Python tabular.Tabular类代码示例

 def set_meta( self, dataset, overwrite = True, **kwd ):
     """Sets the metadata information for datasets previously determined to be in bed format."""
     i = 0
     if dataset.has_data():
         for i, line in enumerate( file(dataset.file_name) ):
             metadata_set = False
             line = line.rstrip('\r\n')
             if line and not line.startswith('#'):
                 elems = line.split('\t')
                 if len(elems) > 2:
                     for startswith in data.col1_startswith:
                         if line.lower().startswith( startswith ):
                             if len( elems ) > 3:
                                 if overwrite or not dataset.metadata.element_is_set( 'nameCol' ):
                                     dataset.metadata.nameCol = 4
                             if len(elems) < 6:
                                 if overwrite or not dataset.metadata.element_is_set( 'strandCol' ):
                                     dataset.metadata.strandCol = 0
                             else:
                                 if overwrite or not dataset.metadata.element_is_set( 'strandCol' ):
                                     dataset.metadata.strandCol = 6
                             metadata_set = True
                             break
             if metadata_set: break
         Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i )

 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_meta( self, dataset, copy_from=None ):
     Tabular.init_meta( self, dataset, copy_from=copy_from )
     self.column_names = ['DB',  'DB Object ID', 'DB Object Symbol', 'Qualifier',  'GO ID',
                          'DB:Reference (|DB:Reference)', 'Evidence Code', 'With (or) From', 
                          'Aspect', 'DB Object', 'DB Object Synonym (|Synonym)', 'DB Object Type', 
                          'Taxon(|taxon)', 'Date', 'Assigned By', 'Annotation Extension', 'Gene Product Form ID', 
                          ]

 def set_meta(self, dataset, **kwd):
     Tabular.set_meta(self, dataset, **kwd)
     dataset.metadata.markerCol = 1
     header = open(dataset.file_name, 'r').readlines()[0].strip().split('\t')
     dataset.metadata.columns = len(header)
     t = ['numeric' for x in header]
     t[0] = 'string'
     dataset.metadata.column_types = t
     return True

 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 set_meta(self, dataset, overwrite=True, skip=None, max_data_lines=None, **kwd):
        Tabular.set_meta(self, dataset, overwrite, skip, max_data_lines)
        tis_args = set()
        try:
            fh = open(dataset.file_name)

            for line in fh:
                fields = line.strip().split("\t")
                try:
                    tis_args.add(fields[0])
                except IndexError:
                    pass
            dataset.metadata.args = []
            dataset.metadata.args += tis_args

        finally:
            fh.close()

 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):
     """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 display_peek( self, dataset ):
     """Returns formated html of peek"""
     return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] )

 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 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 make_html_table( self, dataset ):
     return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] )

 def display_peek( self, dataset ):
     return Tabular.make_html_table( self, dataset, column_names=self.column_names )

 def display_peek( self, dataset ):
     """Returns formated html of peek"""
     return Tabular.make_html_table( self, dataset, column_names=self.column_names )

 def set_meta( self, dataset, **kwd ):
     Tabular.set_meta( self, dataset, **kwd )