read_fasta()/write_fasta() can read/write
FASTA format file into/from named character. If you feel frustrate with
DNAbin or other stophisticated class, and find youself using
read/write_line and str_extract/replace/...
repeatedly, may be you can consider this package.
system.file('extdata', 'aligned-multiline.fasta', package = 'rutil') |>
read_fasta()
#> # A tibble: 61 × 2
#> name seq
#> <chr> <chr>
#> 1 Acanthisitta_chloris_Jarvis --------------------------------------------…
#> 2 Amazona_aestiva_protein MRFWGGGWTLRXT-SEMGNXS----------VQRMRE-------…
#> 3 Anas_platyrhynchos_Jarvis --------------------------------------------…
#> 4 Anser_cygnoides_protein --------------------------------------------…
#> 5 Antrostomus_carolinensis_Jarvis --------------------------------------------…
#> 6 Apaloderma_vittatum_Jarvis --------------------------------------------…
#> 7 Aptenodytes_forsteri_Jarvis --------------------------------------------…
#> 8 Apteryx_australis_protein --------------------------------------------…
#> 9 Aquila_chrysaetos_protein --------------------------------------------…
#> 10 Balearica_regulorum_Jarvis --------------------------------------------…
#> # … with 51 more rows
system.file('extdata', 'aligned-multiline.fasta', package = 'rutil') |>
read_fasta(unalign = TRUE)
#> # A tibble: 61 × 2
#> name seq
#> <chr> <chr>
#> 1 Acanthisitta_chloris_Jarvis AGVLALWALTTHGMYIQDFWRTWLRGLRFFLAVGIFFCVVALVA…
#> 2 Amazona_aestiva_protein MRFWGGGWTLRXTSEMGNXSVQRMREGPGGVLALWALITHVMYV…
#> 3 Anas_platyrhynchos_Jarvis RAGVLALWALITHVMYVQDYWRTWLKGLRFFLFIGILFSALSVV…
#> 4 Anser_cygnoides_protein MYVQDYWRTWLKGLRFFLFIGILFSALSVVGFCTFLVLAITKHQ…
#> 5 Antrostomus_carolinensis_Jarvis AGVLALWALITHVMYVQDYWRTWLKGLRFFLFIGILFSALSVVG…
#> 6 Apaloderma_vittatum_Jarvis RAGVLALWALTTHVMYVQDYWRTWLKGLRFFLFIGILFSALSAV…
#> 7 Aptenodytes_forsteri_Jarvis AGVLALWALITHVMYVQDYWRTWLKGLRFFLFIGILFSALSVVG…
#> 8 Apteryx_australis_protein MHLSFPLESDYWRTWLKGLRFFLFIGILFSALSVVGFCTFLVLA…
#> 9 Aquila_chrysaetos_protein MFSGCIQPFPEWLLMFLCVLALWALITHVMYVQDYWRTWLKGLR…
#> 10 Balearica_regulorum_Jarvis AGVLALWALITHVMYVQDYWRTWLKGLRFFLFIGILFSALSVVG…
#> # … with 51 more rows