omicverse.alignment.mafft

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omicverse.alignment.mafft#

omicverse.alignment.mafft(input_fasta, output_dir, output_name='aligned.fasta', mode='auto', threads=4, extra_args=None, mafft_path=None, auto_install=True, overwrite=False)[source]#

Run MAFFT multiple sequence alignment.

Parameters:

  • input_fasta (str) – Path to unaligned FASTA (ASV centroids, 16S sequences, …).

  • output_dir (str) – Directory for the aligned FASTA + log. Required (no $HOME).

  • output_name (str (default: 'aligned.fasta')) – Filename for the aligned FASTA inside output_dir.

  • mode (str (default: 'auto')) – MAFFT strategy flag: 'auto' (default; --auto picks FFT-NS-1 / L-INS-i depending on size), 'fftns', 'linsi', 'einsi', 'ginsi', or 'retree1' (fastest).

  • threads (int (default: 4)) – Passed as --thread. MAFFT supports --thread -1 for auto-detect.

  • extra_args (Optional[Sequence[str]] (default: None)) – Appended verbatim to the mafft command line (coerced to str).

  • mafft_path (Optional[str] (default: None)) – Explicit path to the mafft binary.

  • auto_install (bool (default: True)) – Try conda install -c bioconda mafft if absent.

  • overwrite (bool (default: False)) – Re-run even if the aligned file already exists.

Return type:

{"input": …, "aligned": …, "log": …} — absolute paths.

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