Learn more about Bioinformatics Toolbox

sffinfo - Return information about SFF file

Syntax

InfoStruct = sffinfo(File)

Description

InfoStruct = sffinfo(File) returns a MATLAB structure containing summary information about a Standard Flowgram Format (SFF) file.

Input Arguments

File	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.

Output Arguments

InfoStruct

MATLAB structure containing summary information about an SFF file. The structure contains the following fields. Field Description Filename Name of the file. FileModDate Modification date of the file. FileSize Size of the file in bytes. Version Version number of the file. FlowgramCode Code of the format used to encode flowgram values. NumberOfReads Number of sequence reads in the file. NumberOfFlowsPerRead Number of flows for each read. FlowChars Bases used in each flow. KeySequence String of bases in the key sequence.

Examples

The SFF file, SRR013472.sff, used in this example is not provided with the Bioinformatics Toolbox software. You can download sample SFF files from:

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=main&m=main&s=main

Return a summary of the contents of an SFF file:

info = sffinfo('SRR013472.sff')

info = 

                Filename: 'SRR013472.sff'
             FileModDate: '23-Feb-2009 15:14:36'
                FileSize: 6632392
                 Version: [0 0 0 1]
            FlowgramCode: 1
           NumberOfReads: 3546
    NumberOfFlowsPerRead: 440
               FlowChars: [1x440 char]
             KeySequence: 'TCAG'

See Also

fastainfo | fastaread | fastawrite | fastqinfo | fastqread | fastqwrite | saminfo | samread | sffread

Tutorials

• Working with SFF Files from the 454 Genome Sequencer FLX System

Related Links

• http://www.454.com/
• http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=main&m=main&s=main

© 1984-2010- The MathWorks, Inc.    -   Site Help   -   Patents   -   Trademarks   -   Privacy Policy   -   Preventing Piracy   -   RSS