Comments (5)
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
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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 ?
from metablastr.
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
from metablastr.
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 ''
from metablastr.
You need to remove system.file(...)
around your path. This isn't a similar error as stated above.
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Related Issues (12)
- blast_best_reciprocal_hit nucleotide-protein comparison task error HOT 1
- Error: Internal error in `dict_hash_with()`: Dictionary is full.
- How can I load sequences from a CSV file and do the massive Blast search locally?
- Error in .Call2("new_input_filexp", filepath, PACKAGE = "XVector") : cannot open file '' HOT 2
- Package release request HOT 2
- blast_nt for nucleotide against NCBI database HOT 3
- additional functionality when extracting random sequences HOT 5
- Feature Request: exclude sequences with Ns
- Feature Request: extract the same regions from multiple samples
- Feature request : add taxon id for each blast hit HOT 3
- Reg: Reciprocal hits from already run blast outcomes HOT 5
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