Sequence Manipulation Utilities

Tools for reading and writing biological sequences in multiple formats, including 'FASTA', 'PHYLIP', 'CLUSTAL', 'STOCKHOLM', 'MEGA' and 'GenBank'. Supports interleaved and sequential layouts where applicable, and reads or writes gzip, bzip2 and xz compressed files transparently. Converts between formats, renames sequences via a two-column mapping, summarizes sequence counts, lengths, GC content and ambiguous characters, and manipulates sequence sets (e.g., filtering by patterns and computing consensus sequences from alignments). Also includes functions to download nucleotide records from NCBI by accession.

seqmagick: Sequence Manipulation Utilities

Tools for reading and writing biological sequences in multiple formats, including ‘FASTA’, ‘PHYLIP’, ‘CLUSTAL’, ‘STOCKHOLM’, ‘MEGA’ and ‘GenBank’. Supports interleaved and sequential layouts where applicable, and reads or writes gzip, bzip2 and xz compressed files transparently. Converts between formats, renames sequences via a two-column mapping, summarizes sequence counts, lengths, GC content and ambiguous characters, and manipulates sequence sets (e.g., filtering by patterns and computing consensus sequences from alignments). Also includes functions to download nucleotide records from NCBI by accession.

:writing_hand: Authors

YuLab@SMU https://yulab-smu.top

:page_facing_up: Supported file formats

Format	Read	Write
FASTA (.fas/.fa/.fasta)	:heavy_check_mark:	:heavy_check_mark:
PHYLIP (.phy)	:heavy_check_mark:	:heavy_check_mark:
CLUSTAL (.clw)	:heavy_check_mark:	-
STOCKHOLM (.sth)	:heavy_check_mark:	-
MEGA (.meg)	:heavy_check_mark:	-
GenBank (.gb)	:heavy_check_mark:	-
NCBI (online)	:heavy_check_mark:	-

Both sequential and interleaved layouts are supported for FASTA and PHYLIP. Compressed files (gzip, bzip2, xz) are handled transparently.

:hammer: Installation

Install from CRAN:

install.packages("seqmagick")

Or grab the development version from GitHub:

if (!requireNamespace("remotes", quietly=TRUE))
    install.packages("remotes")
remotes::install_github("YuLab-SMU/seqmagick")

:bulb: Quick Examples

library(seqmagick)

fas <- system.file("extdata/HA.fas", package = "seqmagick")

## reading/writing FASTA files
x <- fa_read(fas)
fa_write(x[1:5], "sub.fa.gz")     # gzip/bzip2/xz supported

## a quick summary (counts, lengths, GC content)
fa_summary(fas)

## sequence manipulation
bs_filter(x, 'ATGAAAGTAAAA', by='sequence')   # keep matching sequences

## renaming sequences via two-column mapping
map <- data.frame(old = names(x)[1:2],
                  new = c("HA_HK", "HA_BR"))
y <- bs_rename(x, map)

## format conversion (requires aligned sequences)
fas2phy("aln.fas", "aln.phy")
phy2fas("aln.phy", "aln.fas")

## download nucleotide records from NCBI
seqs <- ncbi_fa_read(acc = c("AB115403", "CY084969"))

For more details, please see the online vignette.

If you use seqmagick, please cite: