KeyError: 'pmhc_a_aa'

[Tianran1]

Hi, I am new to tcrdist. When I want to compute the distance between two sets using "compute_rect_distances", it always gives me the KeyError: 'pmhc_a_aa'. Does anyone know how to fix it? Thanks

[kmayerb]

can you provide the code you used to generate this error?

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On Tue, Oct 11, 2022 at 12:30 AM Tianran1 ***@***.***> wrote: Hi, I am new to tcrdist. When I want to compute the distance between two sets using "compute_rect_distances", it always gives me the KeyError: 'pmhc_a_aa'. Does anyone know how to fix it? Thanks — Reply to this email directly, view it on GitHub <#76>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALD2PVYC662UGTCOHTTRSMTWCUJRDANCNFSM6AAAAAARB7Q4UY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Tianran1]

Hi, I just used the example code from your pipeline.

"""
import pandas as pd
from tcrdist.repertoire import TCRrep

df = pd.read_csv("dash.csv")
df2 = pd.read_csv("dash2.csv")
df = df.head(10) #(1)
tr = TCRrep(cell_df = df, #(2)
df2 = df2,
organism = 'mouse',
chains = ['alpha','beta'],
db_file = 'alphabeta_gammadelta_db.tsv')

assert tr.pw_alpha.shape == (10,10)
assert tr.pw_beta.shape == (10,10)

tr.compute_rect_distances() # (3)
assert tr.rw_alpha.shape == (10,1924)
assert tr.rw_beta.shape == (10,1924)

df3 = df2.head(100)

tr.compute_rect_distances(df = tr.clone_df, df2 = df3) # (4)
assert tr.rw_alpha.shape == (10,100)
assert tr.rw_beta.shape == (10,100)

tr.compute_rect_distances( df = tr.clone_df.iloc[0:2,], # (5)
df2 = df3)
assert tr.rw_alpha.shape == (2,100)
assert tr.rw_beta.shape == (2,100)
"""

I only changed the df2 to be df as well because I cannot find the dash2.csv.
Could you have a look?
Many thanks.

[kmayerb]

TCRrep has no argument df2. what you want is something like this: """ df = pd.read_csv("dash.csv").head(10) df2 = pd.read_csv("dash.csv") tr = TCRrep(cell_df = df, organism = 'mouse', chains = ['alpha','beta'], compute_distances = False) tr2 = TCRrep(cell_df = df2, organism = 'mouse', chains = ['alpha','beta'], compute_distances = False) tr.compute_rect_distances( df = tr.clone_df, df2 = tr2.clone_df) """ Does this help?

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On Tue, Oct 11, 2022 at 11:16 AM Tianran1 ***@***.***> wrote: Hi, I just used the example code from your pipeline. """ import pandas as pd from tcrdist.repertoire import TCRrep df = pd.read_csv("dash.csv") df2 = pd.read_csv("dash2.csv") df = df.head(10) #(1) tr = TCRrep(cell_df = df, #(2) df2 = df2, organism = 'mouse', chains = ['alpha','beta'], db_file = 'alphabeta_gammadelta_db.tsv') assert tr.pw_alpha.shape == (10,10) assert tr.pw_beta.shape == (10,10) tr.compute_rect_distances() # (3) assert tr.rw_alpha.shape == (10,1924) assert tr.rw_beta.shape == (10,1924) df3 = df2.head(100) tr.compute_rect_distances(df = tr.clone_df, df2 = df3) # (4) assert tr.rw_alpha.shape == (10,100) assert tr.rw_beta.shape == (10,100) tr.compute_rect_distances( df = tr.clone_df.iloc[0:2,], # (5) df2 = df3) assert tr.rw_alpha.shape == (2,100) assert tr.rw_beta.shape == (2,100) """ I only changed the df2 to be df as well because I cannot find the dash2.csv. Could you have a look? Many thanks. — Reply to this email directly, view it on GitHub <#76 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALD2PV7XRSOZIBOLYIRG3HTWCWVGDANCNFSM6AAAAAARB7Q4UY> . You are receiving this because you commented.Message ID: ***@***.***>

[Tianran1]

Hi, thanks very much. Now it works. Then maybe you need to change the pipeline example since it's not correct.

[kmayerb]

thanks can you send me the link to the example you were initially using.

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On Tue, Oct 11, 2022 at 11:56 PM Tianran1 ***@***.***> wrote: Hi, thanks very much. Now it works. Then maybe you need to change the pipeline example since it's not correct. — Reply to this email directly, view it on GitHub <#76 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALD2PV453RWV2Z3TYZHH22DWCZOK3ANCNFSM6AAAAAARB7Q4UY> . You are receiving this because you commented.Message ID: ***@***.***>

[kmayerb]

will change this: https://tcrdist3.readthedocs.io/en/latest/tcrdistances.html#i-want-distances-from-1-tcr-to-many-tcrs

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On Wed, Oct 12, 2022 at 2:09 PM tcrdist 3 ***@***.***> wrote: thanks can you send me the link to the example you were initially using. On Tue, Oct 11, 2022 at 11:56 PM Tianran1 ***@***.***> wrote: > Hi, thanks very much. Now it works. Then maybe you need to change the > pipeline example since it's not correct. > > — > Reply to this email directly, view it on GitHub > <#76 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ALD2PV453RWV2Z3TYZHH22DWCZOK3ANCNFSM6AAAAAARB7Q4UY> > . > You are receiving this because you commented.Message ID: > ***@***.***> >

[kmayerb]

I think the test works because dash2.csv already has precomputed the other CDR columns, I agree this is a confusing example. Thanks for bringing it to my attention. https://github.com/kmayerb/tcrdist3/blob/master/dash2.csv

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On Wed, Oct 12, 2022 at 2:11 PM tcrdist 3 ***@***.***> wrote: will change this: https://tcrdist3.readthedocs.io/en/latest/tcrdistances.html#i-want-distances-from-1-tcr-to-many-tcrs On Wed, Oct 12, 2022 at 2:09 PM tcrdist 3 ***@***.***> wrote: > thanks can you send me the link to the example you were initially using. > > > On Tue, Oct 11, 2022 at 11:56 PM Tianran1 ***@***.***> > wrote: > >> Hi, thanks very much. Now it works. Then maybe you need to change the >> pipeline example since it's not correct. >> >> — >> Reply to this email directly, view it on GitHub >> <#76 (comment)>, >> or unsubscribe >> <https://github.com/notifications/unsubscribe-auth/ALD2PV453RWV2Z3TYZHH22DWCZOK3ANCNFSM6AAAAAARB7Q4UY> >> . >> You are receiving this because you commented.Message ID: >> ***@***.***> >> >