gschofl / blastr Goto Github PK

Hi Gerhard and Philipp

Thank you for developing a nice package.

I'm trying to convert a commandline blastn query to a remote database into an rBLAST::blast query. I noticed that your README.md states that your package "... allows both local and remote queries...". When I look in the documentation for the rBLAST::blast command I see a nice example of querying a local database while not one for querying a remote database (e.g. using the BLAST_args argument). Such example would be fantastic. Can you help?

The command i'm trying to convert is:
blastn -query barcodes.fa -db nt -remote -out blast_results.tsv -outfmt '6 qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore sscinames sblastnames sskingdoms' -evalue 1e-30 -entrez_query "Fungi[ORGN]"

Best Søren

Dear Gerhard,

I have R and Bioconductor updated:
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.1 (2017-06-30).

I ran the following:
devtools::install_github("gschofl/blastr")

Here is the error message I got:

--library='/usr/lib64/R/library' --install-tests

• installing source package ‘blastr’ ...
  ** R
  ** inst
  ** tests
  ** preparing package for lazy loading
  Error : object ‘fasta.info’ is not exported by 'namespace:Biostrings'
  ERROR: lazy loading failed for package ‘blastr’
• removing ‘/usr/lib64/R/library/blastr’
  Installation failed: Command failed (1)

Could you help? Thank you!

Hi @gschofl ,

I've used your package for a few small projects; thank you. I wanted to raise the possibility that others might like to use it as well - perhaps its worth submitting to CRAN? I think so.

Thanks,
zach cp