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kmayerb / tcrdist3

flexible CDR based distance metrics
MIT License
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issue with running Radius #78

Open QianhuiXu opened 1 year ago

QianhuiXu commented 1 year ago

Hello,

tcrdist3 is a wonderful tool！ I ran into an issue with running Radius with my own data.

My command : tr.clone_df['neighbors'] = _neighbors_variable_radius( pwmat = tr.pw_beta, radius_list = tr.clone_df['radius'])

Error: AttributeError Traceback (most recent call last) Cell In [17], line 7 3 tr.clone_df['radius'][tr.clone_df['radius'] > 26] = 26 4 # Tabulate index of neighboring clones in the ANTIGEN ENRICHED REPERTOIRE, 5 # at each TCR-specific radius
6 tr.clone_df['neighbors'] = _neighbors_variable_radius( ----> 7 pwmat = tr.pw_beta, 8 radius_list = tr.clone_df['radius']) 9 # Tabulate neighboring sequences in background 10 tr.clone_df['background_neighbors'] = _neighbors_sparse_variable_radius( 11 csrmat = tr.rw_beta, 12 radius_list = tr.clone_df['radius'])

AttributeError: 'TCRrep' object has no attribute 'pw_beta'

I'm really at a loss as to how to proceed, and any guidance would be much appreciated! Thank you for your kind help!

kmayerb commented 1 year ago

Please provide the full code block you were trying to run so I can help you diagnose the problem. Best, K

On Thu, Oct 20, 2022 at 2:32 AM QianhuiXu @.***> wrote:

Hello,

tcrdist3 is a wonderful tool！ I ran into an issue with running Radius with my own data.

My command : tr.clone_df['neighbors'] = _neighbors_variable_radius( pwmat = tr.pw_beta, radius_list = tr.clone_df['radius'])

Error: AttributeError Traceback (most recent call last) Cell In [17], line 7 3 tr.clone_df['radius'][tr.clone_df['radius'] > 26] = 26 4 # Tabulate index of neighboring clones in the ANTIGEN ENRICHED REPERTOIRE, 5 # at each TCR-specific radius 6 tr.clone_df['neighbors'] = _neighbors_variable_radius( ----> 7 pwmat = tr.pw_beta, 8 radius_list = tr.clone_df['radius']) 9 # Tabulate neighboring sequences in background 10 tr.clone_df['background_neighbors'] = _neighbors_sparse_variable_radius( 11 csrmat = tr.rw_beta, 12 radius_list = tr.clone_df['radius'])

AttributeError: 'TCRrep' object has no attribute 'pw_beta'

I'm really at a loss as to how to proceed, and any guidance would be much appreciated! Thank you for your kind help!

— Reply to this email directly, view it on GitHub https://github.com/kmayerb/tcrdist3/issues/78, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALD2PV4CDAEW6CJ6QPG2S43WEEGSBANCNFSM6AAAAAARJ6NAXU . You are receiving this because you are subscribed to this thread.Message ID: @.***>

QianhuiXu commented 1 year ago

Thank you for your help! Could please you tell me about your email address? I would send the full code and input data to you. Thank you very much!

kmayerb commented 1 year ago

Please provide the code snippet in the github issue or a link to download it. Thanks, Kind regards.

On Sun, Oct 23, 2022 at 4:57 AM QianhuiXu @.***> wrote:

Thank you for your help! Could please you tell me about your email address? I would send the full code and input data to you. Thank you very much!

— Reply to this email directly, view it on GitHub https://github.com/kmayerb/tcrdist3/issues/78#issuecomment-1288095672, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALD2PVY5Z4DRZ7DX7KPVBD3WEUR35ANCNFSM6AAAAAARJ6NAXU . You are receiving this because you commented.Message ID: @.***>