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To run Percolator on a Tab-delimited input, use the following options:
$ percolator tab-delimited -X output.xml
where tab-delimited is a valid Tab-delimited file.
To run Percolator on a XML file in PIN format, use the
$ percolator -k pin.xml -X output.xml
Tab-delimited file format
Percolator accepts input in a simple Tab-delimited format where each row contains a per PSM:
id <tab> label <tab> scannr <tab> feature1 <tab> ... <tab> featureN <tab> peptide <tab> proteinId1 <tab> .. <tab> proteinIdM
label is a flag set to
1 for target PSMs, and
-1 for decoys, and scannum should be an integer value. If Percolator is run with
--doc option the first and second feature (fourth and fifth column) should contain the retention time and difference between observed and calculated mass/charge.
These lines should be preceded by one line specifying a column header with the exact String
ScanNr, followed by the names of the individual features separated by tabs, and optionally a Default scoring vector which should contain the String
DefaultDirection in its id (first) column, e.g.
PSMId <tab> Label <tab> ScanNr <tab> feature1name <tab> ... <tab> featureNname <tab> Peptide <tab> Proteins DefaultDirection <tab> - <tab> - <tab> feature1weight <tab> ... <tab> featureNweight [optional]
Supposing pin.xml is a valid XML file in PIN format, it is possible to use Percolator as a converter and generate Tab-delimited files from PIN files by using the following options:
$ percolator -k pin.xml -J tab-delimited
After a successful termination, tab-delimited will contain a valid Tab-delimited file that can be fed to Percolator as described above; the file will be overwritten, or created if not already existing.
It is also still possible to output XML files in PIN format by using a
-k flag instead of the
-o flag for the tab delimited-file format.
PIN and POUT file formats
Since version 1.15, Percolator has its own input format called PIN (for Percolator-IN). PIN files are XML files whose structure is defined by the schema percolator_in.xml.
Similarly, Percolator’s output (called PUT for Percolator-OUT) is defined by the schema percolator_out.xml.
Supposing pin.xml is a valid XML file in PIN format, Percolator can be run using the following options:
$ percolator [options] -k pin.xml -X output.xml
After a successful termination, output.xml will contain Percolator’s output formatted in POUT format; the file will be overwritten, or created if not already existing.