public class ProcessBlastReport extends Object
Driver script that parses a blast report and pumps the result through a configurable chain of filters and handlers.
This command expects to be given a blast report as the first argument, a SearchContentHandler with a no-args constructor as the last argument and any number of SearchContentFilters inbetween. It assumes that all classes can be configured using beany accessors (get/setFoo methods). If you supply the class name as-is, the class will be instantiated. If you give the class name followed by brackets, you can put any number of property names and their values within the brackets.
# echo parsing events to stdout
java ProcessBlastReport blast.out ssbind.Echoer
# echo events that are left after all hits with expectedValue greater
# than 0.1 have been removed
java ssbind.ProcessBlastReport blastFile.out \
"ssbind.FilterByValue(maxVal=0.1 keyName=expectedValue)" \
ssbind.Echoer
# echo the percentageIdentity of all alignments between 100 and 200 in length
java ssbind.ProcessBlastReport blastFile.out \
"ssbind.FilterByValue(minVal=100 maxVal=200 keyName=alignmentSize)" \
"ssbind.PropertyEchoer(keyName=percentageIdentity)"
| Constructor and Description |
|---|
ProcessBlastReport() |