Difference between revisions of "Partition"

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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.

Tutorial

Format of a input regular expression (*.re) file