Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:
/fs/szasmg/metagenomics/Partition/Partition.py [stable] /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest, but possibly unstable builds]
-p Populate the given partition/XML. -b Given the input file, build a partition. -m Metadata file that will be used to populate the partitions. -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata. -f Input fasta file. -s Split the fasta file based on the partition information and output to the directory. -o Name of the output .part file. -c Convert an old partition format into the new xml format.
Format of a input regular expression (*.re) file
Example of an input file that clusters animals by their first letter:
[animals] info = all animals [A] info = animals that start with A regexp = a.* [B] info = animals that start with B regexp = b.* ...