API

Package for parsing and generating FASTA files of biological sequences.

Use the tinyfasta.FastaParser class to parse FASTA files.

To generate FASTA files use the tinyfasta.FastaRecord.create() static method to create tinyfasta.FastaRecord instances, which can be written to file.

class tinyfasta.Sequence

Class representing a biological sequence.

add_sequence_line(sequence_line)

Add a sequence line to the tinyfasta.Sequence instance.

This function can be called more than once. Each time the function is called the tinyfasta.Sequence is extended by the sequence line provided.

Parameters:sequence_line – string representing (part of) a sequence
format_line_length(line_length=80)

Format line length used to represent the sequence.

The full sequence is stored as list of shorter sequences. These shorter sequences are used verbatim when writing out the tinyfasta.FastaRecord over several lines.

Parameters:line_length – length of the sequences used to make up the full sequence
class tinyfasta.FastaRecord(description)

Class representing a FASTA record.

class Description(description)

Description line in a tinyfasta.FastaRecord.

update(description)

Update the content of the description.

This function can be used to replace the existing description with a new one.

Parameters:description – new description string
FastaRecord.add_sequence_line(sequence_line)

Add a sequence line to the tinyfasta.FastaRecord instance.

This function can be called more than once. Each time the function is called the tinyfasta.sequence is extended by the sequence line provided.

Parameters:sequence_line – string representing (part of) a sequence
static FastaRecord.create(description, sequence)

Return a FastaRecord.

Parameters:
  • description – description string
  • sequence – full sequence string
Returns:

tinyfasta.FastaRecord

class tinyfasta.FastaParser(fpath)

Class for parsing FASTA files.