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 (predicted retention time)
additional column for PEPTIDE lines: predicted_pt (predicted proteotypicity)

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: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

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 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 quoting with doubling of embedded quotes,
                                           'escape' for quoting with backslash-escaping of embedded quotes (
                                           default: 'none' valid: 'none', 'double', 'escape')
  -no_ids                                  Suppresses output of identification data.
                                           

Options for featureXML input files:
  -feature:minimal                         Set this flag to write only three attributes: RT, m/z, and intensi
                                           ty.
  -feature:add_metavalues <min_frequency>  Add columns for meta values which occur with a certain frequency 
                                           (0-100%). Set to -1 to omit meta values (default). (default: '-1'
                                           min: '-1' max: '100')

                                           

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).
  -id:add_metavalues <min_frequency>       Add columns for meta values which occur with a certain frequency 
                                           (0-100%). Set to -1 to omit meta values (default). (default: '-1'
                                           min: '-1' max: '100')
  -id:add_hit_metavalues <min_frequency>   Add columns for meta values which occur with a certain frequency 
                                           (0-100%). Set to -1 to omit meta values (default). (default: '-1'
                                           min: '-1' max: '100')

                                           

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_i
                                           ncreasing')
  -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 elemen
                                           ts)

                                           
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.

version2.3.0 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 Suppresses 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

add_metavalues-1 Add columns for meta values which occur with a certain frequency (0-100%). Set to -1 to omit meta values (default).-1:100

+++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

add_metavalues-1 Add columns for meta values which occur with a certain frequency (0-100%). Set to -1 to omit meta values (default).-1:100

add_hit_metavalues-1 Add columns for meta values which occur with a certain frequency (0-100%). Set to -1 to omit meta values (default).-1:100

+++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