/Bio/AlignIO
copying lib/python/anarci/Bio/AlignIO/EmbossIO.py -> build/lib.linux-x86_64-2.7/anarci/Bio/AlignIO
copying lib/python/anarci/Bio/AlignIO/__init__.py -> build/lib.linux-x86_64-2.7/anarci/Bio/AlignIO
copying lib/python/anarci/Bio/AlignIO/Interfaces.py -> build/lib.linux-x86_64-2.7/anarci/Bio/AlignIO
copying lib/python/anarci/Bio/AlignIO/StockholmIO.py -> build/lib.linux-x86_64-2.7/anarci/Bio/AlignIO
copying lib/python/anarci/Bio/AlignIO/PhylipIO.py -> build/lib.linux-x86_64-2.7/anarci/Bio/AlignIO
running build_scripts
creating build/scripts-2.7
copying and adjusting bin/ANARCI -> build/scripts-2.7
copying bin/muscle -> build/scripts-2.7
copying bin/muscle_macOS -> build/scripts-2.7
changing mode of build/scripts-2.7/ANARCI from 644 to 755
changing mode of build/scripts-2.7/muscle from 700 to 755
changing mode of build/scripts-2.7/muscle_macOS from 700 to 755
running install_lib
running install_scripts
copying build/scripts-2.7/ANARCI -> /usr/local/bin
changing mode of /usr/local/bin/ANARCI to 755
changing mode of /usr/local/bin/muscle_macOS to 755
changing mode of /usr/local/bin/muscle to 755
running install_egg_info
Removing /usr/local/lib/python2.7/dist-packages/anarci-1.3.egg-info
Writing /usr/local/lib/python2.7/dist-packages/anarci-1.3.egg-info
Downloading germlines from IMGT and building HMMs...
RUN_pipeline.sh: line 8: python: command not found
RUN_pipeline.sh: line 13: python: command not found
Alignment input open failed.
couldn't open ./curated_alignments/ALL.stockholm for reading
Error: File existence/permissions problem in trying to open HMM file ./HMMs/ALL.hmm.
HMM file ./HMMs/ALL.hmm not found (nor an .h3m binary of it)
Traceback (most recent call last):
File "setup.py", line 75, in <module>
shutil.copy( "curated_alignments/germlines.py", ANARCI_LOC )
File "/usr/lib/python2.7/shutil.py", line 139, in copy
copyfile(src, dst)
File "/usr/lib/python2.7/shutil.py", line 96, in copyfile
with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: 'curated_alignments/germlines.py'
Please see and let me know if you have any suggestions to successfully install ANARCI locally.
Thank you
TypeError: string indices must be integers
type error, if using ANARCI local version.
i use this sequence:
QVQLVQSGAEVKRPGASVKVSCKASGYTFTNDIIHWVRQAPGQRLEWMGWINAGYGNTQYSQNFQDRVSITRDTSASTAYMELISLRSEDTAVYYCAREPLWFGESSPHDYYGMDVWGQGTTVTVS
Error: Something really went wrong that has not been handled
string indices must be integers
<_io.TextIOWrapper name='' mode='w' encoding='UTF-8'> Error: string indices must be integers
cmd:
ANARCI -i QVQLVQSGAEVKRPGASVKVSCKASGYTFTNDIIHWVRQAPGQRLEWMGWINAGYGNTQYSQNFQDRVSITRDTSASTAYMELISLRSEDTAVYYCAREPLWFGESSPHDYYGMDVWGQGTTVTVS --restrict heavy
Error during installation
Following the instructions and trying to install with python setup.py install --user raises the following error;
Traceback (most recent call last):
File "/Users/rodrigo/repos/HADDOCK-antibody-antigen/src/ANARCI/build_pipeline/./FormatAlignments.py", line 480, in <module>
main()
File "/Users/rodrigo/repos/HADDOCK-antibody-antigen/src/ANARCI/build_pipeline/./FormatAlignments.py", line 454, in main
jalignments = format_j_genes(jalignments)
File "/Users/rodrigo/repos/HADDOCK-antibody-antigen/src/ANARCI/build_pipeline/./FormatAlignments.py", line 179, in format_j_genes
pr = Popen( [ "muscle_macOS", "-in", ffile, "-gapopen", "-10", "-out", al_filename, ], stdout=PIPE, stderr=PIPE )
File "/Users/rodrigo/software/anaconda3/envs/haddock-antibody/lib/python3.9/subprocess.py", line 951, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/Users/rodrigo/software/anaconda3/envs/haddock-antibody/lib/python3.9/subprocess.py", line 1821, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'muscle_macOS'
Alignment input open failed.
couldn't open ./curated_alignments/ALL.stockholm for reading
Error: File existence/permissions problem in trying to open HMM file ./HMMs/ALL.hmm.
HMM file ./HMMs/ALL.hmm not found (nor an .h3m binary of it)
Traceback (most recent call last):
File "/Users/rodrigo/repos/HADDOCK-antibody-antigen/src/ANARCI/setup.py", line 61, in <module>
shutil.copy( "curated_alignments/germlines.py", ANARCI_LOC )
File "/Users/rodrigo/software/anaconda3/envs/haddock-antibody/lib/python3.9/shutil.py", line 427, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/Users/rodrigo/software/anaconda3/envs/haddock-antibody/lib/python3.9/shutil.py", line 264, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: 'curated_alignments/germlines.py'
Inconsistent results with the official website
I am using the sequence to be run on http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred/anarci/ QVQLVESGGGVVQPGRSLRLSCAASGFTFSVYGMNWVRQAPGKGLEWVAIIWYDGDNQYYADSVKGRFTISRDNSKNTLYLQMNGLRAEDTAVYYCARDLRTGPFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLEIVLTQSPDFQSVTPKEKVTITCRASQSIGSSLHWYQQKPDQSPKLLIKYASQSFSGVPSRFSGSGSGTDFTLTINSLEAEDAAAYYCHQSSSLPFTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
The result was given as two alignments, one is human_H, one is human_K.
But when I debugged locally on my laptop(mac OS), alignments are rat_H and human_K. Only when I set allowed_species = ["human"], it worked, and I don't think it would be the correct way.
Can you guide me how to run the program to output the same results as the website do?
Error in Installation
I have cloned the repository for ANARCI and tried to install it, but got the following error:
I have no idea what could have gone wrong in my installation process since all I've done was "python3 setup.py install --user"
Thanks!
‘X’ amino in result
X amino acid appears in the processed result, what does it mean?
Saving an output using the API
I am trying to use the API to generate a csv output with the assigned germline result, but I am getting this error:
/usr/local/lib/python3.8/dist-packages/anarci/anarci.py in anarci(sequences, scheme, database, output, outfile, csv, allow, hmmerpath, ncpu, assign_germline, allowed_species, bit_score_threshold)
842 if output:
843 if csv:
--> 844 csv_output(sequences, numbered, details, outfile)
845 else:
846 outto, close=sys.stdout, False
NameError: name 'details' is not defined
And this is my script:
from anarci import anarci
from Bio import SeqIO
file = '/home/marcus/Documents/rcsb_pdb_1AO7.fasta'
output = '/home/marcus/Documents/rcsb_pdb_1AO7'
seq_dict = {rec.id : str(rec.seq) for rec in SeqIO.parse(file, "fasta")}
fasta_dict = list(seq_dict.items())
anarci(fasta_dict, scheme="imgt", output = True, csv = True, assign_germline = True, outfile = output)
Any ideas what could be the problem?
Many thanks
Errors in installation
Just trying to get ANARCI running on my mac...seems problematic.
After experiencing/troubleshooting the ANARCI installation instructions per the traditional 'sudo python3 setup.py install' here, I instead tried 'pip3 install .'
which produced this:
and, when testing ANARCI on command line, I get the error...
...which tracks to the ANARCI script in ANARCI-master/bin/ANARCI as...
I guess I should start with the first error, first.
A quick search on "error 'anarci.egg-info' " doesn't yield much.
Anyone?
macOS Big Sur (v 11.0.1)
python 3.11
HMMER 3.1b2 installed
biopython installed
biopython is not declared as a dependency
Hi, please declare within the requirements in the README, that biopython is a dependency of anarci.
Thanks.
submodule_search_location installation issues
Hello,
When I try to install ANARCI on a linux machine, I get the following after running
python setup.py install --user
Has this been seen before? Are there any fixes or suggestions for this issue? Thanks.
Writing /home/jadolfbr/.local/lib/python3.6/site-packages/anarci-1.3-py3.6.egg-info
Traceback (most recent call last):
File "setup.py", line 38, in <module>
ANARCI_LOC = importlib.util.find_spec("anarci").submodule_search_locations[0]
AttributeError: 'NoneType' object has no attribute 'submodule_search_locations'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "setup.py", line 40, in <module>
sys.stderr.write(e.message)
AttributeError: 'AttributeError' object has no attribute 'message'
IMGT numbering mismatch inserted residue
The problem occurs when using IMGT numbering of the following sequence:
EVQLVESGGGLVQPGGSLRLSCAASGIILDYYPIGWFRQAPGKEREGVAFITNSDDSTIYTNYADSVKGRFTISRDKNSLYLQMNSLRAEDTAVYYCSSKASFLIGKDDQGIDAGEYDYWGQGTMVTVSS
Here is the output of the ANARCI program (61A is prior to 61):
Input sequence
ANARCI numbered
Domain 1 of 1
Most significant HMM hit
#|species|chain_type|e-value|score|seqstart_index|seqend_index|
#|alpaca|H|1.2e-52|168.6|0|129|
Scheme = imgt
H 1 E
H 2 V
H 3 Q
H 4 L
H 5 V
H 6 E
H 7 S
H 8 G
H 9 G
H 10 -
H 11 G
H 12 L
H 13 V
H 14 Q
H 15 P
H 16 G
H 17 G
H 18 S
H 19 L
H 20 R
H 21 L
H 22 S
H 23 C
H 24 A
H 25 A
H 26 S
H 27 G
H 28 I
H 29 I
H 30 L
H 31 -
H 32 -
H 33 -
H 34 -
H 35 D
H 36 Y
H 37 Y
H 38 P
H 39 I
H 40 G
H 41 W
H 42 F
H 43 R
H 44 Q
H 45 A
H 46 P
H 47 G
H 48 K
H 49 E
H 50 R
H 51 E
H 52 G
H 53 V
H 54 A
H 55 F
H 56 I
H 57 T
H 58 N
H 59 S
H 60 D
H 61 A D
H 61 S
H 62 T
H 63 I
H 64 Y
H 65 T
H 66 N
H 67 Y
H 68 A
H 69 D
H 70 S
H 71 V
H 72 K
H 73 -
H 74 G
H 75 R
H 76 F
H 77 T
H 78 I
H 79 S
H 80 R
H 81 D
H 82 -
H 83 -
H 84 K
H 85 N
H 86 S
H 87 L
H 88 Y
H 89 L
H 90 Q
H 91 M
H 92 N
H 93 S
H 94 L
H 95 R
H 96 A
H 97 E
H 98 D
H 99 T
H 100 A
H 101 V
H 102 Y
H 103 Y
H 104 C
H 105 S
H 106 S
H 107 K
H 108 A
H 109 S
H 110 F
H 111 L
H 111 A I
H 111 B G
H 111 C K
H 111 D D
H 112 E D
H 112 D Q
H 112 C G
H 112 B I
H 112 A D
H 112 A
H 113 G
H 114 E
H 115 Y
H 116 D
H 117 Y
H 118 W
H 119 G
H 120 Q
H 121 G
H 122 T
H 123 M
H 124 V
H 125 T
H 126 V
H 127 S
H 128 S
//
Does this antibody exist
Hi, we are trying to validate some of the outliers in testing. Can you tell me if you have an example antibody sequence that will hit these statements?
ANARCI/lib/python/anarci/schemes.py
Line 150 in 4392da2
Missing at 10th and 73th position
Hi~
I have run anarci numbering with imgt scheme on 463 human v region genes from imgt.org. However, I found that all of them missing numbering at the 73th position and most of them missing numbering at the 10th position.
here is my stats:
Is that because of the anarci model or the imgt numbering scheme? (asked by an IT staff without much biology background)
Thanks in advance for help: )
Fatal Error: No module named 'anarci'
Getting following error during install
running install_egg_info
Writing ../anarci_prefix/lib/python3.6/site-packages/anarci-1.3-py3.6.egg-info
Something isn't right.
in bin directory, files are created, and I get following when i try to use help
Fatal Error: No module named 'anarci'
I am using RHEL 7.8, and tried with python 3.8.5 and python 3.6.5
Inconsistent licensing
Thank you for developing this useful piece of F/LOSS. While evaluating the terms of use of ANARCI, I have noticed there are mentions of at least two different licenses:
- File
LICENCEcontains the text of BSD-3-Clause license, seemingly declaring single all-governing license for the project; - File
bin/ANARCIand couple others contain the text of GPL-3-or-later license. The same executable also prints text "Freely distributed under the GNU General Public License (GPLv3)" which is slightly different from aforementioned GPL-3-or-later.
In addition, it should probably be mentioned that files under build_pipeline/IMGT_sequence_files/ are licensed as CC BY-NC-ND 4.0 and, strictly speaking, renders the whole package usable for non-commercial uses only (as per IMGT terms of use).
Using ANARCI through Parapred
Hello,
I have a issue with using anarci with through parapred. When importing anarci, cannot import .germlines. Actually in lib there is no germlines.py file. Do you know how to solve it?
Following is the error command:
ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'
/usr/local/lib64/python3.6/site-packages/Bio/SearchIO/init.py:211: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release.
BiopythonExperimentalWarning)
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/parapred-1.0.1-py3.6.egg/parapred/full_seq_processor.py", line 32, in get_CDR_simple
File "/root/.local/lib/python3.6/site-packages/anarci/init.py", line 3, in
from .anarci import *
File "/root/.local/lib/python3.6/site-packages/anarci/anarci.py", line 68, in
from .germlines import all_germlines
ModuleNotFoundError: No module named 'anarci.germlines'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/bin/parapred", line 33, in
sys.exit(load_entry_point('parapred==1.0.1', 'console_scripts', 'parapred')())
File "/usr/local/lib/python3.6/site-packages/parapred-1.0.1-py3.6.egg/parapred/parapred.py", line 227, in main
File "/usr/local/lib/python3.6/site-packages/parapred-1.0.1-py3.6.egg/parapred/parapred.py", line 197, in process_full_VH_VL_sequence
File "/usr/local/lib/python3.6/site-packages/parapred-1.0.1-py3.6.egg/parapred/full_seq_processor.py", line 34, in get_CDR_simple
Exception:
ImportError function get_CDR_simple() requires the python module anarci
Available from http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.php
pip installable version
Hi oxpig team
Is there a pip installable version of anarci? Thanks
"python setup.py install --user" got the "Permission denied: '/usr/bin/ANARCI'" error
Thanks for developing such a great tool for antibody sequencing numbering. Unfortunately, I encountered an issue when I tried to install the latest version.
OS: Rocky Linux 9.1
Python version: 3.9.14
- hmmer-3.3.2 is installed and the directory of the executables is in the
$PATH - cloned the latest code repository (git clone https://github.com/oxpig/ANARCI.git)
- tried to install with the command
python setup.py install --user - got the error
error: [Errno 13] Permission denied: '/usr/bin/ANARCI'
When running python setup.py install with --user or --home="~", the ANARCI_LOC and ANARCI_BIN still follow the global setting:
ANARCI_LOC = /usr/local/lib64/python3.9/site-packages/anarci
ANARCI_BIN = /usr/bin/
To work around the issue, manually specify the ANARCI_LOC and ANARCI_BIN when running python setup.py install --user
ANARCI_LOC = "/home/user/.local/lib/python3.9/site-packages/anarci"
ANARCI_BIN = "/home/user/.local/bin"
From my best understanding, the class CustomInstallCommand may have to check if --user is specified and change the values of ANARCI_LOC and ANARCI_BIN to the user's local setting.
error - undefined variable in anarci.py line 844
A variable named details is used in anarci.py line 844 even though it's previously not defined, creating an error.
Error: unsupported operand type(s) for +: 'NoneType' and 'int'
When I use ANARCI to number antibodies, sometimes this error occurs.
And this error always appears at the end of the program.
What should I do?
Bug in check_for_j function
If hmmer path is not found in environment but a custom hmmer path is given., the check_for_j function will not know that.
def anarci(sequences, scheme="imgt", database="ALL", output=False, outfile=None, csv=False, allow=set(["H","K","L","A","B","G","D"]),
hmmerpath="", ncpu=None, assign_germline=False, allowed_species=None, bit_score_threshold=80):
......
......
### hmmerpath should be given here
check_for_j( sequences, alignments, scheme ,hmmerpath)
Then edit the check_for_j function itself:
def check_for_j( sequences, alignments, scheme , hmmerpath):
.....
.....
# Try to identify a J region in the remaining sequence after the 104. A low bit score threshold is used.
_, re_states, re_details = run_hmmer( [(sequences[i][0], sequences[i][1][cys_si+1:])],
bit_score_threshold=10 ,hmmerpath=hmmerpath)[0]
Incorrect alignment against rhesus_K, forcing to human_K gives correct alignment
I downloaded and installed ANARCI on 15-Nov-2021. Using a 107-residue VL sequence (AIQM...VEIK), it selects rhesus_K and --assign_germline gives |rhesus|IGKV1S1701|0.92|IGKJ101|1.00| with an incorrect alignment. Gaps are at IMGT positions 21, 30-35, 58-64, 74, 82-83, 110-112. The terminal Cys of FW3 is not at position 104, but 105! It appears that the rhesus_K HMM is broken.
Calling ANARCI with --use_species human gives |human|IGKV1-601|0.99|IGKJ101|1.00| with the correct alignment: gaps at 30-35, 58-64, 73, 81-82, 110-113. This corresponds to http://www.imgt.org/IMGTrepertoire/Proteins/alleles/index.php?species=Macaca%20mulatta&group=IGKV&gene=IGKV1S17 .
Is there a place where a tested version of ALL.hmm can be downloaded?
hmmerpath
vi +187 ANARCI
call to run_anarci also needs hmmerpath=args.hmmerpath,
allowed_species/use_species consistency
In the CLI tool, the flag for narrowing down species is --use_spcies=human while in the Python package, the corresponding argument is allowed_species in the run_anarci and anarci functions.
The code also breaks when you specify a species;
ANARCI -i EVQLQQSGAEVVRSGASVKLSCTASGFNIKDYYIHWVKQRPEKGLEWIGWIDPEIGDTEYVPKFQGKATMTADTSSNTAYLQLSSLTSEDTAVYYCNAGHDYDRGRFPYWGQGTLVTVSA --assign_germline --use_species=human | head -n 10
# Input sequence
# ANARCI numbered
# Domain 1 of 1
# Most significant HMM hit
#|species|chain_type|e-value|score|seqstart_index|seqend_index|
#|mouse|H|2e-54|174.1|0|119|
# Most sequence-identical germlines
#|species|v_gene|v_identity|j_gene|j_identity|
#|human|IGHV1-69-2*01|0.65|IGHJ4*01|0.86|
However, this is what I see when I run the Python package
>>> anarci([(1,"EVQLQQSGAEVVRSGASVKLSCTASGFNIKDYYIHWVKQRPEKGLEWIGWIDPEIGDTEYVPKFQGKATMTADTSSNTAYLQLSSLTSEDTAVYYCNAGHDYDRGRFPYWGQGTLVTVSA")], allowed_species='human', assign_germline=True)[1]
# [[{'id': 'mouse_H',
'description': '',
'evalue': 2e-54,
'bitscore': 174.1,
'bias': 0.3,
'query_start': 0,
'query_end': 120,
'species': 'mouse',
'chain_type': 'H',
'scheme': 'imgt',
'query_name': 1,
'germlines': {}}]]
Different Results webapp vs python
Hi, I just installed ANARCI and got it working for the most part. Currently, I am looking at a few single amino acid sequences to validate the results.
First, I add a sequence on into the textfield on http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred/anarci/ , check "restrict to Igs", and click "annotate".
Then, I run the python module to essentially repeat the same annotation:
from anarci import anarci
numbering, _, _ = anarci(
sequences=[('id0', sequence)],
scheme='imgt',
allow=['H'],
assign_germline=True,
allowed_species=['human'])
assert len(numbering) == 1
domain_numbering, start_idx, end_idx = numbering[0][0]
For a sequence from the example file (e.g. sequence = 'EVQLQQSGAEVVRSGASVKLSCTASGFNIKDYYIHWVKQRPEKGLEWIGWIDPEIGDTEYVPKFQGKATMTADTSSNTAYLQLSSLTSEDTAVYYCNAGHDYDRGRFPYWGQGTLVTVSAAKTTPPSVYPLAP') the results are identical. However, if I start adding my own sequences, the results differ.
E.g. with sequence = 'EVQLLESGGGLVQPGGSPRLSCAAFGSTFSSYGMHWVRQAPGKGLEWVAVISYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAMYYCAFGRTVEAEFDY' the domain numbering towards the end of the sequence differes, especially for the CDR3s.
They seem to be truncated or generally a little bit shorter.
If you use the webapp with this sequence you will get species human, domain type H, from indices 0 to 101. The output of the python module has indices 0 to 98. The last 2 amino acids of the sequence in the webapp are R, T with coordinates 117, 118. In the python module they are F, G with coordinates 106, 117.
It seems that the last gap got somehow mixed up.
I checked the CDR lengths of around 1k amino acid sequences and while CDR1s and CDR2s are almost exactly the same, CDR3s are always smaller in the python module compared to the webapp.
Note
When I first tried to install anarci, I ran pip install anarci with an active conda environment. The installation succeeded but running anarci() raised with ..HMMs/ALL.hmm.. not found. So, I uncommented setup.py:23-26 and installed again. Then, it worked.
Can't assign labels while creating an issue
Typo in description
The description of the GitHub repo contains a typo in ClassIfication
valid fasta does not pass
This fasta seems totally valid but I get "Error: Unknown amino acid letter found in sequence: 5, 6, _, 7, 8, 9, 1, U, 3, 0, B, 4, X, O, -, 2, /" , probably it does not separate header and sequence well, check your parser.
S3987Nr1-PBMC_heavy_with_clones_top_100_sequences.fasta.txt
Can you return the sequence's "Gene and allele" like the website of imgt? thank you!
Numbering was found to decrease along the sequence
I get an error that says "numbering was found to decrease along the sequence" when using the command line tool but do not get the same error when i use the same sequence on the python tool. Have you ever seen this issue before/know a solution?
How to identify a nanobody
Hello, all.
I have a question about the usage of ANARCI. Can this tool identify a nanobody by protein sequence?
Clear instructions on how to install on Mac with M1?
Hi, a month ago I managed to install ANARCI on a MacBook Pro M1 (MacOS Monterey) through a dedicated terminal that opens with Rosetta 2.
However, after somehow messing up my conda environment, I decided to start fresh with a new environment and that meant I needed to re-install ANARCI.
Unfortunately, this time it's not possible to work with it.
I reach up to the hmmer installation point (which is the main dependency and is completed with no problems) and then when I install ANARCI from the setup.py (I run python setup.py install) I can't seem to import it from inside a python file (I get an error about architecture and stuff).
However, when I do conda list or pip list, I can see it listed there.
I was wondering if you've tried it and/or if you have any advice on how to do it?
I am afraid I might have done something wrong with the installation of biopython.
Also, which is the most correct way to install it? Is it through pip install anarci, conda install -c bioconda anarci or through the setup.py method?
Many many thanks in advance!
Write warning messages to STDERR
The following warning is written to STDOUT:
ANARCI/lib/python/anarci/anarci.py
Line 346 in c2fd0f7
I suggest writing all warnings/errors to STDERR (seems to be done elsewhere in the project), otherwise there is a risk to jam the output stream, for example, if ANARCI is used in Python scripts that write files to STDOUT.
Inconsistent position IMGT 21 in kappa chain
With the newest version of ANARCI, I'm getting weird behavior in the kappa chain (IGKV2-30*01).
Submitting without J region gives correct numbering:
anarci --scheme imgt -i DVVMTQSPLSLPVTLGQPASISCRSSQSLVYSDGNTYLNWFQQRPGQSPRRLIYKVSNRDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQGT
L 1 D
L 2 V
L 3 V
...
L 19 A
L 20 S
L 21 I <----
L 22 S
L 23 C
...
Submitting with J region produces a gap at position 21:
anarci --scheme imgt -i DVVMTQSPLSLPVTLGQPASISCRSSQSLVYSDGNTYLNWFQQRPGQSPRRLIYKVSNRDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQGTFGQGTKVEIK
L 1 D
L 2 V
L 3 V
...
L 19 A
L 20 S
L 21 - <----
L 22 I
L 23 S
L 24 C
...
Which shifts the whole remainder of the chain after position 21 by one position number.
The invalid letters in input sequence
I have a sequence "EVRLVESGGGLVRPGRSLRLSCAASGFTFSDYNMAWVRQAPKKGLEWVTIISNDDRHAYYRDSVKGRFTISRDNAKSTLFLQLDSLRTEDTAXXYCXXXSXXXGSXXXFDYWGXXVMVTVSA".
The Xs come from the "NNN" in the DNA sequence, since sometimes the sequencing results are not accurate in some positions. What I need is as the website gives:
but what I get from the python version anarci is: "Error: Unknown amino acid letter found in sequence: X".
Is there a way to make things like the results from the website? Thanks for help in advance: )
Installation error
I cloned the repository of ANARCI and tried to install it using python setup.py install --user (I did this after the installation of HMM and biopython). but I got this error:
Would you please help with this?
Thank you very much and really looking forward to hearing from you.
how to identify CDR after numbering sequence
Hi ,all.
Because SCALOP will miss H-CDR3, is there annother tool could identify CDR region? After numbering the antibody sequence, whether it's the right way to extract CDR region according to the position of CDR Definitions ? Any other suggestions would be appreciated.
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.