First format in sintax format and then in dada2 format
Usage
format2dada2(
fasta_db = NULL,
taxnames = NULL,
output_path = NULL,
from_sintax = TRUE,
pattern_to_remove = NULL,
...
)Arguments
- fasta_db
A link to a fasta files
- taxnames
A list of names to format. You must specify either fasta_db OR taxnames, not both.
- output_path
(optional) A path to an output fasta files. Only used if fasta_db is set.
- from_sintax
(logical, default FALSE) Is the original fasta file in sintax format?
- pattern_to_remove
(a regular expression) Define a pattern to remove. For example, pattern_to_remove = "\|rep.*" remove all character after '|rep' to force
dada2::assignTaxonomy()to not use the database as a Unite-formated database- ...
Additional arguments passed on to
format2sintax()function
Examples
# \donttest{
f <- system.file("extdata", "mini_UNITE_fungi.fasta.gz",
package = "MiscMetabar"
)
format2dada2(fasta_db = f, from_sintax = FALSE)
#> DNAStringSet object of length 5000:
#> width seq names
#> [1] 492 GGAAGGATCATTAACACTAATC...GCTTAGTCACACAAACTTTAC k__Fungi;p__Fungi...
#> [2] 451 CGAGTTTACCACTCCAACCCCT...GTTAAACCCCAACTTCTGAAT k__Fungi;p__Ascom...
#> [3] 457 CCGAGTTTACAACTCCCAAGCC...CAGTTAACCCTAAGTTTTGAT k__Fungi;p__Fungi...
#> [4] 490 AGAAGGGGGAAGAGCAATTCTA...GTTCAACCCCAACTTCTGAAT k__Fungi;p__Ascom...
#> [5] 464 CCAGTTGCAACATACCACTTGT...GTTAAACCCCAACTTCTGAAT k__Fungi;p__Ascom...
#> ... ... ...
#> [4996] 622 CATTATTGAACAAAAAAATGGT...GATTTGGAGAACCAAGATAAA k__Fungi;p__Basid...
#> [4997] 609 ATGAATTGTAACGGGGGTTGAT...CTGATCTGTTCCACTTTCAAC k__Fungi;p__Basid...
#> [4998] 615 ATGGAATTGTAACAGGAGCTGA...AATTCTGTTCAACTTCCACCC k__Fungi;p__Fungi...
#> [4999] 606 ATGAATTGTAACAGGGGCTGAT...TGATCTGTTCCATTTTTCAAC k__Fungi;p__Basid...
#> [5000] 519 TTGGAGTCTGGTTGTTGCTGGC...ATTTTCATTTCATCCTTGCCA k__Fungi;p__Basid...
# }