fastaparser.Reader

Parser/Reader for a given FASTA file. Iterates over the FASTA file using one of two parsing mechanisms:

rich: Returns FastaSequence objects (default). Slower, but feature rich.
quick: Generates objects containing just the FASTA header and sequence attributes for each sequence in the FASTA file. Parses FASTA files faster but lacks some features.

Parameters

The Reader class can be instantiated with the following parameters

fastaparser.Reader(fasta_file, sequences_type=None, infer_type=False, parse_method='rich')

Parameter	Type / Value	Default	Description
fasta_file	file object		An opened file handle (for reading). Must be provided
sequences_type	'nucleotide', 'aminoacid' or None	None	Indicates the type of sequences to expect. `None` if unknown. Optional
infer_type	bool	False	Indicates if `Reader` should try to infer aminoacid sequence type for each sequence. Can only identify aminoacid sequences. Optional
parse_method	'rich' or 'quick'	'rich'	Parse method to use. `'quick'` parsing method just parses the header and the sequence into individual properties, so it's much faster and less memory intensive. If selected, `sequences_type` and `infer_type` parameters are ignored. `'rich'` implements more functionality (`FastaSequence`), but is slower. Optional

TypeError

If fasta_file, sequences_type, infer_type or parse_method are of the wrong type.
If fasta_file is not a file object, is closed or is not readable.

Instances of the Reader class have the following attributes

Attribute	Type / Value	Editable	Description
fasta_file	file object	No	The FASTA file passed as parameter
sequences_type	'nucleotide', 'aminoacid' or None	No	Indicates the type of sequences to expect. Can be `None` if not known
infer_type	bool	No	`True` if `Reader` was set to infer the sequence type, `False` otherwise
parse_method	'rich' or 'quick'	No	Parse method used