genomepy.files.filter_fasta

genomepy.files.filter_fasta(infa: str, outfa: str = None, regex: str = '.*', invert_match: Optional[bool] = False) → list

Filter fasta file based on regex.

Parameters

• infa (str) – Filename of the input fasta file.

• outfa (str, optional) – Filename of the output fasta file. If None, infa is overwritten.

• regex (str, optional) – Regular expression used for selecting sequences. Matches everything if left blank.

• invert_match (bool, optional) – Select all sequence not matching regex if set.

Returns

removed contigs

Return type

list