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1 """
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2 Complete Genomics datatypes
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3 Birgit Crain - Complete Genomics, Inc
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4 """
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5
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6 import pkg_resources
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7 pkg_resources.require( "bx-python" )
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8
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9 import logging
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10 from galaxy.datatypes import data
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11 from galaxy import util
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12 from cgi import escape
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13 from galaxy.datatypes import metadata
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14 from galaxy.datatypes import tabular
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15 from galaxy.datatypes.metadata import MetadataElement
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16 from galaxy.datatypes.tabular import Tabular
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17 import galaxy_utils.sequence.vcf
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18 from galaxy.datatypes.sniff import *
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19
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20 log = logging.getLogger(__name__)
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21
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22 class CG_Var( Tabular ):
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23 file_ext = 'cg_var'
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24 def __init__(self, **kwd):
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25 """Initialize CG_Var datatype"""
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26 Tabular.__init__( self, **kwd )
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27 self.column_names = ['locus', 'ploidy', 'allele', 'chromosome', 'begin', 'end',
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28 'varType', 'reference', 'alleleSeq', 'varScoreVAF',
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29 'varScoreEAF', 'varQuality', 'hapLink', 'xRef'
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30 ]
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31 def display_peek( self, dataset ):
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32 """Returns formated html of peek"""
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33 return Tabular.make_html_table( self, dataset, column_names=self.column_names )
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34
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35 class CG_MasterVar( Tabular ):
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36 file_ext = 'cg_mastervar'
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37 def __init__(self, **kwd):
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38 """Initialize CG_MasterVar datatype"""
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39 Tabular.__init__( self, **kwd )
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40 self.column_names = ['locus', 'ploidy', 'chromosome', 'begin', 'end', 'zygosity',
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41 'varType', 'reference', 'allele1Seq', 'allele2Seq',
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42 'allele1VarScoreVAF', 'allele2VarScoreVAF', 'allele1VarScoreEAF',
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43 'allele2VarScoreEAF', 'allele1VarQuality', 'allele2VarQuality',
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44 'allele1HapLink', 'allele2HapLink', 'allele1XRef', 'allele2XRef',
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45 'evidenceIntervalId', 'allele1ReadCount', 'allele2ReadCount',
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46 'referenceAlleleRead', 'totalReadCount', 'allele1Gene',
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47 'allele2Gene pfam', 'miRBaseId', 'repeatMasker', 'segDupOverlap',
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48 'relativeCoverageDiploid', 'calledPloidy',
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49 'relativeCoverageNondiploid', 'calledLevel'
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50 ]
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51
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52 def display_peek( self, dataset ):
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53 """Returns formated html of peek"""
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54 return Tabular.make_html_table( self, dataset, column_names=self.column_names )
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55
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56 class CG_Gene( Tabular ):
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57 file_ext = 'cg_gene'
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58 def __init__(self, **kwd):
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59 """Initialize CG_Gene datatype"""
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60 Tabular.__init__( self, **kwd )
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61 self.column_names = ['index', 'locus', 'allele', 'chromosome', 'begin', 'end',
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62 'varType', 'reference', 'call', 'xRef', 'geneId',
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63 'mrnaAcc', 'proteinAcc', 'symbol', 'orientation', 'component',
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64 'componentIndex', 'hasCodingRegion', 'impact', 'nucleotidePos',
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65 'proteinPos', 'annotationRefSequence', 'sampleSequence',
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66 'genomeRefSequence', 'pfam'
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67 ]
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68
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69 def display_peek( self, dataset ):
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70 """Returns formated html of peek"""
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71 return Tabular.make_html_table( self, dataset, column_names=self.column_names )
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