fastawrite

Write to file using FASTA format

collapse all in page

    Syntax

    fastawrite(File,Data)
    fastawrite(File,Header,Sequence)

    Description

    fastawrite(File,Data) writes the contents of Data to File, a FASTA-formatted file. If you specify an existing FASTA-formatted file,fastawrite appends the data to the file, instead of overwriting the file. For the FASTA-format specifications, visit FASTA.

    example

    fastawrite(File,Header,Sequence) writes the specified header and sequence information to File, a FASTA-formatted file.

    example

    Examples

    collapse all

    Open Live Script

    Retrieve the sequence for the human p53 gene from the GenBank database.

    seq = getgenbank('NM_000546');

    Read the coordinates of the coding region in the CDS line.

    start = seq.CDS.indices(1)
    start = 143

    stop = seq.CDS.indices(2)
    stop = 1324

    Extract the coding region.

    codingSeq = seq.Sequence(start:stop);

    Write the coding region to a FASTA-formatted file, specifying Coding region for p53 for the Header in the file, and p53coding.txt for the file name.

    fastawrite("p53coding.txt","Coding region for p53",codingSeq);

    Open the file to view the content.

    open p53coding.txt
    Open Live Script

    Write two nucleotide sequences to a MATLAB structure containing the fields Header and Sequence.

    data(1).Sequence = "ACACAGGAAA";
data(1).Header = "First Sequence";
data(2).Sequence = "ACGTCAGGTC";
data(2).Header = "Second Sequence";

    Write the sequences to a FASTA-formatted file, specifying my_sequences.txt for the file name.

    fastawrite("my_sequences.txt",data)

    Append a third sequence to the file. Also turn off the append warning message.

    warnState = warning; %Save the current warning state
warning('off','Bioinfo:fastawrite:AppendToFile'); 
fastawrite("my_sequences.txt","Third Sequence","TACTGACTTC")

    Restore the warning to previous setttings.

    warning(warnState)

    Open the file.

    open my_sequences.txt

    Input Arguments

    collapse all

    File name or a path and file name for saving the FASTA-formatted data, specified as a character vector or string scalar. If you specify only a file name, fastawrite saves the file to the MATLAB® Current Folder. If you specify an existing file, fastawrite appends the data to the file, instead of overwriting the file.

    Tip

    To append FASTA-formatted data to an existing file, simply specify that file name. fastawrite adds the data to the end of the file.

    If you are using fastawrite in a script, you can disable the append warning message by entering the following command lines before the fastawrite command:

    warnState = warning %Save the current warning state
warning('off','Bioinfo:fastawrite:AppendToFile');
    Then enter the following command line after the fastawrite command:
    warning(warnState) %Reset warning state to previous settings

    Data Types: char | string

    Sequence data to be written to File, specified as one of the following.

    • Character vector or string scalar containing a sequence.

    • Structure containing the fields Header and Sequence.

    • Structure containing sequence information from the GenBank® or GenPept database. The genbankread, getgenbank, genpeptread, or getgenpept functions return such structures.

    • Character array, where each row is a sequence.

    Data Types: char | string | structure | array

    Header information about the sequence, specified as a character vector or string scalar.

    Data Types: char | string

    Amino acid or nucleotide sequence using the standard IUB/IUPAC letter or integer codes, specified as a character vector or string scalar. For a list of valid characters, see Amino Acid Lookup or Nucleotide Lookup.

    Data Types: char | string

    Version History

    Introduced before R2006a

    See Also

    | | | | | | | | | | | | |