Interface

MatthewThe edited this page Apr 5, 2017 · 18 revisions

Percolator can handle two types of input files: tab-delimited (recommended) and XML. Input files can be generated from search engine outputs using our converters.

Getting started

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 -k flag:


$ 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.

Converters

The percolator-converters package contain a set of converters from the output format of sequest/crux (sqt2pin), x!tandem (tandem2pin) and ms-gf+ (msgf2pin) format to tab delimited-file format.

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.

You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.