FASTAFile

class pyopenms.FASTAFile

Bases: object

Cython implementation of _FASTAFile

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1FASTAFile.html

__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?)