get the names of all the sequences of fasta file

get the names of all the sequences of a fasta file, and perform cleaning of the names of the sequences

get.fasta.name(infile, clean_name = FALSE)

Arguments

infile	character string representing the name of the fasta file.
clean_name	logical, representing cleaning of the names will be performed.

Value

a character vector containing the names of the sequences

References

http://www.genomatix.de/online_help/help/sequence_formats.html

Author

Jinlong Zhang <jinlongzhang01@gmail.com>

Note

Punctuation characters and white space be replaced by "_". Definition of Punctuation characters can be found at regex.

See also

read.fasta, regex

Examples

  cat(
  ">seq_2", "GTCTTATAAGAAAGAATAAGAAAG--AAATACAAA-------AAAAAAGA",
  ">seq_3", "GTCTTATAAGAAAGAAATAGAAAAGTAAAAAAAAA-------AAAAAAAG",
  ">seq_5", "GACATAAGACATAAAATAGAATACTCAATCAGAAACCAACCCATAAAAAC",
  ">seq_8", "ATTCCAAAATAAAATACAAAAAGAAAAAACTAGAAAGTTTTTTTTCTTTG",
  ">seq_9", "ATTCTTTGTTCTTTTTTTTCTTTAATCTTTAAATAAACCTTTTTTTTTTA",
  file = "trn1.fasta", sep = "\n")
get.fasta.name("trn1.fasta")
#> [1] "seq_2" "seq_3" "seq_5" "seq_8" "seq_9"
unlink("trn1.fasta")