Bioinformatics Toolbox™

fastawrite - Write to file using FASTA format

Syntax

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

Arguments

`File`	String specifying either a file name or a path and file name for saving the FASTA-formatted data. If you specify only a file name, the file is saved to the MATLAB^® Current Directory.
`Data`	Any of the following: String 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`.
`Header`	String or name of variable containing information about the sequence. This text will be included in the header of the FASTA-formatted file, `File`.
`Sequence`	String 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.

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, and the data will be added 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 entering the following command line after the fastawrite command:

warning(warnState) %Reset warning state to previous settings

Examples

Writing a Coding Region to a FASTA-Formatted File

Retrieve the sequence for the human p53 gene from the GenBank database.
```
seq = getgenbank('NM_000546');
```

Find the CDS line in the FEATURES information.

cdsline = strmatch('CDS',seq.Features)

cdsline =

    23

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

[start,stop] = strread(seq.Features(cdsline,:),'%*s%d..%d')

start =

   252

stop =

   1433

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);
```

Saving Multiple Sequences to a FASTA-Formatted File

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)
```

Display the FASTA-formatted file, my_sequences.txt.

type('my_sequences.txt')

>First sequence
ACACAGGAAA

>Second sequence
ACGTCAGGTC

Appending Sequences to a FASTA-Formatted File

If you haven't already done so, create the FASTA-formatted file, my_sequences.txt, described in Saving Multiple Sequences to a FASTA-Formatted File.

Append a third sequence to the file.

fastawrite('my_sequences.txt','Third sequence','TACTGACTTC')