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Teichlab / cell2tcr

Inference of TCR motifs
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Input format #4

Open ainarill opened 3 weeks ago

ainarill commented 3 weeks ago

Hi! nice tool! I am struggling to run the pipeline. Could you explain a little bit more what is the format that you need in order to run your code? How can we bridge exactly the data format from scirpy to your input object?

lisadratva commented 1 week ago

Hi @ainarill ,

Thanks for your comment! Your data has to be a pandas dataframe. If your columns don't have the typical scirpy names, you can rename them as shown in the tutorial and written out again here:

# format to match Scirpy
for i, j in zip(
    ['individual', 'IR_VDJ_1_junction_aa','IR_VDJ_1_v_call','IR_VDJ_1_j_call','IR_VJ_1_junction_aa','IR_VJ_1_v_call','IR_VJ_1_j_call'], # Scirpy format - leave unchanged
    ['your_patient_id', 'your_tcr_b_aa','your_tcr_b_v','your_tcr_b_j','your_tcr_a_aa','your_tcr_a_v','your_tcr_a_j']): # your format - modify to match your column names
    df.loc[:,i] = df.loc[:,j].copy()

Simply replace 'your_XXX' with your column names. Hope this helps!