Hello All,
I have a COI FASTA alignment file with 11926 sequences spanning 668 species.
According to my code, a total of 361 species are represented by 6 or more
sequences.
I need to extract these 361 species (along with all their associated
sequences) from the alignment but am having issues.
Here is my code:
library(ape)
library(pegas)
library(spider)
library(stringr)
seqs <- read.dna(file = file.choose(), format = "fasta") # import data
and convert to matrix
seqs.mat <- as.matrix(seqs)
spp <- substr(dimnames(seqs.mat)[[1]], 1, 50) # extract sequence labels
res <- str_remove(spp, "^[^|]+\\|") # remove BOLD Process ID
res <- table(res)[which(table(res) >= 6)] # species with 6 or more
records
names(res) # 361 species names
The problem is that `names(res)' contains unique species names.rather than
repeated species names (according to the BOLD process ID).
I also need the sequences. There are between 6-421 sequences across the 361
species (11143 sequences total).
Does anyone have any ideas on next steps here?
Once this is done, I would then write the sequences to a file via
`write.dna()`
If clarification is needed, please let me know.
Thanks.
Cheers,
Jarrett
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