`AlignmentFormatMode`#

class biotite.application_v2.mmseqs.AlignmentFormatMode(*values)[source]#

Bases: IntEnum

Output modes accepted by the convertalis command.

Attributes:

BLAST_TABLE: A BLAST-like tabular format.
SAM: The SAM alignment format.
BLAST_TABLE_WITH_LENGTH: Like BLAST_TABLE, with the query and target length appended.
HTML: A rendered HTML report.
BLAST_TABLE_WITH_HEADERS: Like BLAST_TABLE, preceded by a row of column names.
CALPHA_PDB: The superimposed C-alpha coordinates as PDB, only in Foldseek.

Notes

Only BLAST_TABLE and BLAST_TABLE_WITH_HEADERS support selecting the reported columns via the format_output option.

BLAST_TABLE = 0#

SAM = 1#

BLAST_TABLE_WITH_LENGTH = 2#

HTML = 3#

BLAST_TABLE_WITH_HEADERS = 4#

CALPHA_PDB = 5#