Partition
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Summary
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]
Options
-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.
Tutorial
Format of an input regular expression (*.re) file
The format of an
[name] key1 = value1 key2 = value2 ... [name2] key1 = value1 ...
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.* ...
Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).