CODEWITHSUNDEEP
biopython
Kaumz
Kaumz

Reputation: 51

Biopython SeqIO error: local variable 'qual' referenced before assignment

I send some samples for Sanger sequencing to a commercial facility. I'm able to read the files they send using the command

from Bio import SeqIO
from Bio import Seq
rec = SeqIO.read("isolation-round4/3dr23_Forward.ab1",'abi-trim').seq

But recently, due to a move, we had to send the samples elsewhere for sequencing. Now, if I try to run the same command on the output I get an error:

UnboundLocalError: local variable 'qual' referenced before assignment in File "C:\Users\Anaconda3\lib\site-packages\Bio\SeqIO\AbiIO.py", line 462, in AbiIterator letter_annotations={"phred_quality": qual}

I would appreciate any help in dealing with this. Here are two files, one that works and one that does not, if you would like to have a look.

Thanks in advance for your help!

Upvotes: 0

Views: 47

Answers (1)

Peter Cock
Peter Cock

Reputation: 1614

Bug should have already been fixed in Biopython 1.77

Update: See https://github.com/biopython/biopython/issues/3221 - turned out to be a new unexpected configuration of the ABI software producing files with no quality scores.

Upvotes: 1

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