sidhomj/DeepTCR

Can´t load own Data using DTCR_SS.Get_Data

junyho486 opened this issue · 7 comments

junyho486 commented

TRB.txt
I have TCRseq Data which was annotated by IGB and preprocessed for DeepTCR as indicated in the tutorial.
I have 9 Samples with many TCRs, here is an excerpt of the Data for one Sample:

cdr3_aa	v_call	d_call	j_call	Count
ASSARQDLQQY	TRBV2*01	TRBD1*01	TRBJ2-7*01	39890
ASKDRALLRAV	TRBV21-1*01	TRBD1*01	TRBJ2-7*01	32323
ASSFSATNTGELF	TRBV5-1*01	TRBD2*01	TRBJ2-2*01	26637
ASSPGEQNTGELF	TRBV7-8*01	TRBD2*01	TRBJ2-2*01	26258
ASSGAGTGGYNEQF	TRBV12-3*01	TRBD1*01	TRBJ2-1*01	16692
ASSFSGHTGELF	TRBV7-2*01	TRBD2*01	TRBJ2-2*01	13838
ASSVETGTEKY	TRBV7-9*01	TRBD1*01	TRBJ2-3*01	13831
PPVIWTATSST	TRBV24-1*01	TRBD1*01	TRBJ2-7*01	13819
ASSSGLAGAYEQY	TRBV7-2*02	TRBD2*01	TRBJ2-7*01	13216
ASSFGVSGANVLT	TRBV7-9*03	TRBD2*01	TRBJ2-6*01	11449
ASSGLAGGPGTGELF	TRBV9*01	TRBD2*02	TRBJ2-2*01	11292
ASSPLAGGVAQF	TRBV7-6*01	TRBD2*02	TRBJ2-1*01	11019
ASSSTGQGNSYEQY	TRBV28*01	TRBD1*01	TRBJ2-7*01	10466

If I run the Tutorial using the example Data from the Repository for supervised Sequence Classification, loading Data, cluster etc. works perfectly (except for DTCR_SS.Train() which throws:

[AttributeError: 'DeepTCR_SS' object has no attribute 'test_pred']()

DTCR_SS.Monte_Carlo_CrossVal, DTCR_SS.K_Fold_CrossVal etc. work.

If I then replace the Folders in Data/Murine_Antigens with my Samples, DTCR_SS.Get_Data() which usually takes just a moment to load the data gets stuck (stopped it after 40min).

Even after only using TCRs >= 1000 Reads which results in Tables between 50-80 rows, does not resolve the issue.

import sys
sys.path.append('../../')
from DeepTCR.DeepTCR import DeepTCR_SS

# Instantiate training object
DTCR_SS = DeepTCR_SS('Tutorial')

#Load Data from directories
DTCR_SS.Get_Data(directory='../../Data/TRB',Load_Prev_Data=False,aggregate_by_aa=True,
               aa_column_beta=0,count_column=4,v_beta_column=1,j_beta_column=3)

Output:

Loading Data ...

Is there anything that could cause this kind of Bug?

Attached you will find the data for one Sample for TCR-seqs > 1000 (as .txt file saved .tsv)

Thank you in Advance for your help!

sidhomj commented

that bug should be fixed now in v 2.1.17.

As for the Get_Data method, it takes files that are csv/tsv. just change the extension of the file and it should work.

junyho486 commented

Well, I did a clean install today, like so:

  1. conda create -n DEEPTCR python=3.8.0
  2. conda activate DEEPTCR
  3. pip3 install DeepTCR // pip3 install git+https://github.com/sidhomj/DeepTCR.git -> same bug
  4. conda install ipykernel
  5. ipykernel install --user DEEPTCR

The Files do have .tsv format, I just changed to .txt for uploading them on github.

sidhomj commented

Sorry. are both bugs still there? or just the latter?

junyho486 commented

Thank you for the quick response!

I installed DeepTCR several times today trying to find the bug. Currently I am running the stable installation and see both bugs.

junyho486 commented

Edit: I reinstalled into a new env using pip3 install git+https://github.com/sidhomj/DeepTCR.git and the first bug seems to be resolved, but the second one persists.

sidhomj commented

second bug fixed. it was an issue with the expected order of columns in the files. I fixed the loading function so the order does not matter anymore. let me know if it works now!

junyho486 commented

Thank you so much! I was struggling with this one all day...
Now both issues are resolved for the unsupervised and supervised model!

Ps: Also congrats for creating DeepTCR it is a very impressive tool!