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simple wrapper around the Unimod amino acid modificatins database

Project description

David's useful Unimod Wrapper
=============================


This is a simple python module to wrap the Unimod XML file in a readily
accessible form for python programemrs.
A copy of the unimod.xml file is included.

Dependencies
============
No dependencies that are not in a standard >2.4 python distribution.

Usage
=====

1. simple usage. Use the built in file.

>>> import Unimod.unimod
>>> db=Unimod.unimod.database

2. Use your own file
>>> import Unimod.Database
>>> db=Unimod.Database.Database(file="my unimod file")

3. Getting element info
Use the get_element(label) method and a dictionary is returned.
>>> db.get_element('H')
{'avge_mass': '1.00794', 'title': 'H', 'full_name': 'Hydrogen', 'mono_mass': '1.007825035'}

All labels are supported, and additionally the common isotopes as labels as well

>>> db.get_element('O')
{'avge_mass': '15.9994', 'title': 'O', 'full_name': 'Oxygen', 'mono_mass': '15.99491463'}
>>> db.get_element('18O')
{'avge_mass': '17.9991603', 'title': '18O', 'full_name': 'Oxygen18', 'mono_mass': '17.9991603'}
>>> db.get_element('16O')
{'avge_mass': '15.9994', 'title': 'O', 'full_name': 'Oxygen', 'mono_mass': '15.99491463'}

4. getting modification info

Use the get_label(modification) method
>>> db.get_label('Phospho')
{'delta_mono_mass': '79.966331',
'group_of_poster': 'admin',
'delta_avge_mass': '79.9799',
'username_of_poster': 'unimod',
'title': 'Phospho',
'delta_composition': 'H O(3) P',
'sites': {
'C': {'position': 'Anywhere', 'hidden': 'true', 'site': 'C', 'classification': 'Post-translational', 'spec_group': '5'},
'D': {'position': 'Anywhere', 'hidden': 'true', 'site': 'D', 'classification': 'Post-translational', 'spec_group': '3'},
'H': {'position': 'Anywhere', 'hidden': 'true', 'site': 'H', 'classification': 'Post-translational', 'spec_group': '4'},
'K': {'position': 'Anywhere', 'hidden': 'true', 'site': 'K', 'classification': 'Other', 'spec_group': '7'},
'S': {'position': 'Anywhere', 'hidden': 'false', 'site': 'S', 'classification': 'Post-translational', 'spec_group': '1'},
'R': {'position': 'Anywhere', 'hidden': 'true', 'site': 'R', 'classification': 'Post-translational', 'spec_group': '6'},
'T': {'position': 'Anywhere', 'hidden': 'false', 'site': 'T', 'classification': 'Post-translational', 'spec_group': '1'},
'Y': {'position': 'Anywhere', 'hidden': 'false', 'site': 'Y', 'classification': 'Post-translational', 'spec_group': '2'}
},
'spec_group': {
'1': ['T', 'S'],
'3': ['D'],
'2': ['Y'],
'5': ['C'],
'4': ['H'],
'7': ['K'],
'6': ['R']
},
'date_time_posted': '2002-08-19 19:17:11',
'date_time_modified': '2011-11-25 10:55:54',
'full_name': 'Phosphorylation',
'record_id': '21',
'approved': 'true'
}

In this dictionary are two fields, 'sites' which contains info for each amino acid, and 'spec_group' which contains the specificity grouping for the modification.

5. Searching for labels
Pass a regular expression in text form to the list_labels method.

>>> db.list_labels('.*Phospho.*')
['Phosphoguanosine', 'Phosphopantetheine', 'PhosphoHex', 'Phosphopropargyl', 'PhosphoribosyldephosphoCoA', 'PhosphoHexNAc', 'Phosphoadenosine', 'PhosphoUridine', 'Phosphogluconoylation', 'Label:13C(9)+Phospho', 'Phospho']

Author
======

Dr David Martin, University of Dundee, UK. d.m.a.martin@dundee.ac.uk

Copyright
=========

(c) David Martin 2012

License
=======

Unimod data is redistributed under the terms of the licensing described on the
Unimod website http://www.unimod.org - in short you can redistribute the data
included as long as you permit unrestricted subsequent redistribution.

The software code is licensed under the Creative Commons Attribution License
http://creativecommons.org/licenses/by/3.0/ You may use, alter and publish work
based on the code as long as you acknowledge the use of the code with an
appropriate statement such as this in the copyright/attribution/help text: "Includes the python Unimod wrapper by Dr David Martin, University of Dundee".







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