Comments (5)
zktuong
commented on August 15, 2024
Hi Sara, yes sorry i need to update the documentation.
The behaviour is as before in that a_b_c refers to the heavy chain and d_e_f refers the light chain for (V_J gene pairing, CDR3 length, and sequence similarity respectively) but the last update #124 made it easier to extract the light chain numbering assignments.
hmm but you have raised a possible bug. I thought i had add in a full_pairing_label option to the call to revert the clone id definitions to the original 4 part definition but looks like this isn't working as intended if you are getting the 6 part clone ids with a normal run.
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saramoein372
commented on August 15, 2024
Hi,
Thank you so much. I am using the same code I was using before. How I
should change the command to get the four label ID?
Thanks,
Sara
…On Tue, Feb 8, 2022, 4:53 PM Zewen Kelvin Tuong ***@***.***> wrote:
Hi Sara, yes sorry i need to update the documentation.
The behaviour is as before in that a_b_c refers to the heavy chain and
d_e_f refers the light chain for (V_J gene pairing, CDR3 length, and
sequence similarity respectively) but the last update #124
<#124> made it easier to extract
the light chain numbering assignments.
hmm but you have raised a possible bug. I thought i had add in a
full_pairing_label option to the call to revert the clone id definitions
to the original 4 part definition but looks like this isn't working as
intended if you are getting the 6 part clone ids with a normal run.
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zktuong
commented on August 15, 2024
Hi Sara,
If you run it as ddl.tl.find_clones(vdj, full_pairing_label = True), it should revert back to the 4-part id.
I named this new option wrongly but it's working as intended (to toggle between the 6-part vs 4-part ids). I will mostly likely rename the option to something more sensible in a future update.
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saramoein372
commented on August 15, 2024
Thank you!
Sara
…On Tue, Feb 8, 2022, 6:56 PM Zewen Kelvin Tuong ***@***.***> wrote:
Hi Sara,
If you run it as ddl.tl.find_clones(vdj, full_pairing_label = True), it
should revert back to the 4-part id.
I named this new option wrongly but it's working as intended (to toggle
between the 6-part vs 4-part ids). I will mostly likely rename the option
to something more sensisble in a future update.
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zktuong
commented on August 15, 2024
the option has been renamed from full_pairing_label to collapse_label in v0.2.0
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Related Issues (20)
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