Difference between revisions of "Partition"

From Cbcb
Jump to navigation Jump to search
Line 3: Line 3:
 
*/fs/szasmg/metagenomics/Partition/Partition.py [latest stable]
 
*/fs/szasmg/metagenomics/Partition/Partition.py [latest 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 ==
 +
-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.

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.