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aakechin / NGS-PrimerPlex

NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design
GNU General Public License v3.0
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RUN test.py fail #59

Open zoe1122824 opened 11 months ago

zoe1122824 commented 11 months ago

I installed and ran it using Docker, but when running test.py, it seems to be stuck. I think there should be nine steps, right? Also, I tried running the getGeneRegionS.py , but it also gets stuck.

thank you!

`` Screenshot from 2023-11-24 17-42-00 Screenshot from 2023-11-24 17-42-17

aakechin commented 11 months ago

@zoe1122824 Thank you for the question. The NGS-PrimerPlex output may be different sometimes due to the use of primer3 module. Now, we're working on removing this module from NGS-PrimerPlex, and then it will be much simpler to perform NGS-PrimerPlex tests. So, I recommend you to ignore this test. Considering the 2nd question, it is a normal problem for genes which have many synonyms. And many different human genome genes have the same synonyms. And APC is one of such genes. So, you need to open chr2.gb and chr5.gb and search there for the "APC" gene (see screenshots). We can see that chr2 contains APC gene, which is synonym to "PROC" gene. But chr5 contains APC gene which is the main name fot the gene. So, you need to rename this gene in such a way that it will be unambiguously interpreted by the program, e.g., BTPS2. APC_gene_for_GitHub_Issue

zoe1122824 commented 11 months ago

I appreciate your response. However, regarding the second question, I'm not entirely clear on your meaning. Could you please specify how to modify gene names? Do you mean to change the gene name by modifying the APC gene to BTPS2 in the chr5.gb file? Thank you

aakechin commented 11 months ago

@zoe1122824 You need to replace APC with BTPS2 in the example_gene_list_file.txt.

zoe1122824 commented 11 months ago

@aakechin Thank you very much. It can run now.