as.fasta — as.fasta • msaR

functionality to convert objects to a fasta string. Currently this can handle character objects which are interpreted as filenames or several of the popular means of storing sequence data: DNAbin, DNAStringSet, AAStringSet, RNAStringSet, BStringSet, DNAMultipleAlignment, RNAMultipleAlignment, or AAMultipleAlignment.

as.fasta(seqs)

Arguments

seqs	(Required.) the sequence/alignment to be displayed. A character vector, `DNAbin`, `DNAStringSet`, `AAStringSet`, or `RNAStringSet`.

Value

A character string in fasta format.

Examples

seqfile <- system.file("sequences","AHBA.aln",package="msaR")
as.fasta(seqfile)
#> [1] ">Hygrocin_AHBA\n--atg--------------------------------------------------------agcaatgatgtgcgactgcga-------tccgagctgcccgcatggccgcagtacggcgacgaggagcgcgaggccctcatccgggctctggatcaggggcaatggtggcgtatcgggggcggtgaggtcgacgccttcgaggcggagttcgccgcggcccatgggagcgagcacgccctggcggtcaccaatgggacgcatgcgctggagctcgccctcgaagtgctcggggtcggcaccgactccgaggtgatcgttcccgcgttcaccttcatctcgtcctcgcaggcggctcagcggctgggcgcggtggccgtgcccgtggacgtggacccggacacgtactgcatcgatccctcggcggtcgaggcagccatcggcccgaaaacccgcgcgatcatgccggtgcacatggcgggccagatgtgcgacatggacgcgctgggcaagctgtccgccgactcgggggtgccgctgatccaggacgcggcccatgcgcacggtgcgcggtggcgcggtcagaaggtcggtgagctgggctcggtcgccgcgttcagcttccagaacggaaagctgatgacggccggtgagggcggcgccgtgctcttccccgatgccgagatgtacgagaggggcttcgtccggcacagctgtggacgtccgcgcaccgaccgcggctacttccaccgcacctcgggctccaacttccggctgaacgagttctccgcatccgtactgcgcgcccaactcgcccgcctggacggccagatcaccacgcgtgagcagcgctggccggtgctgagccggctgctcgccgaaatccccggtgtggtaccgcagtcgcgcgacgaccgcggtgaccgcaatccgcactacatggcgatgttccgggtgccgggcatcaccgaggagcgccgcgcgaaggtcgtcgacaccctcatcgagcgcggggtgcccgcgtttgtcgcgttccgcgcggtctaccgtacggacgccttctgggaggtcgcggcgccggatctgacggtggacgaactcgcccgccgctgcccgcactccgaggcgctcacccgcgactgcctttggctgcaccaccgggtgctgctgggcagcgaggagcagatgcacgaagtggccgccgtcgtcgccgatgtgctcgcgggcgcatga\n>Macbecin_AHBA\n--atg-----------------------------------------------------------agcaattctccggacgca----ggcatcgagttcccggcctggccgcagcacgacgacgccgagcgcacggccctgctgcgcgcgctggaccagggccagtggtggcgggtcggcggcagcgaggtcgacgagttcgagcgcgagttcgccgagtaccacggcgcgggccacgcgctcgccgtcaccaacgggacgcacgcgctggagctggcgctccaggtgctcgacgtgggccccggcgccgaggtgatcgtgcccgccttcaccttcatctcgtcctcgcaggccgtgcagcgcctcggcgcggtcgccgtgcccgtggacgtcgaccccgacacctactgcctggacgtcgccgccgccgaggccgccgtcacctcccgcacctcggcgatcatgcccgtgcacatggcgggccagttcgccgacatggaccggctggacaagctgtccacgagcaccggcgtgccggtcctgcaggacgccgcccacgcccacggcgcccactggcgcggcaagcgggtcggcgagctcgggtcgatcgccacgttcagcttccagaacggcaagctgatgacggcgggcgagggcggggccgtgctgttcgaggacgaggcccagtgggagaaggcgttcgtcctgcacagctgcggcaggcccaagggcgaccgcggctacttccacctcacctcgggctcgaacttccggatgaacgagttctccgccgccgtgctgcgcgcccagctcggcaggctggactcgcagatcgcgaccaggcaggcccgctggccggtgctgtccgcgctgctggcggggatcgacggcgtcgtgccgcagaccgtcgacccgcgcagcgaccgcaacccgagctacatggcgatgttccggatgcccggcgtcaccgaggagcggcgcaacgcggtggtggacgagctggtgcggcgcgggatcccggcgttcatggcgttccgggcggtctaccgcacccaggcgttctgggagaccggcgcgcccgacctgaccaccgaggagctggccgcccggtgcccggtgtcggaggagatcacccgcgactgcgtgtggctgcaccaccgggtgctgctgggcaccgaggagcagctgcaccggcttgccgccgtcgtggccgacgtggtcgcgggcgcgtga\n>Ansatrienin_AHBA\n--gtg--------------------------------------------------------cacctgaaggccccgcagaag-------ctggagttccccgcctggccgcagttcgactcgaccgagcgcgaggccctgctgcgcacgctcgacagcggccggtggtggcggatcaccggggacgaggtcgtctcgttcgagcgggagttcgcgcaggcccacggcgcccggcacgcgctcgccgtcaccacgggcacgcacgccctcgaactcgtcctggaggtcatgggcgccgggcctggcaccgaggtgatcgtgcccgcgttcaccttcatctcctcctcgcaggccgcccagcggctcggcgcggtcgtcgtccccgtcgacgtcgacccggacacctactgcgtcgacccggccgccgtgcgggccgcgatcaccgagcgcaccagggcgatcatgcccgtgcacatggcgggccagctcgccgacatggacgcgctgcgcgccctgtccgccgagaccggcgtcccgctgctccaggacgccgcgcacgcccacggcgcgcggtggcgcggcgagcccctcggcgcgctcggctcgatcgccgccttcagcttccagaacggcaagctgatgaccgcgggcgagggcggcgccgtgctgctcccggacggggaccagcacgaggaggcgttcctgcgccacgcctgcgggcgcccgctcgccgaccgggcctaccaccaccgcacggccgggtcgaacttccgcatgaacgagttctccgccgcgctgctgcgcgcccagctcggcaggctccagcagcagaccgacgtgcgcgagcggcactggcccgtgctgtcgcggctgctcgccgaggtgcccggcgtcgtcccgcaggggaccgacccgcgctgcgaccgcaacccgcactacatggccatgttccaggtccccggcatcggcgaggagcgccgcgcccgcctggtcgacgcgctggtcgagcgcggagtcccggcgttcgccgggttccgcgcgatctaccgcaccgccgcgttctgggagcgcgccgcccccgacaccacggtggacgccctcgcccgcgcctgcccggtcacggaagcgctcagcagcgactgcgtgtggctgcaccaccgggtgctgctgggggcggaggagcagatgccgctggtggcggaggccgtcgcctgcgcgctggaggaggcctga\n>Ansamitocin_AHBA\n--gtg--------------------------------------------------------cacctgaaggccccgcagaag-------ctggagttccccgcctggccgcagttcgactcgaccgagcgcgaggccctgctgcgcacgctcgacagcggccggtggtggcggatcaccggggacgaggtcgtctcgttcgagcgggagttcgcgcaggcccacggcgcccggcacgcgctcgccgtcaccacgggcacgcacgccctcgaactcgtcctggaggtcatgggcgccgggcctggcaccgaggtgatcgtgcccgcgttcaccttcatctcctcctcgcaggccgcccagcggctcggcgcggtcgtcgtccccgtcgacgtcgacccggacacctactgcgtcgacccggccgccgtgcgggccgcgatcaccgagcgcaccagggcgatcatgcccgtgcacatggcgggccagctcgccgacatggacgcgctgcgcgccctgtccgccgagaccggcgtcccgctgctccaggacgccgcgcacgcccacggcgcgcggtggcgcggcgagcccctcggcgcgctcggctcgatcgccgccttcagcttccagaacggcaagctgatgaccgcgggcgagggcggcgccgtgctgctcccggacggggaccagcacgaggaggcgttcctgcgccacgcctgcgggcgcccgctcgccgaccgggcctaccaccaccgcacggccgggtcgaacttccgcatgaacgagttctccgccgcgctgctgcgcgcccagctcggcaggctccagcagcagaccgacgtgcgcgagcggcactggcccgtgctgtcgcggctgctcgccgaggtgcccggcgtcgtcccgcaggggaccgacccgcgctgcgaccgcaacccgcactacatggccatgttccaggtccccggcatcggcgaggagcgccgcgcccgcctggtcgacgcgctggtcgagcgcggagtcccggcgttcgccgggttccgcgcgatctaccgcaccgccgcgttctgggagcgcgccgcccccgacaccacggtggacgccctcgcccgcgcctgcccggtcacggaagcgctcagcagcgactgcgtgtggctgcaccaccgggtgctgctgggggcggaggagcagatgccgctggtggcggaggccgtcgcctgcgcgctggaggaggcctga\n>Divergolide_AHBA\n--atgacgagaggttttcaccctggttatcgtgcgggccgagaatcattcgaggagggctggcgaacaatgctggacaaggaactcgacctggatttcccggcgtggccgcagtacgacgacaccgagcgtgccgggctcgtccgtgccctggagcagggacagtggtggcgtatcggcggcagtgaggtggacgagttcgagcgcgagttcgccgaggcgaacggtgccccgcacgcgctcgcggtgacgaccggcacgcacgccctggaactggcactgcaggtgctcggcgtcggccccggcaccgaggtcgtcgtgccggcgttcaccttcatctcgtcgtcgcaggccgcgcagcgactgggcgcggtggccgtcccggtcgacgtcgacctggacacgtactgcctggaccccgaggcggtggcggcggcgatcacgccgcgcaccgcggcgatcatgccggtgcacatggccggtcagatctgcgacatggacgccctcggcaagctgtcggcggactccggcgtcccgctgctgcacgacgccgcgcacgcgcacggcgggcggtggcgcgaccagggcgtgtcggcgctgggcacgatggcggcgttcagcttccagaacggcaagctgatgaccgcgggcgagggcggcgcggtcaccttcccggacagcgagcagtacgagacggcgttcctccggcacagctgcggccgcccccgcacggaccgcacctaccggcaccagacctccggctccaacttccggatgaacgagttcaccgcgagcgtgctgcgcgcccaactggcccggctcgacggccagatcgacacccgggagcagcgctggccggtgctggccggacaactcgcgcggatcacgggcgtgctgccgcaggccaccgacgaccggtgcacccgcaacccgcactacatggccatgttccgggtgcccggcatctccgaacagcagcgcaacgaactggtcgacgcgctggtggcccgcggcctgccggccttcgcggcgttccgcgcgatccatcgcaccaaggcgttctgggagaccggggcgcccgacgaaccggtcgaggcgatcgcccggcggtgcccgaacagcgaggcgctgtccaccgactgcgtctggctgcaccaccggaccctgctcggcaccgaggagcagatgcacgccgtcgccgaggtcgtctccgacgcgctggcggcgtcgtga\n>Rubradirin_AHBA\n--atg--------------------------------------------------------------agtccgcgaccgagg-------ccgacctttccggattggccgcaattcgatgacaccgaacgccgagctcttgatcgtgcgctgtcccagggccagtggtggcgcatgggtggcagcgaggtggacagcttcgagcgggagttcgccggataccacggtgcccaccacgccctcgccgtcaccaacggcacgcacgcgctggagctcgccctgcaggtgctgggtgcgggaccgggcaccgaagtgatcgtgccggcgttcaccttcatctcctcgtcccaggccgctcagcggatcggggccgtcgccgtgccggtggacgtcgatccggagacctacaacatcgacgcgaccgccaccgccgaggcgatcacaccgcggacccgggtgatcatgccggtgcacatggcgggtctcatggccgacatggacgcactggacaagctcgcctccgatgccggcgtccggatccttcaggacgcggcccacgcgcacggtgcccggtggcggggcaagcgcgtgggcgagctgggctcgatcgcggcgttcagcttccagaacggcaagctgatgaccgcgggcgagggcggcgcggtgctgttcttggacccggacgactacgagaaggcattcctgcatcactcctgcggccggccgcgcaccgaccgcaactatcaccaccaggtggccggcaccaacatgcggatgaacgagttctcggccgccgtcctgcgcgctcagctgggccgcctcgacggccagatcgagctgcgcgagcagcggtggcggttgctgtcgcagctcttggcccagatccccggcgtccggccgcagggcggtgatgcgcgggccgaccggaatccgcactacatggcgatgttccggcttcccggctggtcggaggagcgtcgcaacctcctcgtcgatcgcctggtcgacgcggggatcccggcgttcgcgggcttccgcgccatctaccgcaccgcggcgttctgggagaccggcgcacccgaggagtccgtcgacgcggtcgccaagcggtgccccaacgccgacgcgatcagccaggactgcgtctggctgcaccaccgcaccctgctcgcgtcggagcaggctctcaccgacaccgccgccatcgtggccgaccaggtggccgccggatga\n>Napthomycin_AHBA\n--atg--------------------------------------------------------------aacgcgcgaccggca-------ccggaattcccgaagtggccgcagtacgacgacgaagagcggaccggactgatccgggccctggaacaaggccagtggtggcgcatgggcggggaggaagtcgactccttcgagcgtgagttcgccgacttccacggcgccccgcacgccctggccgtcaccaacggcacccaggccctcgaactcgccctccaggtgctgggcgtcggtccggggaccgaggtcatcgtgccggccttcaccttcatctcctcctcccaggccgcccagcgcatcggcgcggtcgccgtccccgtcgacgtcgacccgggcacgtacaacatcgacgtcgccgcggccgccgccgccgtcaccccgcgcacccgggcgatcatgcccgtgcacatggccggtctgccggccgacatggacgccctcggcaagctcgccgccgacaccggcgtatcgatcgtgcaggacgcggcccacgcccagggcgcccgctggcagggcaagcgggtcggcgaactcggttcggtcgccgtgttctccttccagaacggcaagttgatgaccgccggtgagggcggcgccgtcctgttccccgacagcggcctgcacgaggcggcgttcctgcggcacagctgcggtcggccgcgtaccgaccgccactaccggcacgaggtcgcgggcaccaacatgcggctcaacgagttctccgccgccgtgctgcgcgcccagctgcgccgcctgcccgcccagaccgaactgcgcgacaagcggtgggcgctgctgtcccggctgctcggcgccatcgacggcgtcgtaccgcagagcggtgacgcccgcgccgaccagaacacgcactacatggcgatgttccgggtccccggcatctccgaggagacccgtaacgcgctggtcgaccggctggtcgacgccgggctgcccgccttcgccgcgttccgcgccatccaccgcaccgacgccttctgggaggtcggcgcccccgacgagaccgtggagcagatcgccgagcgctgcccgaacaccgaggccatcagcgacgactgcgtctggctgcaccaccgggtgctcctcgccgaggagcgggacctggagatcacggccgagatcatcgcggacgcagtggccgccatatga\n>Neoansalactam_AHBA\nacatg--------------------------------------------------------------aacgcgcgacggacg-------ccagagttccccacctggccgcagtacgacgacggcgagcgcaccggcctgatccgggccctggagcagggccagtggtggcgcatgggaggctcggaggtggactccttcgagagtgagttcgcggacttccacggtgccccacacgctttggccgtcaccaacggcacccacgccctggagttggcgttgcagtgtctgggcgtcgggccgggcaccgaggtcatcgtgccggccttcaccttcatctcctcctcccaggccgctcagcggctgggagcggttgccgtccccgtcgacgtcgatctcgatacctacaacatcgacgtggctgccgcggcttccgccgtcacccccctcaccaaggcgatcatgcctgtgcacatggcggggctcatcgccgacatggacgcgctcggcgaactctccgccgacaccggtgtgcctcttctccaggacgccgcccacgcacacggtgcccgctggcagggcaaacgggtgggcgagttgggtacggtcgcctcgttcagcttccagaacggcaagctgatgaccgccggcgagggcggtgcgctgctcctgcccgacgaggagacctacgaggccgcgttcctgcggcacagttgtggccggtcacgtaccgaccgccgatacatgcaccagaccgccggcaccaacatgcggctcaacgagttctccgcggccgtgctccgcgcccagctgggccgcctcgacgcccagatcacgctccgcgatcagcgctggacgctgctgtcccggctgctcggtgagatcgacggcgtcgtaccccagggcagcgacccgcgcgccgaccggaactcccactacatggcgatgttccggatccccggcatatccgaggaggcccgcaacgccctcgtcgacacgctcgtcgaggccggcctgcccgccttcgccgccttccgggcgatctaccgcaccgacgcgttctgggagacggccgcgcccgacaccaccgtcgacaagctcgccgaaagctgcccgcacaccgaggcgatcagcaccgactgcatctggctgcaccatcgagtgctgctcgcctcggaggaggccctccacaccacagccgagatcatcgccgacgccgtggccgcacggtga\n>Ansalactam_AHBA\n---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gcgccgcgcatgctttggccgtcaccaacggcacccatgccctggaactggcgctgcagtgtctgggtgtcggtccgggcacggaggtcatcgtgccggccttcactttcatctcctcgtcccaggccgctcagcggctcggcgcggtcgccgtccccgtcgacgtcgatctcgacacgtacaacatcgacgtggctgccgcggcggccgccgtcacccctcgcaccagggtgatcatgcccgtgcacatggcggggctcatcgctgacatggacgcgctcgacaagctctccgcggacaccggcgtgcccgtgctgcaggacgccgcccacgcgcacggtgcccgatggcagggcaaacgggtgggcgagttgggcacggtcgccaccttcagcttccagaacggcaagctgatgaccgccggcgagggtggtgccctgctcttccccgacgaggagacgtacgaggccgccttcctgcggcacagctgtggccggccgcgcaccgaccgccactacatgcaccagaccgccggcaccaacatgcggctcaacgagttctctgcctccgtgctccgcgcccaactgagccgcctcgacgcccagctcacgctgcgcgatgagcgctggacactgctgtcccggctgctcggcaagatcgacggcgtcgtaccccaggggggcgatgcgcgcgcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n>Arifamycini\n--atg--------------------------------------------------------------aacgcacgacaggcg-------cccgaattcccccaatggccgcagtacgacgacgcagagcgggacggcctgatccgtgcgctggagcagggccagtggtggcgcatgggcggcagcgaggtggacgcgttcgagcacgagttcgccgcgcaccacggcgccgcgcacgcgctggcggccaccaccgggacgcacgcgctcgaactcgccctgcagtgcatgggcgtcgggccgggcaccgaggtgatcgtgccggccttcaccttcatctcctcctcccaggcggcccagcggctcggcgcggtcgcggtcccggtcgacgtcgacgccggcacctacaacctcgacccggcggcggtctccgccgccctcaccccccgcacccgcgtgatcatgccggtgcacatggccgggctcatggcggacatggacgcgctcggcaagatctccgccgagtccggggtgccgctgctgcaggacgccgcgcacgcccacggcgcgcgctggcaggggcggcgcgtcggcgagctcggcggcgtcgcggcgttcagcttccagaacggcaaactgatgaccgcgggcgagggcggcgcggtgctgttcccggacggcgacatgtacgagacggcgttcctgcgccacagttgcggccgcccccgggacgaccgccgctacttccaccggatcgcgggctccaacctgcggatgaacgagttctcggcggcggtgctgcgggcccagctgcgccgcctcgacgagcagatcgcggtccgggacgagcgctggaagctgctgtccccgctgctcgcgcggatcgacggcgtcgtcccgcaggcggacgacgtgcgcgccgaccggcactcgcactacatggcgatgttccgcgtccccgggatcaccgaggagcggcgcaacgccctcgtcgaccgcctcgtcgccgccggcgtgcccgcgttcgccgcgttccgcgcgatccaccgcaccgaggcgttctgggagatcggggcgcccgcggagacgccggacgcgatcggggagcgctgccccaacaccgaggccatcagccgcgactgcgtctggctgcaccaccgcgtcctgctggcgggggagccggagatccgcgccgccgccgagatcatcgccgacctcgtggcctccgcatga\n>Chaxamycin_AHBA\n--atg--------------------------------------------------------------aacgcgcgacaggca-------ccagaattcccccgctggcctcagtacgacgagaccgagcgggacggcctgatccgtgcgctggaacagggccagtggtggcgcatgggcggcgacgaggtcgactccttcgagcgggagttcgccgagcaccacggcgccccccacgcgctggcggtcaccaacggcacccacgcgctggaactcgccctgcaatgcctgggcgtcggcccgggcaccgaagtcatcgtgccggccttcaccttcatctcctcctcgcaggccgcccagcggctcggcgccgtcgccgtccccgtcgacgtccacccggacacctactgcatcgacgccgccgcggtcgccgccgccgtcaccccccgcacccgcgccatcatgccggtgcacatggccgggctcatcgcggacatggacgccctggcgaagatctccgccgacaccggggtccccctgctccaggacgccgctcacgcccacggtgcccgctggcagggcaaacgcgtcggtgaactgggcagcgtcgccgcgttcagcttccagaacggcaagctgatgaccgccggcgagggcggcgccctcctcttcccggacacggagctgtacgaggcggcgttcctgcggcacagctgcggccgcccccgcgacgaccgccgctacctgcaccgcaccgcgggctccaacctgcgcatgaacgagttctccgcggccgtgctgcgcgcccagctgagccgcctcgaccagcagatcgccctgcgggaggagcgctggaccctgctgtcccggctgctcgccgccatcgacggcgtcgtcccgcagggcggcgacgtgcgcgtggaccgcaagtcgcactacatggcgatgttccgggtccccggcctcggcgaggagcggcgcaacgccctggtcgaccggctcgtggaggcgggcctgcccgcgttcgccgcgttccgcgcgatctaccgcaccgacgccttctgggagatcggcgcacccgacgagacccccgacgccatcgccgcccgctgcccccacaccgaagccatcagccaggactgcgtctggctgcaccaccgcgtcctgctcgccggggaagcggagatgcacgccaccgccgagatcatcgccgacctcgtggcccgcgcgtga"
help("as.fasta")

if (FALSE) {
if (requireNamespace("Biostrings")) {
   seqs <- readDNAStringSet(seqfile)
   as.fasta(seqs)
 }
}