Package csb :: Package bio :: Package io :: Module hhpred :: Class HHOutputParser |
[frames] | no frames]

# Class HHOutputParser

source code

    object --+
             |
            HHOutputParser

Parser for HHsearch result (*.hhr) files.

Instance Methods
__init__(self, alignments=True) x.__init__(...) initializes x; see help(type(x)) for signature | source code
__repr__(self) repr(x) | source code
HHpredHitList |
parse_file(self, hhr_file, header_only=False) Parse all hits from this HHpred result file. | source code
HHpredHitList |
parse_string(self, output, header_only=False) Get all hits from an `output` string. | source code
Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Properties
bool | alignments True if hit alignments will be parsed
Inherited from `object`: `__class__`

Method Details

### __init__(self, alignments=True) (Constructor) | source code
x.__init__(...) initializes x; see help(type(x)) for signature Parameters: `alignments` (bool) - if set to False, the parser will skip the alignments section of the file Overrides: object.__init__ (inherited documentation)

### __repr__(self) (Representation operator) | source code
repr(x) Overrides: object.__repr__ (inherited documentation)

### parse_file(self, hhr_file, header_only=False) | source code
Parse all hits from this HHpred result file. Parameters: `hhr_file` (str) - input HHR file name Returns: HHpredHitList parsed hits Raises: `HHOutputFormatError` - if the hhr file is corrupt

### parse_string(self, output, header_only=False) | source code
Get all hits from an `output` string. Parameters: `output` (str) - HHpred standard output Returns: HHpredHitList parsed hits Raises: `HHOutputFormatError` - if the output is corrupt

Property Details

### alignments True if hit alignments will be parsed Get Method: unreachable.alignments(self) - True if hit alignments will be parsed Set Method: unreachable.alignments(self, value) Type: bool