Mercurial > repos > completegenomics > cg_cgatools_linux
view cgatools/lib/galaxy/datatypes/completegenomics.py @ 0:182426b32995 draft default tip
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author | completegenomics |
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date | Mon, 18 Jun 2012 20:15:00 -0400 |
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""" Complete Genomics datatypes Birgit Crain - Complete Genomics, Inc """ import pkg_resources pkg_resources.require( "bx-python" ) import logging from galaxy.datatypes import data from galaxy import util from cgi import escape from galaxy.datatypes import metadata from galaxy.datatypes import tabular from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes.tabular import Tabular import galaxy_utils.sequence.vcf from galaxy.datatypes.sniff import * log = logging.getLogger(__name__) class CG_Var( Tabular ): file_ext = 'cg_var' def __init__(self, **kwd): """Initialize CG_Var datatype""" Tabular.__init__( self, **kwd ) self.column_names = ['locus', 'ploidy', 'allele', 'chromosome', 'begin', 'end', 'varType', 'reference', 'alleleSeq', 'varScoreVAF', 'varScoreEAF', 'varQuality', 'hapLink', 'xRef' ] def display_peek( self, dataset ): """Returns formated html of peek""" return Tabular.make_html_table( self, dataset, column_names=self.column_names ) class CG_MasterVar( Tabular ): file_ext = 'cg_mastervar' def __init__(self, **kwd): """Initialize CG_MasterVar datatype""" Tabular.__init__( self, **kwd ) self.column_names = ['locus', 'ploidy', 'chromosome', 'begin', 'end', 'zygosity', 'varType', 'reference', 'allele1Seq', 'allele2Seq', 'allele1VarScoreVAF', 'allele2VarScoreVAF', 'allele1VarScoreEAF', 'allele2VarScoreEAF', 'allele1VarQuality', 'allele2VarQuality', 'allele1HapLink', 'allele2HapLink', 'allele1XRef', 'allele2XRef', 'evidenceIntervalId', 'allele1ReadCount', 'allele2ReadCount', 'referenceAlleleRead', 'totalReadCount', 'allele1Gene', 'allele2Gene pfam', 'miRBaseId', 'repeatMasker', 'segDupOverlap', 'relativeCoverageDiploid', 'calledPloidy', 'relativeCoverageNondiploid', 'calledLevel' ] def display_peek( self, dataset ): """Returns formated html of peek""" return Tabular.make_html_table( self, dataset, column_names=self.column_names ) class CG_Gene( Tabular ): file_ext = 'cg_gene' def __init__(self, **kwd): """Initialize CG_Gene datatype""" Tabular.__init__( self, **kwd ) self.column_names = ['index', 'locus', 'allele', 'chromosome', 'begin', 'end', 'varType', 'reference', 'call', 'xRef', 'geneId', 'mrnaAcc', 'proteinAcc', 'symbol', 'orientation', 'component', 'componentIndex', 'hasCodingRegion', 'impact', 'nucleotidePos', 'proteinPos', 'annotationRefSequence', 'sampleSequence', 'genomeRefSequence', 'pfam' ] def display_peek( self, dataset ): """Returns formated html of peek""" return Tabular.make_html_table( self, dataset, column_names=self.column_names )