Mercurial > repos > edward-kirton > hmmer
view hmmer.py @ 1:66f8262e1686
add datatype
author | eskirton@lbl.gov |
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date | Mon, 05 Mar 2012 22:51:04 -0800 |
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""" Hmmer classes """ import data import logging import re import string from cgi import escape from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes import metadata import galaxy.model from galaxy import util from sniff import * log = logging.getLogger(__name__) class Hmm( data.Text ): """Class for hmmer database files""" file_ext = 'hmm' def init_meta( self, dataset, copy_from=None ): data.Text.init_meta( self, dataset, copy_from=copy_from ) class HmmPressed( Hmm ): """Class describing a hmmer database produced by hmmpress""" file_ext = 'hmmPressed' composite_type='basic' MetadataElement( readonly=True, optional=True, visible=False, no_value=0 ) def __init__(self,**kwd): data.Data.__init__(self, **kwd) self.add_composite_file('hmm.h3m') self.add_composite_file('hmm.h3i') self.add_composite_file('hmm.h3f') self.add_composite_file('hmm.h3p') def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = "Folder of multiple files" dataset.blurb = "Folder of multiple files" else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' def display_peek( self, dataset ): try: return dataset.peek except: return "Folder of multiple files" def get_mime(self): """Returns the mime type of the datatype""" return 'text/plain'