Comments (1)
Hi @wcfung14,
Thank you very much for making me aware of this issue!
When performing blast_best_reciprocal_hit()
, users can now specify tasks in both directions when selecting search_type = protein_to_nucleotide
(task = c("tblastn", "blastx")
) or search_type = nucleotide_to_protein
(task = c("blastx", "tblastn")
).
Example:
blast_test_reciprocal <- blast_best_reciprocal_hit(
query = system.file('seqs/qry_aa.fa', package = 'metablastr'), # protein sequence
subject = system.file('seqs/sbj_nn_best_hit.fa', package = 'metablastr'), # nucleotide sequence
search_type = "protein_to_nucleotide",
task = c("tblastn", "blastx"),
evalue = 0.000001,
output.path = tempdir(),
db.import = FALSE)
# A tibble: 20 x 21
# Groups: query_id [20]
query_id subject_id perc_identity num_ident_match… alig_length
<chr> <chr> <dbl> <int> <int>
1 311313|PAC… AT1G01210… 95.3 102 107
2 311315|PAC… AT1G01190… 94.2 502 533
3 311317|PAC… AT1G01170… 85.6 83 97
4 333544|PAC… AT1G01110… 93.6 494 528
5 333551|PAC… AT1G01040… 92.0 1812 1970
6 333554|PAC… AT1G01010… 72.1 328 455
7 470155|PAC… AT1G01220… 96.7 1021 1056
8 470156|PAC… AT1G01200… 95.8 228 238
9 470161|PAC… AT1G01140… 98.5 446 453
10 470171|PAC… AT1G01090… 95.2 413 434
11 470177|PAC… AT1G01060… 89.2 578 648
12 470180|PAC… AT1G01030… 95.5 343 359
13 470181|PAC… AT1G01020… 91.1 224 246
14 909860|PAC… AT1G01180… 92.6 287 310
15 909871|PAC… AT1G01080… 87.3 262 300
16 909874|PAC… AT1G01050… 100 213 213
17 918854|PAC… AT1G01160… 84.9 152 179
18 918855|PAC… AT1G01150… 72.6 207 285
19 918858|PAC… AT1G01120… 99.2 525 529
20 918864|PAC… AT1G01070… 95.1 348 366
# … with 16 more variables: mismatches <int>, gap_openings <int>,
# n_gaps <int>, pos_match <int>, ppos <dbl>, q_start <int>,
# q_end <int>, q_len <int>, qcov <dbl>, qcovhsp <dbl>,
# s_start <int>, s_end <int>, s_len <int>, evalue <dbl>,
# bit_score <dbl>, score_raw <dbl>
Please let me know if this works for you after re-installing metablastr
.
Best wishes,
Hajk
from metablastr.
Related Issues (12)
- 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
- function blast_protein_to_protein with argument is.subject.db = TRUE doesn't work with nr database HOT 5
- 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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