Conversion Between OpenMS XML Formats and Text Formats#
Export of OpenMS XML formats#
As TOPP offers no functionality for statistical analysis, this step is normally done using external statistics packages. In order to export the OpenMS XML formats into an appropriate format for these packages the TOPP TextExporter can be used.
It converts the the following OpenMS XML formats to text files:
featureXML
idXML
consensusXML
The use of the TextExporter
is is very simple:
TextExporter -in infile.idXML -out outfile.txt
Import of feature data to OpenMS#
OpenMS offers a lot of visualization and analysis functionality for feature data.
Feature data in text format, e.g. from other analysis tools, can be imported using the TextImporter
. The default
mode accepts comma separated values containing the following columns: RT, m/z, intensity. Additionally meta data
columns may follow. If meta data is used, meta data column names have to be specified in a header line. Without headers:
1201 503.123 1435000
1201 1006.246 1235200
Or with headers:
RT m/z Int isHeavy myMeta
1201 503.123 1435000 true 2
1201 1006.246 1235200 maybe 1
Example invocation:
TextImporter -in infile.txt -out outfile.featureXML
The tool also supports data from msInspect,SpecArray and Kroenik(Hardkloer sibling), just specify the -mode
option
accordingly.
Import of protein/peptide identification data to OpenMS#
Peptide/protein identification data from several identification engines can be converted to idXML format using the IDFileConverter tool.
It can currently read the following formats:
Sequest output folder
pepXML file
idXML file
It can currently write the following formats:
pepXML
idXML
This example shows how to convert pepXML to idXML:
IDFileConverter -in infile.pepXML -out outfile.idXML