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iracooke/thermoid_to_scan_onlyid.sh

Created December 9, 2015 05:22
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File Cleanup for PRIDE
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thermoid_to_scan_onlyid.sh
#!/bin/bash
# Converts an mzID file from Thermo nativeID format to scan number only nativeID format
file=$1
sed -i.bak s/controllerType\=[0-9]\ controllerNumber\=[0-9]\ // $file
sed -i.bak s/Thermo\ nativeID\ format/scan\ number\ only\ nativeID\ format/ $file
sed -i.back s/MS\:1000768/MS\:1000776/ $file
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iracooke commented Dec 9, 2015

For some reason our MS-GF outputs end up with Thermo native ID. The ontology specifies this as

ControllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger

It can easily be converted to scan number only native ID format which looks like

Scan=xsd:nonNegativeInteger

This script used sed to convert the IDs and then update the SpectrumIDFormat tag to reflect the change

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