OpenMS: 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	$\longrightarrow$ TextExporter $\longrightarrow$	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:

first column: RUN / PROTEIN / UNASSIGNEDPEPTIDE / FEATURE / PEPTIDE (indicator for the type of data in the current row)
a RUN line contains information about a protein identification run; further columns: run_id, score_type, score_direction, data_time, search_engine_version, parameters
a PROTEIN line contains data of a protein identified in the previously listed run; further columns: score, rank, accession, coverage, sequence
an UNASSIGNEDPEPTIDE line contains data of peptide hit that was not assigned to any feature; further columns: rt, mz, score, rank, sequence, charge, aa_before, aa_after, score_type, search_identifier, accessions
a FEATURE line contains data of a single feature; further columns: rt, mz, intensity, charge, width, quality, rt_quality, mz_quality, rt_start, rt_end
a PEPTIDE line contains data of a peptide hit annotated to the previous feature; further columns: same as for UNASSIGNEDPEPTIDE

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:

first column: MAP / RUN / PROTEIN / UNASSIGNEDPEPTIDE / CONSENSUS / PEPTIDE (indicator for the type of data in the current row)
a MAP line contains information about a sub-map; further columns: id, filename, label, size (potentially followed by further columns containing meta data, depending on the input)
a CONSENSUS line contains data of a single consensus feature; further columns: rt_cf, mz_cf, intensity_cf, charge_cf, width_cf, quality_cf, rt_X0, mz_X0, ..., rt_X1, mz_X1, ...
"..._cf" columns refer to the consensus feature itself, "..._Xi" columns refer to a sub-feature from the map with ID "Xi" (no quality column in this case); missing sub-features are indicated by "nan" values
see above for the formats of RUN, PROTEIN, UNASSIGNEDPEPTIDE, PEPTIDE lines

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

Output format produced for the consensus_centroids parameter:

one line per consensus centroid
columns: rt, mz, intensity, charge, width, quality

Output format produced for the consensus_elements parameter:

one line per sub-feature (element) of a consensus feature
first column: H / L (indicator for new/repeated element)
H indicates a new element, L indicates the replication of the first element of the current consensus feature (for plotting)
further columns: rt, mz, intensity, charge, width, rt_cf, mz_cf, intensity_cf, charge_cf, width_cf, quality_cf
"..._cf" columns refer to the consensus feature, the other columns refer to the sub-feature

Output format produced for the consensus_features parameter:

one line per consensus feature (suitable for processing with e.g. R)
- columns: same as for a CONSENSUS line above, followed by additional columns for identification data
- additional columns: peptide_N0, n_diff_peptides_N0, protein_N0, n_diff_proteins_N0, peptide_N1, ...
- "..._Ni" columns refer to the identification run with index "Ni", n_diff_... stands for "number of different ..."; different peptides/proteins in one column are separated by "/"

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

idXML input:

first column: RUN / PROTEIN / PEPTIDE (indicator for the type of data in the current row)
see above for the formats of RUN, PROTEIN, PEPTIDE lines
additional column for PEPTIDE lines: predicted_rt

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:

TextExporter -- Exports various XML formats to a text file.
Version: 1.10.0 Mar  7 2013, 08:30:22, Revision: unknown

Usage:
  TextExporter <options>

Options (mandatory options marked with '*'):
  -in <file>*                                   Input file  (valid formats: 'featureXML', 'consensusXML', 
                                                'idXML', 'mzML')
  -out <file>                                   Output file (mandatory for featureXML and idXML) (valid forma
                                                ts: 'csv')
  -separator <sep>                              The used separator character(s); if not set the 'tab' charact
                                                er is used (default: '	')
  -replacement <string>                         Used to replace occurrences of the separator in strings befor
                                                e writing, if 'quoting' is 'none' (default: '_')
  -quoting <method>                             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 quo
                                                tes (default: '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 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 files:
  -consensusfeature:consensus_centroids <file>  Output file for centroids of consensus features (valid format
                                                s: 'csv')
  -consensusfeature:consensus_elements <file>   Output file for elements of consensus features (valid formats
                                                : 'csv')
  -consensusfeature:consensus_features <file>   Output file for consensus features and contained elements 
                                                from all maps (writes 'nan's if elements are missing) (valid
                                                formats: 'csv')
  -consensusfeature: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_decre
                                                asing', 'quality_increasing')
  -consensusfeature:sort_by_maps                Apply a stable sort by the covered maps, lexicographically
  -consensusfeature: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.

version1.10.0 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 quotesnone,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

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 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

+++consensusfeatureOptions for consensusXML files

consensus_centroids Output file for centroids of consensus featuresoutput file*.csv

consensus_elements Output file for elements of consensus featuresoutput file*.csv

consensus_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