This tools merges several OTU maps into one OTU map. It has an option to skip over certain prefixes that should not appear in the merged output file.
MergeOtuMaps requires Java 8 to be installed on your device. Download Java 8 here or install via your distribution's package manager.
Download the latest version of MergeOtuMaps here. To generate the usage run:
java -jar <MergeOtuMaps_jar> --help
MergeOtuMaps takes several OTU maps and merges them in a single file.
You can ignore certain prefixes in the OTU maps so these entries
are not included in the output file using the
To merge two OTU maps and ignore the prefix
java -jar <MergeOtuMaps_jar> \ -I OtuMap1 \ -I OtuMap2 \ -o MergedOtuMaps \ -p seq8
Usage for MergeOtuMaps:
|Option||Required||Can occur multiple times||Description|
|--log_level, -l||no||no||Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'|
|--help, -h||no||no||Print usage|
|--version, -v||no||no||Print version|
|--input, -I||yes||yes (unlimited)||Input OTU map. Flag needs to be specified at least 2 times: -I OTUmap1 -I OTUmap2. There is no limit to the number of OTU maps that can be merged.|
|--output, -o||yes||no||Output OTU map file.|
|--skipPrefix, -p||no||yes (unlimited)||Prefix that will not be included in the output file. Flag can be used multiple times.|
MergeOtuMaps is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of BIOPET pipelines.
MergeOtuMaps is build using sbt. Before submitting a pull request, make sure all tests can be passed by
sbt test from the project's root. We recommend using an IDE to work on MergeOtuMaps. We have had
good results with this IDE.