Package csb :: Package bio :: Package io :: Module hhpred :: Class HHOutputParser

Class HHOutputParser

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

Class HHOutputParser

__init__(self, alignments=True) (Constructor)

__repr__(self) (Representation operator)

parse_file(self, hhr_file, header_only=False)

parse_string(self, output, header_only=False)

alignments

init(self, alignments=True)
(Constructor)

repr(self)
(Representation operator)