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Runsheng / primervcf

primderdiffer submodule: primervcf
GNU General Public License v2.0
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LENGTH cutoff for the minimum length of a deletion is giving error #4

Closed Him22 closed 1 year ago

Him22 commented 1 year ago

Hi Runsheng,

Using the LENGTH (-l) cutoff option for the minimum length of a deletion to be selected for primer design is giving following error, without giving --length (-l) option it is working fine I want to design the primers for regions having deletion of >= 20 nt.

vcf2del.py -f QR25.vcf -o QR25_del.bed -l 20 Traceback (most recent call last): File "mambaforge/envs/py39/bin/vcf2del.py", line 29, in bed_l=get_deletion_region(args.file, key="del", len_cutoff=args.length) File "mambaforge/envs/py39/lib/python3.9/site-packages/primervcf/vcfparser.py", line 92, in get_deletion_region if del_len>=len_cutoff and "n" not in record.REF: # no gap in the reference TypeError: '>=' not supported between instances of 'int' and 'str'

please help to resolve this issue. Best regards Himanshu

Runsheng commented 1 year ago

Sorry for the old bug. Should have been fixed in the github repo.

Would you please help to test the new fix with github install using the following code?

git clone https://github.com/Runsheng/primervcf.git
cd primervcf
pip install .

Best regards, Runsheng

Runsheng commented 1 year ago

close with 0.1.5 in pip