Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages

Example 1: File Handling

General information about peak and feature maps

If you want some general information about a peak or feature map, use the FileInfo tool.

Validation of XML files

If you are experiencing problems while processing an XML file you can check if the file does validate against the XML schema using the FileInfo tool.

Validation is available for several file formats including MzData, FeatureXML, IdXML.

Converting your files to mzData

The TOPP tools work only on the HUPO-PSI mzData format. If you need to convert mzXML or ANDI/MS data to mzData, you can do that using the FileConverter, e.g.
FileConverter -in infile.mzXML -out outfile.mzData
If you use the format names as file extension, the tool derives the format from the extension. For other extensions, the file formats of the input and output file can be given explicitly.

Converting between DTA and mzData

Sequest DTA files can be extracted from a mzData file using the DTAExtractor:
DTAExtractor -in infile.mzData -out outfile
The retention time of a scan, the precursor mass-to-charge ratio (for MS/MS scans) and the file extension are appended to the output file name.

To combine several files (e.g. DTA files) to an mzData file use the FileMerger:

FileMerger -in infile_list.txt -out outfile.mzData
The retention times of the scans can be generated, taken from the infile_list.txt or can be extrated from the DTA file names. See the FileMerger documentation for details.

Extracting part of the data from a file

If you want to extract part of the data from an mzData file, you can use the FileFilter tool. It allows filtering for RT, m/z and intensity range or for MS level. To extract the MS/MS scans between retention time 100 and 1500, you would use the following command:
FileFilter -in infile.mzData -levels 2 -rt 100:1500 -out outfile.mzData

Generated Tue Apr 1 15:36:40 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1