annotate galaxyp_util.py @ 0:9156a440afed draft default tip

Improved some datatype handling

from galaxy.datatypes.tabular import Tabular
import logging

log = logging.getLogger(__name__)


class PepXmlReport(Tabular):
    """pepxml converted to tabular report"""
    file_ext = "tsv"

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

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


class ProtXmlReport(Tabular):
    """protxml converted to tabular report"""
    file_ext = "tsv"
    comment_lines = 1

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

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