Mercurial > repos > edward-kirton > hmmscan

annotate hmmer/hmmer.py @ 0:914f50b4c8c1 default tip

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author edward-kirton
date Tue, 07 Jun 2011 16:41:43 -0400
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914f50b4c8c1 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 """
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2 Hmmer classes
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3 """
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4
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5 import data
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6 import logging
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7 import re
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8 import string
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9 from cgi import escape
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10 from galaxy.datatypes.metadata import MetadataElement
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11 from galaxy.datatypes import metadata
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12 import galaxy.model
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13 from galaxy import util
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14 from sniff import *
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15
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16 log = logging.getLogger(__name__)
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17
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18 class Hmm( data.Text ):
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19 """Class for hmmer database files"""
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20
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21 file_ext = 'hmm'
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22
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23 def init_meta( self, dataset, copy_from=None ):
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24 data.Text.init_meta( self, dataset, copy_from=copy_from )
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25
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26 class HmmPressed( Hmm ):
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27 """Class describing a hmmer database produced by hmmpress"""
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28
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29 file_ext = 'hmmPressed'
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30 composite_type='basic'
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31
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32 MetadataElement( readonly=True, optional=True, visible=False, no_value=0 )
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33
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34 def __init__(self,**kwd):
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35 data.Data.__init__(self, **kwd)
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36 self.add_composite_file('hmm')
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37 self.add_composite_file('hmm.h3m')
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38 self.add_composite_file('hmm.h3i')
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39 self.add_composite_file('hmm.h3f')
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40 self.add_composite_file('hmm.h3p')
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41 def set_peek( self, dataset, is_multi_byte=False ):
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42 if not dataset.dataset.purged:
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43 dataset.peek = "Folder of multiple files"
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44 dataset.blurb = "Folder of multiple files"
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45 else:
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46 dataset.peek = 'file does not exist'
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47 dataset.blurb = 'file purged from disk'
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48 def display_peek( self, dataset ):
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49 try:
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50 return dataset.peek
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51 except:
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52 return "Folder of multiple files"
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53 def get_mime(self):
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54 """Returns the mime type of the datatype"""
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55 return 'text/plain'