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 __init__(self, **kwd):
"""
Initialize gg datatype, by adding UCSC display apps
"""
Tabular.__init__(self, **kwd)
self.add_display_app('ucsc', 'Genome Graph', 'as_ucsc_display_file',
'ucsc_links')
def __init__(self, **kwd):
Tabular.__init__(self, **kwd)
self.column_names = [
'ID', 'local_max', 'min_count_aTIS', 'R_aTis', 'min_count_5UTR',
'R_5UTR', 'min_count_CDS', 'R_CDS', 'min_count_3UTR', 'R_3UTR',
'min_count_no_trans', 'R_no_trans', 'SNP'
]
self.columns = 13
def __init__(self, **kwd):
Tabular.__init__(self, **kwd)
self.column_names = [
'Protein', 'Peptide', 'Assumed Charge',
'Neutral Pep Mass (calculated)', 'Neutral Mass', 'Retention Time',
'Start Scan', 'End Scan', 'Search Engine',
'PeptideProphet Probability', 'Interprophet Probabaility'
]
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 __init__(self, **kwd):
Tabular.__init__(self, **kwd)
self.column_names = [
"Entry Number", "Group Probability",
"Protein", "Protein Link", "Protein Probability",
"Percent Coverage", "Number of Unique Peptides",
"Total Independent Spectra", "Percent Share of Spectrum ID's",
"Description", "Protein Molecular Weight", "Protein Length",
"Is Nondegenerate Evidence", "Weight", "Precursor Ion Charge",
"Peptide sequence", "Peptide Link", "NSP Adjusted Probability",
"Initial Probability", "Number of Total Termini",
"Number of Sibling Peptides Bin", "Number of Instances",
"Peptide Group Designator", "Is Evidence?"]
def __init__(self, **kwd):
Tabular.__init__(self, **kwd)
self.column_names = [
"Entry Number", "Group Probability",
"Protein", "Protein Link", "Protein Probability",
"Percent Coverage", "Number of Unique Peptides",
"Total Independent Spectra", "Percent Share of Spectrum ID's",
"Description", "Protein Molecular Weight", "Protein Length",
"Is Nondegenerate Evidence", "Weight", "Precursor Ion Charge",
"Peptide sequence", "Peptide Link", "NSP Adjusted Probability",
"Initial Probability", "Number of Total Termini",
"Number of Sibling Peptides Bin", "Number of Instances",
"Peptide Group Designator", "Is Evidence?"]
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 __init__(self, **kwd):
Tabular.__init__(self, **kwd)
self.column_names = [
"ID",
"local_max",
"min_count_aTIS",
"R_aTis",
"min_count_5UTR",
"R_5UTR",
"min_count_CDS",
"R_CDS",
"min_count_3UTR",
"R_3UTR",
"min_count_no_trans",
"R_no_trans",
"SNP",
]
self.columns = 13
def __init__(self, **kwd):
Tabular.__init__(self, **kwd)
self.column_names = ['Column', 'Name', 'Alias']
def __init__(self, **kwd):
Tabular.__init__(self, **kwd)
def __init__(self, **kwd):
Tabular.__init__( self, **kwd )
self.column_names = ['Protein', 'Peptide', 'Assumed Charge', 'Neutral Pep Mass (calculated)', 'Neutral Mass', 'Retention Time', 'Start Scan', 'End Scan', 'Search Engine', 'PeptideProphet Probability', 'Interprophet Probabaility']
def __init__(self, **kwd):
"""Initialize genomdiff datatype"""
Tabular.__init__(self, **kwd)
def __init__(self, **kwd):
"""
Initialize featurelistt datatype
"""
Tabular.__init__(self, **kwd)
self.column_names = []
def __init__(self, **kwd):
"""
Initialize featurelistt datatype
"""
Tabular.__init__(self, **kwd)
self.column_names = []
def __init__(self, **kwd):
"""Initialize interval datatype, by adding UCSC display app"""
Tabular.__init__(self, **kwd)
self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' )
def __init__(self, **kwd):
Tabular.__init__(self, **kwd)
def __init__(self, **kwd):
Tabular.__init__(self, **kwd)
"""Initialize RsemResults datatype"""
self.comment_lines = 1
def __init__(self, **kwd):
"""Initialize datatype, by adding GBrowse display app"""
Tabular.__init__(self, **kwd)
self.add_display_app ('c_elegans', 'display in Wormbase', 'as_gbrowse_display_file', 'gbrowse_links' )
def __init__(self, **kwd):
Tabular.__init__( self, **kwd )
self.column_names = [ 'Column', 'Name', 'Alias' ]
def __init__(self, **kwd):
"""
Initialize gg datatype, by adding UCSC display apps
"""
Tabular.__init__(self, **kwd)
self.add_display_app('ucsc', 'Genome Graph', 'as_ucsc_display_file', 'ucsc_links')
def __init__(self, **kwd):
Tabular.__init__( self, **kwd )
self.column_names = ['ID','local_max','min_count_aTIS','R_aTis','min_count_5UTR','R_5UTR','min_count_CDS','R_CDS','min_count_3UTR','R_3UTR','min_count_no_trans','R_no_trans']
self.columns = 12
def __init__( self, **kwd ):
Tabular.__init__( self, **kwd )
self.add_display_app( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' )
self.add_display_app( 'gbrowse', 'display in Gbrowse', 'as_gbrowse_display_file', 'gbrowse_links' )
def __init__(self, **kwd):
"""Initialize QTLMap:Genealogy datatype"""
Tabular.__init__(self, **kwd)
