Date: 2026-01-31

# seqmagick: sequence manipulation

#### Guangchuang Yu

#### 2026-01-31

# 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:

    ## R version 4.5.2 (2025-10-31 ucrt)
    ## Platform: x86_64-w64-mingw32/x64
    ## Running under: Windows 11 x64 (build 26200)
    ##
    ## Matrix products: default
    ##   LAPACK version 3.12.1
    ##
    ## locale:
    ## [1] LC_COLLATE=C
    ## [2] LC_CTYPE=Chinese (Simplified)_China.utf8
    ## [3] LC_MONETARY=Chinese (Simplified)_China.utf8
    ## [4] LC_NUMERIC=C
    ## [5] LC_TIME=Chinese (Simplified)_China.utf8
    ##
    ## time zone: Asia/Shanghai
    ## tzcode source: internal
    ##
    ## attached base packages:
    ## [1] stats4    stats     graphics  grDevices utils     datasets  methods
    ## [8] base
    ##
    ## other attached packages:
    ## [1] seqmagick_0.1.8     Biostrings_2.78.0   Seqinfo_1.0.0
    ## [4] XVector_0.50.0      IRanges_2.44.0      S4Vectors_0.48.0
    ## [7] BiocGenerics_0.56.0 generics_0.1.4      magrittr_2.0.4
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] crayon_1.5.3      cli_3.6.5         knitr_1.51        rlang_1.1.7
    ##  [5] xfun_0.56         otel_0.2.0        jsonlite_2.0.0    htmltools_0.5.9
    ##  [9] sass_0.4.10       rappdirs_0.3.4    rmarkdown_2.30    evaluate_1.0.5
    ## [13] jquerylib_0.1.4   prettydoc_0.4.1   fastmap_1.2.0     yaml_2.3.12
    ## [17] lifecycle_1.0.5   compiler_4.5.2    fs_1.6.6          digest_0.6.39
    ## [21] R6_2.6.1          bslib_0.9.0       tools_4.5.2       yulab.utils_0.2.3
    ## [25] cachem_1.1.0

# References