Package Bio :: Package SearchIO :: Module _utils
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Module _utils

source code

Common SearchIO utility functions.
Functions [hide private]
 
get_processor(format, mapping)
Returns the object to process the given format according to the mapping.
source code
 
singleitem(attr=None, doc='')
Returns a property that fetches the given attribute from the first item in a SearchIO container object.
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allitems(attr=None, doc='')
Returns a property that fetches the given attributes from all items in a SearchIO container object.
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fullcascade(attr, doc='')
Returns a getter property with a cascading setter.
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optionalcascade(cont_attr, item_attr, doc='')
Returns a getter property with a cascading setter.
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fragcascade(attr, seq_type, doc='')
Returns a getter property with cascading setter, for HSPFragment objects.
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Variables [hide private]
  __package__ = 'Bio.SearchIO'
Function Details [hide private]

get_processor(format, mapping)

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Returns the object to process the given format according to the mapping.
Parameters:
  • format (string, lower case) - format name
  • mapping (dictionary {string: object}) - mapping of format name and its processor object

fullcascade(attr, doc='')

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Returns a getter property with a cascading setter.

This is similar to optionalcascade, but for SearchIO containers that have at least one item (HSP). The getter always retrieves the attribute value from the first item. If the items have more than one attribute values, an error will be raised. The setter behaves like partialcascade, except that it only sets attributes to items in the object, not the object itself.

optionalcascade(cont_attr, item_attr, doc='')

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Returns a getter property with a cascading setter.

This is used for the id and description properties of the container objects with zero or more items. These items have their own private attributes that stores query and/or hit ID and description. When the container has zero items, attribute values are always retrieved from the container's attribute. Otherwise, the first item's attribute is used.

To keep the container items' query and/or hit ID and description in-sync, the setter cascades any new value given to the items' values.

fragcascade(attr, seq_type, doc='')

source code 

Returns a getter property with cascading setter, for HSPFragment objects.

Similar to partialcascade, but for HSPFragment objects and acts on query or hit properties of the object if they are not None.