function blast_protein_to_protein with argument is.subject.db = TRUE doesn't work with nr database

[cparsania]

I have nr blast database downloaded from NCBI, which contains the files given in the attached snapshot. When I run the command below, it throws the as shown. I wonder, what input should I give as a blast-able database ?

blast_test <- blast_protein_to_protein(
        query   =  "aa_query.fasta",
        subject = "path/to/nr/db/nr",
        is.subject.db = TRUE,
        output.path = tempdir(),
        db.import  = FALSE ,cores = 4)

Error in .Call2("new_input_filexp", filepath, PACKAGE = "XVector") : 
  cannot open file '/Users/chiragparsania/Documents/Database/nr_protein_db/nr'

[HajkD]

Hi @cparsania

Many thanks for this input.

There will be functions named blast_protein_to_ncbi_nr(), blast_nuceotide_to_ncbi_nt(), etc which I haven't implemented fully yet. So this NCBI nr BLAST feature will be available soon.

I intentionally wanted all blast_*_to_*() functions to be between a query fasta against a subject fasta file to support low-level comparisons and then build on top of them larger search requests against large sequence databases.

I hope this helps and I will try to make sure that this feature will be available soon.

Best wishes, Hajk

[cparsania]

I intentionally wanted all blast_to() functions to be between a query fasta against a subject fasta file

However, the documentation for argument subject is path to subject file in fasta format or blast-able database, which I interpreted as either fasta file or blast format database created using makeblastdb command. Do you think is it worth mentioning argument subject takes fasta only ?

--- Edit

Also, there is an argument is.subject.db which says that logical specifying whether or not the subject file is a file in fasta format (is.subject.db = FALSE; default) or a blast-able database that was formatted with makeblastdb (is.subject.db = TRUE) , which means making this to TRUE allow users to supply nr db. Is that right ?

[HajkD]

Hi @cparsania

Many thanks for coming back to me on this one.

Also, there is an argument is.subject.db which says that logical specifying whether or not the subject file is a file in fasta format (is.subject.db = FALSE; default) or a blast-able database that was formatted with makeblastdb (is.subject.db = TRUE) , which means making this to TRUE allow users to supply nr db. Is that right ?

I now see the confusion and I am very sorry for not being more clear here.

What I meant by is.subject.db is that in cases where users already used makeblastdb to convert their *.fasta file into a blast-able database then they could also use this fasta-database with these functions.

But now I see that this can be misunderstood and I will make this more clear in the documentation. Also, once I implemented the functions to blast against e.g. NCBI nr etc, I will make a reference in the documentation at this point to these new functions.

Thank you very much for your feedback and this allows me to improve the metablastr package.

Best wishes, Hajk

[katievigil]

Hi I am getting a similar error:

sealionfeces <- readDNAStringSet(system.file("H:/ONRdolphinsealionpooled/sealionfecespooled/canu/medaka/consensus.fasta",

• package = "rBLAST")) Error in .Call2("new_input_filexp", filepath, PACKAGE = "XVector") : cannot open file ''

@HajkD

[HajkD]

You need to remove system.file(...) around your path. This isn't a similar error as stated above.