bioseq.fasta


        require(GCModeller);
                               

#' Fasta sequence toolkit
imports "bioseq.fasta" from "seqtoolkit";

.NET clr type export
MSA_result: MSAOutput	the result data of multiple sequence alignment

.NET clr function exports
as.data.frame.fastafile	FastaFile: A FASTA file that contains multiple sequence data. (一个包含有多条序列数据的FASTA文件)
as.data.frame.fastaseq	FastaSeq: The FASTA format file of a bimolecular sequence.(Notice that this file is only contains on sequence.)
size	get the sequence length
chars	get alphabets represents of the fasta sequence
mass	evaluate the molecule mass of the given sequence
seq_formula	evaluate the chemical formula of the given sequence data
seq_sgt	Create algorithm for make sequence embedding
seq_vector	embedding the given fasta sequence as vector
read.seq	Read a single fasta sequence file
read.fasta	read a fasta sequence collection file
read_assembly	read genome assembly fasta sequence file
open.fasta	open the fasta sequence file
parse.fasta	parse the fasta sequence object from the given text data
takes	takes the sequence subset from the given sequence collection by a set of the sequence id
list_index	make sequence list index
write.fasta	write a fasta sequence or a collection of fasta sequence object
translate	Do translation of the nt sequence to protein sequence
MSA.of	Do multiple sequence alignment
read_stockholm	read stockholm MSA file.
as.fasta	Create a fasta sequence collection object from any given sequence collection.
fasta	Create a new fasta sequence objects
fasta.headers	get/set the fasta headers title
fasta.titles	get the fasta titles from a collection of fasta sequence
slicer	create a sequence region slicer for cut a specific sequence region from the given sequence data
cut_seq.linear	cut part of the sequence
open.fingerprint_writer	open a fingerprint matrix writer for write the sequence fingerprint data into a binary BSON file
write_fingerprint	make the sequence fingerprint data of the given nucleotide sequence collection, and then write the generated fingerprint data into the target fingerprint matrix file
read.fingerprint_bson	read the sequence fingerprint data from a binary BSON format fingerprint matrix file
make_clusterTree	make the cluster tree of the given sequence fingerprint data