Read data from FASTA file
FASTAData = fastaread(File)
[Header, Sequence]
= fastaread(File)
... = fastaread(File,
...'IgnoreGaps', IgnoreGapsValue, ...)
... = fastaread(File, ...'Blockread', BlockreadValue,
...)
... = fastaread(File, ...'TrimHeaders', TrimHeadersValue,
...)
File | Either of the following:
|
IgnoreGapsValue | Controls the removal of gap symbols. Choices are true or false (default). |
BlockreadValue | Scalar or vector that controls the reading of a single sequence
entry or block of sequence entries from a FASTA-formatted file containing
multiple sequences. Enter a scalar N to
read the Nth entry in the file. Enter a
1-by-2 vector [ 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. |
TrimHeadersValue | Specifies whether to trim the header after the first
white space character. White space characters include a space (char(32))
and a tab (char(9)). Choices are |
FASTAData | MATLAB structure with the fields Header and Sequence. |
fastaread reads data from a FASTA-formatted
file into a MATLAB structure with the following fields.
| Field | Description |
|---|---|
Header | Header information. |
Sequence | Single letter-code representation of a nucleotide sequence. |
A FASTA-formatted file 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 must use the standard IUB/IUPAC amino acid and nucleotide
letter codes.
For a list of codes, see aminolookup and baselookup.
FASTAData = fastaread(File)FASTAData.HeaderFASTAData.Sequence
[ reads data
from a file into separate variables. If the file contains multiple
sequences, then Header, Sequence]
= fastaread(File)Header and Sequence are
cell arrays of header and sequence information.
... = fastaread( calls File, ...'PropertyName', PropertyValue, ...)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 pairs and structures). These property name/property
value pairs are as follows:
... = fastaread(,
when File,
...'IgnoreGaps', IgnoreGapsValue, ...)IgnoreGapsValue is true,
removes any gap symbol ('-' or '.')
from the sequences. Default is false.
... = fastaread( lets you read in a single sequence entry or block
of sequence entries from a file containing multiple sequences. If File, ...'Blockread', BlockreadValue,
...)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.
... = fastaread( specifies whether to trim the header to the first
white space. File, ...'TrimHeaders', TrimHeadersValue,
...)
aminolookup | baselookup | BioIndexedFile | emblread | fastainfo | fastawrite | fastqinfo | fastqread | fastqwrite | genbankread | genpeptread | multialignread | saminfo | samread | seqprofile | seqviewer | sffinfo | sffread