seqmagick: sequence manipulation

knitr::opts_chunk$set(tidy = FALSE,
           message = FALSE)
library(magrittr)
library(Biostrings)
library("seqmagick")

Download sequences

Genbank

tmpgb <- tempfile(fileext = '.gb')
tmpfa <- tempfile(fileext = '.fa')
download_genbank(acc='AB115403', format='genbank', outfile=tmpgb)
download_genbank(acc='AB115403', format='fasta', outfile=tmpfa)
## readLines(tmpgb)[1:10]
## readLines(tmpfa)

File conversion

fasta and phylip conversion

fa_file <- system.file("extdata/HA.fas", package="seqmagick")
## use the small subset to save compilation time of the vignette
fa2 <- tempfile(fileext = '.fa')
fa_read(fa_file) %>% bs_filter('ATGAAAGTAAAA', by='sequence') %>% fa_write(fa2, type='interleaved')


alnfas <- tempfile(fileext = ".fas")
fa_read(fa2) %>% bs_aln(quiet=TRUE) %>% fa_write(alnfas)

## phylip format is only for aligned sequences
tmpphy <- tempfile(fileext = ".phy")
fas2phy(alnfas, tmpphy, type = 'sequential')

seqmagick supports both sequential and interleaved formats, users can specify the format by type parameter.

phy2fas(tmpphy, alnfas, type = 'interleaved')

interleaved and sequential format conversion

tmpfas <- tempfile(fileext='.fa')
fa_read(fa2) %>% fa_write(tmpfas, type="sequential")
tmpphy2 <- tempfile(fileext = '.phy')
phy_read(tmpphy) %>% phy_write(tmpphy2, type="interleaved")

Sequence manipulation

bs <- fa_read(fa_file)
bs_filter(bs, 'ATGAAAGTAAAA', by='sequence')

aln <- bs_filter(bs, 'ATGAAAGTAAAA', by='sequence') %>% bs_aln(quiet=TRUE)

bs_consensus(aln)

Bugs/Feature requests

If you have any, let me know. Thx!

Session info

Here is the output of sessionInfo() on the system on which this document was compiled:

sessionInfo()

References



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seqmagick documentation built on April 25, 2021, 9:08 a.m.