ImportFastaAlignment: Import a FASTA alignment from a file
In aramette/otu2ot: Calculate oligotypes for aligned FASTA sequences

Description Usage Arguments Details Value Note Author(s) Examples

Import a FASTA alignment from a file and if needed converts the space in the FASTA headers into underscore "_"

1	ImportFastaAlignment(File,fixSpaceinHeaders=TRUE)

`File`	path to the FASTA file
`fixSpaceinHeaders`	logical. If TRUE, replaces spaces in the headers by underscores. The function runs faster if this is turned to FALSE. Alternatively, one can "clean" the headers before importing the alignment to R!

require(seqinr)

The function returns a list containing a vector of names (rows) and a matrix of sequence nber by site List with two items:

`Seqs.names`	FASTA headers
`Seqs.only`	only the FASTA sequences as vectors of bases. This is in a matrix format.

require(seqinr)

Alban Ramette

#require(seqinr)

#write.fasta(sequences="mock-env-aligned.fasta",file.out="mock-env-aligned.fasta")
#mock_env_aligned.list <-  ImportFastaAlignment(File="mock-env-aligned.fasta",fixSpaceinHeaders=TRUE)
#data(mock_env_aligned.list) # resulting list after importing from the previous line

#FastaHeaders <-  mock_env_aligned.list[[1]]
#Sequences  <-   mock_env_aligned.list[[2]]
#SEQUENCES <- toupper(Sequences) #convert sequences to capital letters

#Nseqs <-  nrow(Sequences) #nber of sequences
#Nbases <- ncol(Sequences)#nber of bases