FASTAFile

class pyopenms.FASTAFile

Bases: object

Cython implementation of _FASTAFile

Original C++ documentation is available here

__init__(self) → None

This class serves for reading in and writing FASTA files

Methods

__init__(self)	This class serves for reading in and writing FASTA files
atEnd(self)	Boolean function to check if streams is at end of file
load(self, filename, data)	Loads a FASTA file given by 'filename' and stores the information in 'data'
readNext(self, protein)	Reads the next FASTA entry from file
readStart(self, filename)	Prepares a FASTA file given by 'filename' for streamed reading using readNext()
store(self, filename, data)	Stores the data given by 'data' at the file 'filename'
writeEnd(self)	Closes the file (flush).
writeNext(self, protein)	Stores the data given by protein.
writeStart(self, filename)	Prepares a FASTA file given by 'filename' for streamed writing using writeNext()

atEnd(self) → bool

Boolean function to check if streams is at end of file

load(self, filename: Union[bytes, str, String], data: List[FASTAEntry]) → None

Loads a FASTA file given by ‘filename’ and stores the information in ‘data’

readNext(self, protein: FASTAEntry) → bool

Reads the next FASTA entry from file

If you want to read all entries in one go, use load()

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(self, filename: Union[bytes, str, String]) → None

Prepares a FASTA file given by ‘filename’ for streamed reading using readNext()

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

Reads the next FASTA entry from file

If you want to read all entries in one go, use load()

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(self, filename: Union[bytes, str, String], data: List[FASTAEntry]) → None

Stores the data given by ‘data’ at the file ‘filename’

writeEnd(self) → None

Closes the file (flush). Called implicitly when FASTAFile object does out of scope

writeNext(self, protein: FASTAEntry) → None

Stores the data given by protein. Call writeStart() once before calling writeNext()

Call writeEnd() when done to close the file!

Raises

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

writeStart(self, filename: Union[bytes, str, String]) → None

Prepares a FASTA file given by ‘filename’ for streamed writing using writeNext()

Raises

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

Stores the data given by protein. Call writeStart() once before calling writeNext()

Call writeEnd() when done to close the file!

Raises

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