Hi everyone,
I am currently testing the published HEV 400 bp v1.0.0 scheme from the primer schemes repository and wanted to try using repair-mode on it, to adapt for my samples.
For this purpose I tried using the following command
primalscheme3 repair-mode
--bedfile primer.bed
--msa reference.msa
--config info.json
--output output_dir
(I am using PrimalScheme3 version: 3.2.0 at the moment.)
However, I get the following error:
KeyError: 'msa_data'
It looks like repair-mode expects a config.json containing an msa_data field, whereas the published scheme only contains an info.json.
Is repair-mode intended to work with published schemes from the primer schemes repository? If so, is there a way I could obtain the original config.json (or another compatible configuration file) for the HEV 400 bp v1.0.0 scheme?
For the msa I am using the reference.fasta and aligned it the sequence of the samples I want it adapt to. As I understood, I would't need the original msa that was used for the creation of the scheme?
Thanks very much!
Mona
Hi everyone,
I am currently testing the published HEV 400 bp v1.0.0 scheme from the primer schemes repository and wanted to try using repair-mode on it, to adapt for my samples.
For this purpose I tried using the following command
primalscheme3 repair-mode
--bedfile primer.bed
--msa reference.msa
--config info.json
--output output_dir
(I am using PrimalScheme3 version: 3.2.0 at the moment.)
However, I get the following error:
KeyError: 'msa_data'
It looks like repair-mode expects a config.json containing an msa_data field, whereas the published scheme only contains an info.json.
Is repair-mode intended to work with published schemes from the primer schemes repository? If so, is there a way I could obtain the original config.json (or another compatible configuration file) for the HEV 400 bp v1.0.0 scheme?
For the msa I am using the reference.fasta and aligned it the sequence of the samples I want it adapt to. As I understood, I would't need the original msa that was used for the creation of the scheme?
Thanks very much!
Mona