`synthaser.fasta`¶

This module contains some helper functions for handling FASTA format files/strings.

synthaser.fasta.count(fasta)¶

Counts sequences in an open FASTA file handle.

Iterates file and counts header lines. Then, seeks to start of the file and returns the count.

Parameters:	fasta (file pointer) – An open file handle corresponding to a FASTA file.
Returns:	Total number of sequences in the file.
Return type:	count (int)

synthaser.fasta.create(header, sequence, limit=80)¶

Creates a FASTA format string from a header and sequence.

For example:

>>> fasta = create_fasta('header', 'AAAAABBBBBCCCCC', wrap=5)
>>> print(fasta)
>header
AAAAA
BBBBB
CCCCC

Parameters:	header (str) – Name to use in FASTA definition line (i.e. >header). sequence (str) – The sequence corresponding to the header. limit (int) – Total characters per line before sequence is wrapped.
Returns:	FASTA format string.
Return type:	(str)

synthaser.fasta.wrap(sequence, limit=80)¶

Wraps sequences to limit characters per line.

Parameters:	sequence (str) – Sequence to be wrapped. limit (int) – Total characters per line.
Returns:	Sequence wrapped to maximum limit characters per line.
Return type:	(str)

synthaser.fasta¶