topiary.muscle

Interface to muscle, compatible with muscle 3.8 and 5.1.

topiary.muscle.muscle

Interface to muscle, compatible with muscle 3.8 and 5.1.

topiary.muscle.muscle.align(input_seqs, output_fasta=None, super5=False, silent=False, muscle_cmd_args=[], muscle_binary='muscle')

Run muscle to align sequences.

Parameters:

  • input_seqs (str or pandas.DataFrame) – input to align (fasta file or topiary df)

  • output_fasta (str or None, default=None) – output fasta file to store alignment. Optional if the input is a dataframe; required if the input is a fasta file.

  • super5 (bool) – Use the ‘super5’ mode of muscle 5

  • silent (bool, default=False) – whether or not to suppress all output

  • muscle_cmd_args (list) – list of arguments to pass directly to muscle. Wrapper specifies -align and -output (or -in/-out for old version of the command line), but leaves rest as default. Format should be something like ['-replicates','20',...]. Arguments are not checked by this function, but passed directly to muscle.

  • muscle_binary (str) – location of muscle binary (default assumes ‘muscle’ command is in the $PATH).

Returns:

alignment – If input_seqs is a topiary dataframe, return a copy of the dataframe with the aligned sequences loaded into the alignment column. Otherwise, write to output_fasta file and return None from the function.

Return type:

None or pandas.DataFrame