attachment:__init__.py of JakeFeala - Cardiac Mechanics Research Group

Attachment 'init.py'

import GRID
import Cytoscape
import PSI_MI

_FormatToIterator ={"grid" : GRID.GRIDIterator,
                    "cytoscape" : Cytoscape.InteractionReader
                    }

def parse(handle, format) :
    """Turns an interaction file into a iterator returning InteractionRecords

    handle   - handle to the file.
    format   - string describing the file format.

    If you have the file name in a string 'filename', use:

    import InteractionIO
    my_iterator = InteractionIO.parse(open(filename), format)

    If you have a string 'data' containing the file contents, use:

    import InteractionIO
    from StringIO import StringIO
    my_iterator = InteractionIO.parse(StringIO(data), format)
    """

    #Try and give helpful error messages:
    if isinstance(handle, basestring) :
        raise TypeError("Need a file handle, not a string (i.e. not a filename)")
    if not isinstance(format, basestring) :
        raise TypeError("Need a string for the file format (lower case)")
    if not format :
        raise ValueError("Format required (lower case string)")
    if format <> format.lower() :
        raise ValueError("Format string '%s' should be lower case" % format)

    #Map the file format to a sequence iterator:    
    try :
        iterator_generator = _FormatToIterator[format]
    except KeyError :
        raise ValueError("Unknown format '%s'" % format)

    #Its up to the caller to close this handle - they opened it.
    return iterator_generator(handle)

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Attachment '__init__.py'

Attachment 'init.py'