MMParse parses MetaMaps output files. It was originally written for analysis of nanopore adaptive sampling data.
A Java JAR file can be found in the target directory.
Inputs are two .reads2Taxon files, one for the enriched channels, one for control channels.
To run:
java -jar MMParse.jar -count -control control.reads2Taxon -enriched enriched.read2Taxon -lengths readlengths.txt -taxon 47420 -taxonomy /path/to/taxonomy
The lengths file is a two column tab separated file consiting of read ID and read length. It can be generated using the get_contig_stats.pl script in the bin directory, e.g.:
get_contig_stats.pl -i input.fastq -fastq -r readlengths.txt
The taxon is the target taxon. Any descendent of this taxon will be counted as a hit.
The taxonomy path leads to a directory containing nodes.dmp and names.dmp.
MMParse can also be used to generate a comma separated taxon,count file for importing into MEGAN. Use:
java -jar MMParse.jar -megan -input sample.reads2Taxon -taxonomy /path/to/taxonomy