Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

unsupported operand type(s) for +=: 'int' and 'NoneType' in 2024 #73

Open
Ohmori-Insilico opened this issue Apr 1, 2024 · 0 comments
Open

Comments

@Ohmori-Insilico
Copy link

We are having this problem using the SAM file to identify the off-target with Py3.

(base) user@ohmori-lab-ubuntu:~/Desktop/Guideseq 2024/guideseq/guideseq$ guideseq.py identify \

--aligned Data/aligned/VEGFA1_Tsai.sam
--genome Homo_sapiens_GRCh38ssembly.fa
--outfolder "/home/user/Desktop/Guideseq 2024/guideseq/guideseq/output"
--target_sequence GGGTGGGGGGAGTTTGCTCCNGG
--description "VEGFA1_site1"
[04/02 07:46:48AM][INFO][guideseq] Identifying offtarget sites...
[04/02 07:46:48AM][INFO][identifyOfftargetSites] Processing SAM file /home/user/Desktop/Guideseq 2024/guideseq/guideseq/output/aligned/VEGFA1_Tsai.sam
[04/02 07:47:01AM][ERROR][guideseq] Error identifying offtarget sites.
[04/02 07:47:01AM][ERROR][guideseq] Traceback (most recent call last):
File "/home/user/miniconda3/bin/guideseq.py", line 239, in identifyOfftargetSites
identifyOfftargetSites.analyze(samfile, self.reference_genome, self.identified[sample], annotations,
File "/home/user/miniconda3/bin/identifyOfftargetSites.py", line 314, in analyze
chromosome_position.addPositionBarcode(chromosome, read_position, strand, barcode, primer, count)
File "/home/user/miniconda3/bin/identifyOfftargetSites.py", line 60, in addPositionBarcode
self.chromosome_barcode_dict[chromosome][position][strand][barcode] += count
TypeError: unsupported operand type(s) for +=: 'int' and 'NoneType'

Samfile size: 7GB.
I used UMI, consolidation and aligned data. But problem is still persisted.
Test with EMX1 data from Guideseq insruction, it is working.
Is file size matter ?

Is there any solution to complete this task ?

Thanks a lot.

Neme.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant