charge_czar.py

Description:

Use a support vector machine to classify multiply-charged low-resolution tandem mass spectra as either +2 or +3 and eliminate the low-probability spectrum charge-state assignment.

Usage:

charge_czar.py [options] 
  --in <input filename> 
  [ --out <output filename> | --suffix <output file suffix] 
  [ --annot <annotation filename>]

Input:

<input filename> - A file or directory containing files with tandem mass spectra. The exact form of input (e.g. ms2, dta) should be indicated using one of the options listed below. Default input is a directory containing ms2 files.

Output:

<output filename> - optional output file or directory in which to place the filtered tandem mass spectra output file(s). The format of the output files is the same as the input format. If no output filename is given, output is placed in a file named the same as the input with a suffix <output file suffix> as specified by the –suffix option. If no suffix option is given, the suffix is ".czar.<suffix>", where <suffix> is the original suffix of the input files. This option is mutually exclusive with the –suffix option.
<annotation filename> - An optional four-column tab-delimited output file with the assigned charge state and confidence level for each spectrum. Columns are filename, spectrum scan number, charge state assignment (2, 3 or A for ambiguous), and confidence value (ranges from 0 to 1 indicating the probability of assignment to the +3 charge state).

Options:

--dta – The input files will be in dta format. The names of the files are required to have .dta as a suffix. This option is mutually exclusive with any other input file format options (e.g. the –ms2 option).
--ms2 – The input files will be in ms2 format. The names of the files are required to have .ms2 as a suffix. This option is mutually exclusive with any other input file format options (e.g. the –dta option).
--remove-input – The input files will be removed.
--suffix – The output file suffix to give to each output file. The default is .czar.<suffix>, where <suffix> is the input file suffix, something like .ms2 or .dta. This option is mutually exclusive with the –out.
--two-threshold – The (maximum) probability threshold for calling a spectrum +2. The default is 0.05.
--three-threshold – The (minimum) probability threshold for calling a spectrum +3. The default is 0.90.

Warning messages:

Warning: There are currently no defined warning messages!

Bugs:

The Czar does not have bugs, it has features.

ChargeCzar