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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.

Note
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

TextExporter -- Exports various XML formats to a text file.
Version: 2.0.0 May 29 2015, 13:57:09, Revision: GIT-NOTFOUND

Usage:
  TextExporter <options>

Options (mandatory options marked with '*'):
  -in <file>*                         Input file  (valid formats: 'featureXML', 'consensusXML', 'idXML', 'mzM
                                      L')
  -out <file>                         Output file (mandatory for featureXML and idXML) (valid formats: 'csv')
  -separator <sep>                    The used separator character(s); if not set the 'tab' character is used
  -replacement <string>               Used to replace occurrences of the separator in strings before writing,
                                      if 'quoting' is 'none' (default: '_')
  -quoting <method>                   Method for quoting of strings: 'none' for no quoting, 'double' for quot
                                      ing with doubling of embedded quotes,
                                      'escape' for quoting with backslash-escaping of embedded quotes (defau
                                      lt: 'none' valid: 'none', 'double', 'escape')
  -no_ids                             Supresses output of identification data.
                                      

Options for featureXML input files:
  -feature:minimal                    Set this flag to write only three attributes: RT, m/z, and intensity.

                                      

Options for idXML input files:
  -id:proteins_only                   Set this flag if you want only protein information from an idXML file
  -id:peptides_only                   Set this flag if you want only peptide information from an idXML file
  -id:first_dim_rt                    If this flag is set the first_dim RT of the peptide hits will also be 
                                      printed (if present).

                                      

Options for consensusXML input files:
  -consensus:centroids <file>         Output file for centroids of consensus features (valid formats: 'csv')
  -consensus:elements <file>          Output file for elements of consensus features (valid formats: 'csv')
  -consensus:features <file>          Output file for consensus features and contained elements from all maps
                                      (writes 'nan's if elements are missing) (valid formats: 'csv')
  -consensus:sorting_method <method>  Sorting options can be combined. The precedence is: sort_by_size, sort_
                                      by_maps, sorting_method (default: 'none' valid: 'none', 'RT', 'MZ',
                                      'RT_then_MZ', 'intensity', 'quality_decreasing', 'quality_increasing')
  -consensus:sort_by_maps             Apply a stable sort by the covered maps, lexicographically
  -consensus:sort_by_size             Apply a stable sort by decreasing size (i.e., the number of elements)

                                      
Common TOPP options:
  -ini <file>                         Use the given TOPP INI file
  -threads <n>                        Sets the number of threads allowed to be used by the TOPP tool (default
                                      : '1')
  -write_ini <file>                   Writes the default configuration file
  --help                              Shows options
  --helphelp                          Shows all options (including advanced)

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+TextExporterExports various XML formats to a text file.
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'TextExporter'
in Input file input file*.featureXML,*.consensusXML,*.idXML,*.mzML
out Output file (mandatory for featureXML and idXML)output file*.csv
separator The used separator character(s); if not set the 'tab' character is used
replacement_ Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'
quotingnone Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,
'escape' for quoting with backslash-escaping of embedded quotes
none,double,escape
no_idsfalse Supresses output of identification data.true,false
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue,false
forcefalse Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false
+++featureOptions for featureXML input files
minimalfalse Set this flag to write only three attributes: RT, m/z, and intensity.true,false
+++idOptions for idXML input files
proteins_onlyfalse Set this flag if you want only protein information from an idXML filetrue,false
peptides_onlyfalse Set this flag if you want only peptide information from an idXML filetrue,false
first_dim_rtfalse If this flag is set the first_dim RT of the peptide hits will also be printed (if present).true,false
+++consensusOptions for consensusXML input files
centroids Output file for centroids of consensus featuresoutput file*.csv
elements Output file for elements of consensus featuresoutput file*.csv
features Output file for consensus features and contained elements from all maps (writes 'nan's if elements are missing)output file*.csv
sorting_methodnone Sorting options can be combined. The precedence is: sort_by_size, sort_by_maps, sorting_methodnone,RT,MZ,RT_then_MZ,intensity,quality_decreasing,quality_increasing
sort_by_mapsfalse Apply a stable sort by the covered maps, lexicographicallytrue,false
sort_by_sizefalse Apply a stable sort by decreasing size (i.e., the number of elements)true,false

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:34 using doxygen 1.8.9.1