OpenMS  2.5.0
SequenceCoverageCalculator

Prints information about idXML files.

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:


SequenceCoverageCalculator -- Prints information about idXML files.

Full documentation: http://www.openms.de/documentation/UTILS_SequenceCoverageCalculator.html

Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

To cite OpenMS:

  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.



Usage:

  SequenceCoverageCalculator <options>



Options (mandatory options marked with '*'):

  -in_database <file>*  Input file containing the database in FASTA format (valid formats: 'fasta')

  -in_peptides <file>*  Input file containing the identified peptides (valid formats: 'idXML')

  -out <file>           Optional text output file. If left out, the output is written to the command line. 

                        (valid formats: 'txt')

                        

Common UTIL 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
+SequenceCoverageCalculatorPrints information about idXML files.
version2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1Instance '1' section for 'SequenceCoverageCalculator'
in_database input file containing the database in FASTA formatinput file*.fasta
in_peptides input file containing the identified peptidesinput file*.idXML
out Optional text output file. If left out, the output is written to the command line.output file*.txt
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