Unable to run query on input file

[CSree]

Hi Dr. Bo,
This is Chai, firstly thanks for the GIANA tool , its actually a fascinating idea to use the body’s immune response as a diagnostic tool.

I am writing to request help in querying my set of sequences against a reference . I have attached a section of the input file, this was successfully clustered by the clustering command. Next, I tried to query against the reference provided with the tool, as below. Before this, I clustered hc10s10.txt, and put that rotation file in the same dir, as mentioned on the github page.

python GIANA4.py -q input_giana.tsv -r hc10s10.txt -S 3.3 -o tmp/

Here is the error I got:

Processing tmp_query.txt
Total time elapsed: 0.290075
Maximum memory usage: 0.196432 MB
Build query clustering file. Elapsed 18.401398
Now mering with reference cluster
Traceback (most recent call last):
File "GIANA4.py", line 1207, in
main()
File "GIANA4.py", line 1151, in main
MergeExist(refClusterFile, OutDir+'/'+outFile)
File "/gpfs/scratch/cs5359/Projects/Weberlab_GIANA/GIANA/query.py", line 173, in MergeExist
queryT=pd.read_table(queryClusterFile, skiprows=2, delimiter='\t', header=None)
File "/gpfs/home/cs5359/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1242, in read_table
return _read(filepath_or_buffer, kwds)
File "/gpfs/home/cs5359/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 583, in _read
return parser.read(nrows)
File "/gpfs/home/cs5359/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1704, in read
) = self._engine.read( # type: ignore[attr-defined]
File "/gpfs/home/cs5359/.local/lib/python3.8/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read
chunks = self._reader.read_low_memory(nrows)
File "pandas/_libs/parsers.pyx", line 814, in pandas._libs.parsers.TextReader.read_low_memory
File "pandas/_libs/parsers.pyx", line 875, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 850, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._check_tokenize_status
File "pandas/_libs/parsers.pyx", line 2029, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 4 fields in line 4879, saw 7

I checked both the files, there is nothing different on line 4879. I noticed that the input file input_giana.xlsx on github: TestReal-ADIRP0000023_TCRB.tsv, has 3 additional cols along with the cdr3 and gene info. These 3 cols are frequencyCount, RANK, and info. Are these mandoatory and how do I create these cols for my data?

Thanks in advance
Chai Sree

[s175573]

Yes, please stick to the input format of the example file. Sorry that GIANA query doesn't allow flexible input format.

[LilianaLucca]

Dear GIANA team,

I am also running into errors that I assume to be related to the input format when running GIANA in query mode.
I can run the example query and reference fine, but I get the following error when using my own data:

GIANA: Geometric Isometry based ANtigen-specific tcr Alignment
Ultrafast short peptide alignment exclusively designed for large-scale adaptome analysis

Input columns:

1. CDR3 amino acid sequence (Starting from C, ending with the first F/L in motif [FL]G.G)
2. Variable gene name in Imgt format: TRBVXX-XX*XX
3. Joining gene name (optional)
4. Frequency (optional)
5. Other information (optional)

!!! ALL amino acid letters must be CAPITAL !!!

Reference created. Elapsed 2.678218
Querying Resistec_TcRs_query.txt
Traceback (most recent call last):
File "/Users/liliana.lucca/Python/GIANA.py", line 1257, in
main()
File "/Users/liliana.lucca/Python/GIANA.py", line 1197, in main
MakeQuery(qf, rData, thr=cutoff, thr_s=thr_s)
File "/Users/liliana.lucca/Python/query.py", line 114, in MakeQuery
vss_r=SDu_r[kk]
~~~~~^^^^
KeyError: 22

I tried to rename the reference and query columns to match the example data, namely aminoAcid, vMaxResolved, frequencyCount...., RANK, Info, but to no avail.
Would it be possible to better explain what is the format that query.py expects, since you previously said that it's not flexible?

Thank you very much!

Liliana

[s175573]

It appears that your query file contains CDR3s that are too long and not included in the reference data. You can either remove them (length >=22), or include more TCRs in the reference. Thanks, Bo

…

________________________________ From: LilianaLucca ***@***.***> Sent: Wednesday, January 29, 2025 6:07 AM To: s175573/GIANA ***@***.***> Cc: Li, Bo ***@***.***>; Comment ***@***.***> Subject: [External]Re: [s175573/GIANA] Unable to run query on input file (Issue #11) Dear GIANA team, I am also running into errors that I assume to be related to the input format when running GIANA in query mode. I can run the example query and reference fine, but I get the following error when using my own data: GIANA: Geometric Isometry based ANtigen-specific tcr Alignment Ultrafast short peptide alignment exclusively designed for large-scale adaptome analysis Input columns: 1. CDR3 amino acid sequence (Starting from C, ending with the first F/L in motif [FL]G.G) 2. Variable gene name in Imgt format: TRBVXX-XX*XX 3. Joining gene name (optional) 4. Frequency (optional) 5. Other information (optional) !!! ALL amino acid letters must be CAPITAL !!! Reference created. Elapsed 2.678218 Querying Resistec_TcRs_query.txt Traceback (most recent call last): File "/Users/liliana.lucca/Python/GIANA.py", line 1257, in main() File "/Users/liliana.lucca/Python/GIANA.py", line 1197, in main MakeQuery(qf, rData, thr=cutoff, thr_s=thr_s) File "/Users/liliana.lucca/Python/query.py", line 114, in MakeQuery vss_r=SDu_r[kk] ~~~~~^^^^ KeyError: 22 I tried to rename the reference and query columns to match the example data, namely aminoAcid, vMaxResolved, frequencyCount...., RANK, Info, but to no avail. Would it be possible to better explain what is the format that query.py expects, since you previously said that it's not flexible? Thank you very much! Liliana — Reply to this email directly, view it on GitHub<#11 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKWYQCYP5T3TDM27UQLR3UT2NCY6XAVCNFSM6AAAAABWCSMPBSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRRGMZTKMZVHE>. You are receiving this because you commented.Message ID: ***@***.***> ** This email originated from an EXTERNAL sender to CHOP. Proceed with caution when replying, opening attachments, or clicking links. Do not disclose your CHOP credentials, employee information, or protected health information to a potential hacker**.