metagenlab / updated_simulate_pcr Goto Github PK

Hello there,
I'm trying to run the script with the example given but the code is not running. I'm trying to run it in powershell, I've already installed all the packages required, and still the code just doesn't run. I even tried using a tracer to see the executed lines but there are none, meaning the code isn't even trying to run.
What could be happening or what could I do?

Dear developers,
simulate_PCR works ok wit ATCG bases with the 2019 change to the code.

Unfortunately, i'm struggling to have it working with IUPAC bases. If i use any Primer with IUPAC bases (N, R, Y or such) it outputs 0 amplicons.

Thanks you so much for your help!

Christian Milani, Ph.D.
Associate Professor of Microbiology
Department of Chemistry, Life Sciences and Environmental Sustainability
Parco Area delle Scienze 11/A
University of Parma
43124 Parma
Italy
Tel. +39 (0)521 904785
Fax +39 (0)521 906014
Probiogenomics lab (website)
GenProbio s.r.l. (website)
Email Probiogenomics lab: [email protected]

When having only 1 sequence in query database, blastdbcmd executed by simulte_PCR will look as follow and raise an error since it doesn't accept zero (tested with blast versions 2.2.31, 2.6.0 and 2.9.0).

blastdbcmd -db myfasta.faa -dbtype nucl -outfmt '%s' -entry "gnl|BL_ORD_ID|0" -range 5930607-5931046

Error: NCBI C++ Exception:
T0 "/anaconda/conda-bld/work/ncbi-blast-2.2.31+-src/c++/src/objects/general/Object_id_.cpp", line 96: Error: CObject_id::GetId(): Invalid choice selection: NCBI-General::Object-id.str