knausb
commented
4 years ago Hello, not sure I follow you. It is usually best to create a reproducible example. Below is my attempt.
library(ape)
data(woodmouse)
woodmouse <- as.list(woodmouse)
woodmouse[[3]] <- woodmouse[[3]][1:100]
woodmouse
#> 15 DNA sequences in binary format stored in a list.
#>
#> Mean sequence length: 907.333
#> Shortest sequence: 100
#> Longest sequence: 965
#>
#> Labels:
#> No305
#> No304
#> No306
#> No0906S
#> No0908S
#> No0909S
#> ...
#>
#> Base composition:
#> a c g t
#> 0.307 0.262 0.126 0.306
#> (Total: 13.61 kb)
my_seq <- woodmouse[grep("No306", names(woodmouse))]
my_seq
#> 1 DNA sequence in binary format stored in a list.
#>
#> Sequence length: 100
#>
#> Label:
#> No306
#>
#> Base composition:
#> a c g t
#> 0.35 0.30 0.07 0.28
#> (Total: 100 bases)Created on 2020-03-30 by the reprex package (v0.3.0)
This appears to work as expected. Can you modify this so that I can reproduce the error?
The error you're reporting appears to be from ape::as.matrix.DNAbin(). My understanding is that a DNAbin object may be a vector, matrix, or list. If it's a matrix all sequences need to be the same length. We would expect this in a multiple sequence alignment, but not in a genome where different contigs are of different sizes. Somewhere in the code this function appears to be called on a DNAbin that contains sequences of different length. Please let me know what you find!
lesneski
Hello, I have been having trouble subsetting my fasta file into 1 chromosome while following the instructions on [https://knausb.github.io/vcfR_documentation/subset_data_to_1chrom.html] When I get to the last step, I get a return of "Error in as.matrix.DNAbin(dna2) : DNA sequences in list not of the same length."
All steps prior worked fine - I also tried to run these steps with the pinf_sc50.fasta file available from the package, changing inputs where necessary, but I also couldn't get the subset fasta steps to work.
Thank you in advance.