Partition: Difference between revisions
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== Summary == | ==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: | 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/Partition.py ['''stable'''] | ||
/fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds'''] | /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds'''] | ||
''' Options ''' | '''Options''' | ||
<pre> | <pre> | ||
-p Populate the given partition/XML. | -p Populate the given partition/XML. | ||
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</pre> | </pre> | ||
== Tutorial == | ==Tutorial== | ||
=== Format of a input regular expression (*.re) file === | ===Format of a input regular expression (*.re) file=== | ||
Revision as of 14:14, 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 [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.