Difference between revisions of "Partition"

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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.
      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.