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s175573 / GIANA

Ultrafast TCR clustering algorithm based on geometric isometry
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query mode error #1

Closed alxndravc closed 2 years ago

alxndravc commented 2 years ago

Hi,

I was trying to run Giana in query mode but I keep hitting an error.

All files are in the same directory. The ref and test files both only have 1 column (=CDR3).

  1. reference file: no-dups.txt
  2. clustered reference file: no-dups--RotationEncodingBL62.txt
  3. test file: 001-giana.txt
  4. clustered test file: 001-giana--RotationEncodingBL62.txt

Command used: python GIANA4.1.py -q 001-giana.txt -r no-dups.txt -S 3.3

Error: Traceback (most recent call last): File "/Tools/GIANA/data/data2/GIANA4.py", line 1205, in <module> main() File "//Tools/GIANA/data/data2/GIANA4.py", line 1132, in main rData=CreateReference(rFile) File "/Tools/GIANA/data/data2/query.py", line 35, in CreateReference vgs.append(ww[1]) IndexError: list index out of range Could you please help me?

Many thanks! :)

s175573 commented 2 years ago

Query mode is required to have variable gene input. You can make a second column with identical V genes.

Thanks, Bo

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From: alxndravc @.> Sent: Saturday, February 19, 2022 10:45:34 AM To: s175573/GIANA @.> Cc: Subscribed @.***> Subject: [s175573/GIANA] query mode error (Issue #1)

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Hi,

I was trying to run Giana in query mode but I keep hitting an error.

All files are in the same directory. The ref and test files both only have 1 column (=CDR3).

  1. reference file: no-dups.txt
  2. clustered reference file: no-dups--RotationEncodingBL62.txt
  3. test file: 001-giana.txt
  4. clustered test file: 001-giana--RotationEncodingBL62.txt

Command used: python GIANA4.py -q 001-giana.txt -r no-dups.txt -S 3.3

Error:

Traceback (most recent call last): File "/Tools/GIANA/data/data2/GIANA4.py", line 1205, in main() File "//Tools/GIANA/data/data2/GIANA4.py", line 1132, in main rData=CreateReference(rFile) File "/Tools/GIANA/data/data2/query.py", line 35, in CreateReference vgs.append(ww[1]) IndexError: list index out of range

Could you please help me?

Many thanks! :)

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