Class Hit

Initializes a Hit object.

Arguments:
hsps -- List containing HSP objects.

Hit objects must be initialized with a list containing at least one HSP
object. If multiple HSP objects are used for initialization, they must
all have the same `query_id`, `query_description`, `hit_id`, and
`hit_description` properties.

Overrides: object.__init__

repr(x)

Overrides: object.__repr__

(inherited documentation)

str(x)

Overrides: object.__str__

(inherited documentation)

Adds a HSP object to the end of Hit.

Parameters
hsp -- HSP object to append.

Any HSP object appended must have the same `hit_id` property as the
Hit object's `id` property and the same `query_id` property as the
Hit object's `query_id` property.

Creates a new Hit object whose HSP objects pass the filter
function.

Arguments:
func -- Callback function that accepts a HSP object as its parameter,
        does a boolean check, and returns True or False.

`filter` is analogous to Python's built-in `filter` function, except
that instead of returning a list it returns a `Hit` object. Here is an
example of using `filter` to select for HSPs having bitscores bigger
than 60:

>>> from Bio import SearchIO
>>> qresult = SearchIO.parse('Blast/mirna.xml', 'blast-xml').next()
>>> hit = qresult[3]
>>> evalue_filter = lambda hsp: hsp.bitscore > 60
>>> filtered_hit = hit.filter(evalue_filter)
>>> len(hit)
2
>>> len(filtered_hit)
1
>>> print filtered_hit
Query: 33211
       mir_1
  Hit: gi|301171322|ref|NR_035857.1| (86)
       Pan troglodytes microRNA mir-520c (MIR520C), microRNA
 HSPs: ----  --------  ---------  ------  ---------------  ---------------------
          #   E-value  Bit score    Span      Query range              Hit range
       ----  --------  ---------  ------  ---------------  ---------------------
          0   8.9e-20     100.47      60           [1:61]                [13:73]

Returns the index of a given HSP object, zero-based.

Arguments:
hsp -- HSP object to be looked up.

Creates a new Hit object, mapping the given function to its HSPs.

Arguments:
func -- Callback function that accepts a HSP object as its parameter and
        also returns a HSP object.

`map` is analogous to Python's built-in `map` function. It is applied to
all HSPs contained in the Hit object and returns a new Hit object.

Removes and returns the HSP object at the specified index.

Arguments:
index -- Integer denoting the index of the HSP object to remove.

Sorts the HSP objects.

Arguments:
key -- Function used to sort the HSP objects.
reverse -- Boolean, whether to reverse the sorting or not.
in_place -- Boolean, whether to perform sorting in place (in the same
            object) or not (creating a new object).

`sort` defaults to sorting in-place, to mimick Python's `list.sort`
method. If you set the `in_place` argument to False, it will treat
return a new, sorted Hit object and keep the initial one unsorted

description

Hit description

Get Method:

unreachable.getter(self)

Set Method:

unreachable.setter(self, value)

query_description

Description of the query that produced the hit

Get Method:

unreachable.getter(self)

Set Method:

unreachable.setter(self, value)

id

Hit ID string.

Get Method:

unreachable.getter(self)

Set Method:

unreachable.setter(self, value)

query_id

ID string of the query that produced the hit

Get Method:

unreachable.getter(self)

Set Method:

unreachable.setter(self, value)

hsps

HSP objects contained in the Hit

Get Method:

unreachable.getter(self)

fragments

HSPFragment objects contained in the Hit

Get Method:

unreachable.fragments(self) - HSPFragment objects contained in the Hit