fastaread - Read data from FASTA file

Syntax

FASTAData = fastaread(File) [Header, Sequence] = fastaread(File) ... = fastaread(File, ...'IgnoreGaps', IgnoreGapsValue, ...) ... = fastaread(File, ...'Blockread', BlockreadValue, ...)

Arguments

`File`	FASTA-formatted file (ASCII text file). Enter a file name, a path and file name, or a URL pointing to a file. `File` can also be a MATLAB character array that contains the text for a file name.
`IgnoreGapsValue`	Property to control removing gap symbols. Enter either `true` or `false` (default).
`BlockreadValue`	Property to control reading a single sequence entry or block of sequence entries from a file containing multiple sequences. Enter a scalar `N`, to read the `N`th entry in the file. Enter a 1-by-2 vector [`M1, M2`], to read the block of entries starting at the `M1` entry and ending at the `M2` entry. To read all remaining entries in the file starting at the `M1` entry, enter a positive value for `M1` and enter `Inf` for `M2`.

Return Values

FASTAData MATLAB structure with the fields Header and Sequence.

Description

fastaread reads data from a FASTA-formatted file into a MATLAB structure with the following fields.

Field
`Header`
`Sequence`

A file with a FASTA format begins with a right angle bracket (>) and a single line description. Following this description is the sequence as a series of lines with fewer than 80 characters. Sequences are expected to use the standard IUB/IUPAC amino acid and nucleotide letter codes.

For a list of codes, see aminolookup and baselookup.

FASTAData = fastaread(File) reads a file with a FASTA format and returns the data in a structure. FASTAData.Header is the header information, while FASTAData.Sequence is the sequence stored as a string of letters.

[Header, Sequence] = fastaread(File) reads data from a file into separate variables. If the file contains more than one sequence, then header and sequence are cell arrays of header and sequence information.

... = fastaread(File, ...'PropertyName', PropertyValue, ...) calls fastaread with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. The property name/value pairs can be in any format supported by the function set (for example, name-value string pairs, structures, and name-value cell array pairs). These property name/property value pairs are as follows:

... = fastaread(File, ...'IgnoreGaps', IgnoreGapsValue, ...), when IgnoreGapsValue is true, removes any gap symbol ('-' or '.') from the sequences. Default is false.

... = fastaread(File, ...'Blockread', BlockreadValue, ...) lets you read in a single sequence entry or block of sequence entries from a file containing multiple sequences. If BlockreadValue is a scalar N, then fastaread reads the Nth entry in the file. If BlockreadValue is a 1-by-2 vector [M1, M2], then fastaread reads the block of entries starting at the M1 entry and ending at the M2 entry. To read all remaining entries in the file starting at the M1 entry, enter a positive value for M1 and enter Inf for M2.

Examples

Read the sequence for the human p53 tumor gene.

p53nt = fastaread('p53nt.txt')

Read the sequence for the human p53 tumor protein.

p53aa = fastaread('p53aa.txt')

Read the human mitochondrion genome in FASTA format.

entrezSite = 'http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?';
textOptions = '&txt=on&view=fasta';
genbankID = '&list_uids=NC_001807';
mitochondrion = fastaread([entrezSite textOptions genbankID])