Use this program to convert the results of a Crux Tide + Percolator analysis to limelight XML suitable for import into the limelight web application. Requires PepXML output and that the Percolator output be represented as XML (see --pout-output option in Crux).
- Download the latest release.
- Run the program
java -jar cruxTide2LimelightXML.jarwith no arguments to see the possible parameters. Requires Java 8.
NOTE: Tide currently contains a couple of issues in its pepxml output. Fixes to tide are currently pending; however, you may run the following *nix commands to "fix" the pepxml so that it may be processed by this converter:
In the crux-output directory, create a backup of your tide-search.target.pep.xml file. The run the following commands:
perl -p -i -e 's/num_tol_term=\"\"/num_tol_term=\"2\"/g' tide-search.target.pep.xml
perl -p -i -e 's/date=\".+?\" /date=\"2020-01-07T17:05:18\" /g' tide-search.target.pep.xml
perl -p -i -e 's/mass=\"nan\"/mass=\"0.0\"/g' tide-search.target.pep.xml
perl -0777 -p -i -e 's/<\/modification_info>\n<modification_info.+//g' tide-search.target.pep.xml
Once that's done you may use the converter as:
Usage: java -jar cruxTide2LimelightXML.jar -d path -f path -o path
Example: java -jar cruxTide2LimelightXML.jar -f /path/to/fasta.fa -d /path/to/crux-output -o ./crux.limelight.xml
Options:
-f [Required] Path to FASTA file used in the experiment.
-d [Required] Path to the output directory for Crux, usually called "crux-output"
Contains percolator XML output and pepXML output from Tide.
-o [Required] Path you to which you would like to output the limelight XML.