Partition: Difference between revisions
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-b Given the input file, build a partition. | -b Given the input file, build a partition. | ||
-m Metadata file that will be used to populate the partitions. | -m Metadata file that will be used to populate the partitions. | ||
-h Header information for the metadata, if not present column information | -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. | -f Input fasta file. | ||
-s Split the fasta file based on the partition information and output to the directory. | -s Split the fasta file based on the partition information and output to the directory. | ||
-o Name of the output .part file. | -o Name of the output .part file. | ||
-c Convert an old partition format into the new xml format. | -c Convert an old partition format into the new xml format. | ||
Revision as of 14:04, 13 August 2009
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 [latest 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.