Read data from SFF file
SFFStruct = sffread(
a Standard Flowgram Format (SFF) file and returns the data in a MATLAB® array
SFFStruct = sffread(
sffread(..., ' calls
sffread with optional properties
that use property name/property value pairs. You can specify one or
more properties in any order. Enclose each
single quotation marks. Each
case insensitive. These property name/property value pairs are as
sffread(..., 'Blockread', reads a single sequence entry or block of sequence
entries from an SFF file containing multiple sequences.
sffread(..., 'Feature', specifies the information to include in the return
Character vector or string specifying a file name or path and file name of an SFF file produced by version 1.0 of the Genome Sequencer System data analysis software from 454 Life Sciences. If you specify only a file name, that file must be on the MATLAB search path or in the current folder.
Scalar or vector that controls the reading of a single sequence
entry or block of sequence entries from an SFF file containing multiple
sequences. Enter a scalar
Character vector or string specifying the information to include in the output structure. The
character vector or string includes letters from the alphabet
Array of structures containing information from an SFF file. There is one structure for each read or entry in the file. Each structure contains one or more of the following fields.
The SFF file,
SRR013472.sff, used in these
examples is not provided with the Bioinformatics Toolbox™ software.
You can download sample SFF files from:
Read an entire SFF file:
% Read the contents of an entire SFF file into an % array of structures reads = sffread('SRR013472.sff') reads = 3546x1 struct array with fields: Header Sequence Quality
Read a block of entries from an SFF file:
% Read only the header and sequence information of the % first five reads from an SFF file into an array of structures reads5 = sffread('SRR013472.sff', 'block', [1 5], 'feature', 'hs') reads5 = 5x1 struct array with fields: Header Sequence
Introduced in R2009b