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fastawrite

Write to file using FASTA format

Syntax

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

Arguments

File

Character vector specifying either a file name or a path and file name for saving the FASTA-formatted data. 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.

Data

Any of the following:

  • Character vector containing a sequence

  • MATLAB structure containing the fields Header and Sequence

  • MATLAB structure containing sequence information from the GenBank® or GenPept database, such as returned by genbankread, getgenbank, genpeptread, or getgenpept.

HeaderCharacter vector or name of variable containing information about the sequence. This text appears in the header of the FASTA-formatted file, File.
Sequence

Character vector or name of variable containing an amino acid or nucleotide sequence using the standard IUB/IUPAC letter or integer codes. For a list of valid characters, see Amino Acid Lookup or Nucleotide Lookup.

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 https://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml.

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

Examples

Example 16. Writing a Coding Region to a FASTA-Formatted File
  1. Retrieve the sequence for the human p53 gene from the GenBank database.

    seq = getgenbank('NM_000546');
  2. Read the coordinates of the coding region in the CDS line.

    start = seq.CDS.indices(1)
    
    start =
    
       198
    
    stop = seq.CDS.indices(2)
    
    stop =
    
       1379
  3. Extract the coding region.

    codingSeq = seq.Sequence(start:stop);
  4. 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);
Example 17. Saving Multiple Sequences to a FASTA-Formatted File
  1. 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';
    
  2. Write the sequences to a FASTA-formatted file, specifying my_sequences.txt for the file name.

    fastawrite('my_sequences.txt', data)
    
  3. Display the FASTA-formatted file, my_sequences.txt.

    type('my_sequences.txt')
    
    >First sequence
    ACACAGGAAA
    
    >Second sequence
    ACGTCAGGTC
    
Example 18. Appending Sequences to a FASTA-Formatted File
  1. If you haven't already done so, create the FASTA-formatted file, my_sequences.txt, described previously.

  2. Append a third sequence to the file.

    fastawrite('my_sequences.txt','Third sequence','TACTGACTTC')
    
  3. Display the FASTA-formatted file, my_sequences.txt.

    type('my_sequences.txt')
    
    >First sequence
    ACACAGGAAA
    
    >Second sequence
    ACGTCAGGTC
    
    >Third sequence
    TACTGACTTC

Introduced before R2006a

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