Class QueryResult

Initializes a QueryResult object.

Arguments:
id -- String of query sequence ID.
hits -- Iterator returning Hit objects.
hit_key_function -- Function to define hit keys, defaults to a function
                    that return Hit object IDs.

Overrides: object.__init__

repr(x)

Overrides: object.__repr__

(inherited documentation)

str(x)

Overrides: object.__str__

(inherited documentation)

Adds a Hit object to the end of QueryResult. If the QueryResult
already has a Hit with the same ID, append the new Hit's HSPs into
the existing Hit.

Arguments:
hit -- Hit object to absorb.

This method is used for file formats that may output the same Hit in
separate places, such as BLAT or Exonerate. In both formats, Hit
with different strands are put in different places. However, SearchIO
considers them to be the same as a Hit object should be all database
entries with the same ID, regardless of strand orientation.

Adds a Hit object to the end of QueryResult.

Parameters
hit -- Hit object to append.

Any Hit object appended must have the same `query_id` property as the
QueryResult's `id` property. If the hit key already exists, a
`ValueError` will be raised.

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

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

Here is an example of using `hit_filter` to select Hits whose
description begins with the string 'Homo sapiens', case sensitive:

>>> from Bio import SearchIO
>>> qresult = SearchIO.parse('Blast/mirna.xml', 'blast-xml').next()
>>> def desc_filter(hit):
...     return hit.description.startswith('Homo sapiens')
...
>>> len(qresult)
100
>>> filtered = qresult.hit_filter(desc_filter)
>>> len(filtered)
39
>>> print filtered[:4]
Program: blastn (2.2.27+)
  Query: 33211 (61)
         mir_1
 Target: refseq_rna
   Hits: ----  -----  ----------------------------------------------------------
            #  # HSP  ID + description                                          
         ----  -----  ----------------------------------------------------------
            0      1  gi|262205317|ref|NR_030195.1|  Homo sapiens microRNA 52...
            1      2  gi|262205330|ref|NR_030198.1|  Homo sapiens microRNA 52...
            2      1  gi|262205302|ref|NR_030191.1|  Homo sapiens microRNA 51...
            3      1  gi|262205451|ref|NR_030222.1|  Homo sapiens microRNA 51...

Note that instance attributes (other than the hits) from the unfiltered
QueryResult are retained in the filtered object.

    >>> qresult.program == filtered.program
    True
    >>> qresult.target == filtered.target
    True

Creates a new QueryResult object, mapping the given function to its
Hits.

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

Here is an example of using `hit_map` with a function that discards all
HSPs in a Hit except for the first one:

>>> from Bio import SearchIO
>>> qresult = SearchIO.parse('Blast/mirna.xml', 'blast-xml').next()
>>> print qresult[:8]
Program: blastn (2.2.27+)
  Query: 33211 (61)
         mir_1
 Target: refseq_rna
   Hits: ----  -----  ----------------------------------------------------------
            #  # HSP  ID + description                                          
         ----  -----  ----------------------------------------------------------
            0      1  gi|262205317|ref|NR_030195.1|  Homo sapiens microRNA 52...
            1      1  gi|301171311|ref|NR_035856.1|  Pan troglodytes microRNA...
            2      1  gi|270133242|ref|NR_032573.1|  Macaca mulatta microRNA ...
            3      2  gi|301171322|ref|NR_035857.1|  Pan troglodytes microRNA...
            4      1  gi|301171267|ref|NR_035851.1|  Pan troglodytes microRNA...
            5      2  gi|262205330|ref|NR_030198.1|  Homo sapiens microRNA 52...
            6      1  gi|262205302|ref|NR_030191.1|  Homo sapiens microRNA 51...
            7      1  gi|301171259|ref|NR_035850.1|  Pan troglodytes microRNA...

>>> top_hsp = lambda hit: hit[:1]
>>> mapped_qresult = qresult.hit_map(top_hsp)
>>> print mapped_qresult[:8]
Program: blastn (2.2.27+)
  Query: 33211 (61)
         mir_1
 Target: refseq_rna
   Hits: ----  -----  ----------------------------------------------------------
            #  # HSP  ID + description                                          
         ----  -----  ----------------------------------------------------------
            0      1  gi|262205317|ref|NR_030195.1|  Homo sapiens microRNA 52...
            1      1  gi|301171311|ref|NR_035856.1|  Pan troglodytes microRNA...
            2      1  gi|270133242|ref|NR_032573.1|  Macaca mulatta microRNA ...
            3      1  gi|301171322|ref|NR_035857.1|  Pan troglodytes microRNA...
            4      1  gi|301171267|ref|NR_035851.1|  Pan troglodytes microRNA...
            5      1  gi|262205330|ref|NR_030198.1|  Homo sapiens microRNA 52...
            6      1  gi|262205302|ref|NR_030191.1|  Homo sapiens microRNA 51...
            7      1  gi|301171259|ref|NR_035850.1|  Pan troglodytes microRNA...

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

`hsp_filter` is the same as `hit_filter`, except that it filters
directly on each HSP object in every Hit. If a the filtering removes
all HSP object in a given Hit, the entire Hit will be discarded. This
will result in the QueryResult having less Hit after filtering.

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

`hsp_map` is the same as `hit_map`, except that it applies the given
function to all HSP objects in every Hit, instead of the Hit objects.

Removes the specified hit key and return the Hit object.

Arguments:
hit_key -- Integer index or string of hit key that points to a Hit
           object.
default -- Value that will be returned if the Hit object with the
           specified index or hit key is not found.

By default, `pop` will remove and return the last Hit object in the
QueryResult object. To remove specific Hit objects, you can use its
integer index or hit key.

>>> from Bio import SearchIO
>>> qresult = SearchIO.parse('Blast/mirna.xml', 'blast-xml').next()
>>> len(qresult)
100
>>> for hit in qresult[:5]:
...     print hit.id
...
gi|262205317|ref|NR_030195.1|
gi|301171311|ref|NR_035856.1|
gi|270133242|ref|NR_032573.1|
gi|301171322|ref|NR_035857.1|
gi|301171267|ref|NR_035851.1|

# remove the last hit
>>> qresult.pop()
Hit(id='gi|397513516|ref|XM_003827011.1|', query_id='33211', 1 hsps)

# remove the first hit
>>> qresult.pop(0)
Hit(id='gi|262205317|ref|NR_030195.1|', query_id='33211', 1 hsps)

# remove hit with the given ID
>>> qresult.pop('gi|301171322|ref|NR_035857.1|')
Hit(id='gi|301171322|ref|NR_035857.1|', query_id='33211', 2 hsps)

Returns the index of a given hit key, zero-based.

Arguments:
hit_key -- Hit ID string to look up.

This method is useful for finding out the integer index (usually
correlated with search rank) of a given hit key.

>>> from Bio import SearchIO
>>> qresult = SearchIO.parse('Blast/mirna.xml', 'blast-xml').next()
>>> qresult.index('gi|301171259|ref|NR_035850.1|')
7

Sorts the Hit objects.

Arguments:
key -- Function used to sort the Hit 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 QueryResult object and keep the initial one
unsorted.

hits

Hit objects contained in the QueryResult.

Get Method:

unreachable.hits(self) - Hit objects contained in the QueryResult.

hit_keys

Hit IDs of the Hit objects contained in the QueryResult.

Get Method:

unreachable.hit_keys(self) - Hit IDs of the Hit objects contained in the QueryResult.

items

List of tuples of Hit IDs and Hit objects.

Get Method:

unreachable.items(self) - List of tuples of Hit IDs and Hit objects.

id

QueryResult ID string

Get Method:

unreachable.getter(self)

Set Method:

unreachable.setter(self, value)

description

QueryResult description

Get Method:

unreachable.getter(self)

Set Method:

unreachable.setter(self, value)

hsps

HSP objects contained in the QueryResult.

Get Method:

unreachable.hsps(self) - HSP objects contained in the QueryResult.

fragments

HSPFragment objects contained in the QueryResult.

Get Method:

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