Good day house.
Please I need to use command line (like wget, ) to retrieve nucleotide/amino acid sequences of giardia Thioredoxin reductase from databases like NCBI GenBank, eupathdb and Ensembl.
The method I know (seqinr) requires me entering the "accession numbers" of what I need one by one. But there is no way I can know all the accession numbers of giardia Thioredoxin reductase in the database. So, I need what can search the database and extract all these for me to use.
I could have used BiomaRt or biomartr, but I am having issues installing the package BiocManager which is required for installing the package and BiocLite seems not tho be functional.
So I need to use command line straight rather than any package.
Thanks.
You answered the question yourself: using R and Biomart is the way I would recommend. Some days ago I also trouble with the new BiocManager, but after upgrading my R installation to the latest version it works again.
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