Mercurial > repos > edward-kirton > hmmscan
annotate hmmer/hmmer.py @ 0:914f50b4c8c1 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | edward-kirton |
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date | Tue, 07 Jun 2011 16:41:43 -0400 |
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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' |