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TextExporter

This application converts several OpenMS XML formats (featureXML, consensusXML, and idXML) to text files.

potential predecessor tools $ \longrightarrow $ TextExporter $ \longrightarrow $ potential successor tools
almost any TOPP tool external tools (MS Excel, OpenOffice, Notepad)

The goal of this tool is to create output in a table format that is easily readable in Excel or OpenOffice. Lines in the output correspond to rows in the table; the individual columns are delineated by a separator, e.g. tab (default, TSV format) or comma (CSV format).

Output files begin with comment lines, starting with the special character "#". The last such line(s) will be a header with column names, but this may be preceded by more general comments.

Because the OpenMS XML formats contain different kinds of data in a hierarchical structure, TextExporter produces somewhat unusual TSV/CSV files for many inputs: Different lines in the output may belong to different types of data, and the number of columns and the meanings of the individual fields depend on the type. In such cases, the first column always contains an indicator (in capital letters) for the data type of the current line. In addition, some lines have to be understood relative to a previous line, if there is a hierarchical relationship in the data. (See below for details and examples.)

Missing values are represented by "-1" or "nan" in numeric fields and by blanks in character/text fields.

Depending on the input and the parameters, the output contains the following columns:

featureXML input:

With the no_ids flag, only FEATURE lines (without the FEATURE indicator) are written.

With the feature:minimal flag, only the rt, mz, and intensity columns of FEATURE lines are written.

consensusXML input:

Output format produced for the out parameter:

With the no_ids flag, only MAP and CONSENSUS lines are written.

Output format produced for the consensus_centroids parameter:

Output format produced for the consensus_elements parameter:

Output format produced for the consensus_features parameter:

With the no_ids flag, the additional columns are not included.

idXML input:

With the id:proteins_only flag, only RUN and PROTEIN lines are written.

With the id:peptides_only flag, only PEPTIDE lines (without the PEPTIDE indicator) are written.

With the id:first_dim_rt flag, the additional columns rt_first_dim and predicted_rt_first_dim are included for PEPTIDE lines.

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 1.11.1 Documentation generated on Mon Aug 18 2014 14:41:09 using doxygen 1.8.7