FASTAFile#

class pyopenms.FASTAFile#

Bases: object

Cython implementation of _FASTAFile

__init__()#: Cython signature: void FASTAFile() This class serves for reading in and writing FASTA files

Methods

`__init__`	Cython signature: void FASTAFile() This class serves for reading in and writing FASTA files
`atEnd`	Cython signature: bool atEnd() Boolean function to check if streams is at end of file
`load`	Cython signature: void load(const String & filename, libcpp_vector[FASTAEntry] & data) Loads a FASTA file given by 'filename' and stores the information in 'data'
`readNext`	Cython signature: bool readNext(FASTAEntry & protein)
`readStart`	Cython signature: void readStart(const String & filename)
`store`	Cython signature: void store(const String & filename, libcpp_vector[FASTAEntry] & data) Stores the data given by 'data' at the file 'filename'
`writeEnd`	Cython signature: void writeEnd() Closes the file (flush).
`writeNext`	Cython signature: void writeNext(const FASTAEntry & protein)
`writeStart`	Cython signature: void writeStart(const String & filename)

atEnd()#: Cython signature: bool atEnd() Boolean function to check if streams is at end of file

load()#: Cython signature: void load(const String & filename, libcpp_vector[FASTAEntry] & data) Loads a FASTA file given by ‘filename’ and stores the information in ‘data’

readNext()#

Cython signature: bool readNext(FASTAEntry & protein)

Returns: true if entry was read; false if eof was reached
Raises: Exception:FileNotFound is thrown if the file does not exists
Raises: Exception:ParseError is thrown if the file does not suit to the standard

readStart()#

Cython signature: void readStart(const String & filename)

Raises: Exception:FileNotFound is thrown if the file does not exists
Raises: Exception:ParseError is thrown if the file does not suit to the standard

Returns: true if entry was read; false if eof was reached
Raises: Exception:FileNotFound is thrown if the file does not exists
Raises: Exception:ParseError is thrown if the file does not suit to the standard

store()#: Cython signature: void store(const String & filename, libcpp_vector[FASTAEntry] & data) Stores the data given by ‘data’ at the file ‘filename’

writeEnd()#: Cython signature: void writeEnd() Closes the file (flush). Called implicitly when FASTAFile object does out of scope

writeNext()#

Cython signature: void writeNext(const FASTAEntry & protein)

Raises: Exception:UnableToCreateFile is thrown if the process is not able to write to the file (disk full?)

writeStart()#

Cython signature: void writeStart(const String & filename)

Raises: Exception:UnableToCreateFile is thrown if the process is not able to write to the file (disk full?)

Raises: Exception:UnableToCreateFile is thrown if the process is not able to write to the file (disk full?)