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Runsheng / primervcf

primderdiffer submodule: primervcf
GNU General Public License v2.0
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Function deprecated please use "design_primers" instead #3

Closed Him22 closed 1 year ago

Him22 commented 1 year ago

Dear Runsheng

I am facing the following issue in running the primervcf

primerdesign_vcf.py -g cb5.fa -b QR25_del.bed --prefix QR25 mambaforge/lib/python3.10/site-packages/primer3/bindings.py:580: UserWarning: Function deprecated please use "design_primers" instead warnings.warn('Function deprecated please use "design_primers" instead') Traceback (most recent call last): File "mambaforge/bin/primerdesign_vcf.py", line 76, in flow_walk_deletion( File "mambaforge/lib/python3.10/site-packages/primervcf/primer_indel.py", line 141, in flow_walk_deletion primer_status = del_primer_check(del_single, db, ref_dict, File "mambaforge/lib/python3.10/site-packages/primervcf/primer_indel.py", line 101, in del_primer_check product_l = insilicon_pcr(left, right, db) File "mambaforge/lib/python3.10/site-packages/primerdiffer/primer_check.py", line 78, in insilicon_pcr blast_records_left = primer_blast(primer_left, db) File "mambaforge/lib/python3.10/site-packages/primerdiffer/primer_check.py", line 39, in primer_blast out, err = blastn_cline(stdin=query) File "mambaforge/lib/python3.10/site-packages/Bio/Application/init.py", line 574, in call raise ApplicationError(return_code, str(self), stdout_str, stderr_str) Bio.Application.ApplicationError: Non-zero return code 2 from 'blastn -outfmt 5 -db cb5.fa -task blastn-short', message 'BLAST Database error: No alias or index file found for nucleotide database [cb5.fa] in search path [softwares/primervcf-0.1.0:::]'

Please help to resolve the issue Thank you Himanshu

Runsheng commented 1 year ago

Hi Himanshu,

Thank you for reporting the issue. There are too separate messages in your log.

  1. The "UserWarning: Function deprecated please use "design_primers" instead" should not affect your run result. The warning comes from primer3-py package, the new binding is design_primers instead of designPrimers, however, I need to keep it as it is to maintain the support for py38 and py39.
  2. The blast issue means the makeblastdb function did not run properly in your environment. I have added a double-check command in the new primervcf version (0.1.4). The issue should have been fixed.

You can use pip install primervcf to update the module to 0.1.4. Or you can use the github repo for updates.

Best regards, Runsheng

Him22 commented 1 year ago

Hi Runsheng,

Thank you for you response, The problem was due to the python version installed in my system, I switched to py39 and it worked.

Best regards, Himanshu