Extra ; in barcode_report.tsv

[ktpolanski]

Hello, I've fed another new type of data through TRUST4 to reconstruct contigs from it. While doing so, I encountered an error when trying to run barcoderep-expand.py (technically my modification of it, but the issue still holds when doing --chain 2 with the original code from the repository). Inspecting the file reveals the following problem line, formatted as a minimal working example.

#barcode	cell_type	chain1	chain2	secondary_chain1	secondary_chain2
AGCGTCCTTGAAAG	B	*	IGKV1-39*01,*,IGKJ4*01,IGKC,TGTCAACAGAGTTACACTATCCCTCTCACTTTC,CQQSYTIPLTF,12.00,AGCGTCCTTGAAAG_336,93.75,0	*	IGLV2-14*01,*,IGLJ1*01,IGLC1,TGCAGCTCATATACAAGCAGCAGCACTCTCGGTGTCTTC,CSSYTSSSTLGVF,8.00,AGCGTCCTTGAAAG_71120,100.00,0;

Trying to feed this into the barcode expansion script treats the ; at the end as a delimiter indicating another secondary chain, and then fails at processing it as there's nothing there to process:

$ python3 /mnt/TRUST4/scripts/barcoderep-expand.py -b test.tsv --chain 2 > test_chain2.tsv
Traceback (most recent call last):
  File "/mnt/TRUST4/scripts/barcoderep-expand.py", line 86, in <module>
    abund = float(subCols[6])
IndexError: list index out of range

I haven't seen this before, do you have any idea what would cause the extra ; to appear here? Dealing with it has the file process without issue.

[mourisl]

Thank you for identifying the bug. I have uploaded a new trust-barcoderep.pl script to the github repo. Could you please pull the new version and rerun TRUST4 with the additional command --stage 3 (only regenerating the report files based on previous intermediate files if you want to save some time)? Thank you.

[ktpolanski]

Yep, ran like a charm now! Thanks a lot!