Difference between revisions of "Partition"

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-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
+
-s    Split the fasta file based on the partition information and output to the directory.
      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 14:03, 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.