schrodinger.protein.tasks.muscle module¶
- schrodinger.protein.tasks.muscle.get_muscle_path()¶
Returns the path to the MUSCLE executable.
- Return type
str
- Returns
path to MUSCLE executable file, or None if the executable could not be located.
- class schrodinger.protein.tasks.muscle.MuscleJob(aln, second_aln=None, quiet=True, maintain_order=True, seqtype='auto')¶
Bases:
schrodinger.protein.tasks.clustal.AbstractAlignmentJob
Runs alignment via MUSCLE program
- Note
Muscle by default rearranges the order to put similar sequences together
- __init__(aln, second_aln=None, quiet=True, maintain_order=True, seqtype='auto')¶
- Parameters
aln (ProteinAlignment) – Input sequences
second_aln (ProteinAlignment) – Second alignment for aligning multiple MSAs
maintain_order (bool) – Whether to maintain input order of sequences
seqtype – Sequence type. One of ‘auto’, ‘protein’, ‘rna’ or ‘dna’. In ‘auto’ mode, if >95 of the first 100 letters correspond to nucleotides, the file is treated as the relevant nucleotide type. Otherwise, it is treated as protein.
Dev note: - Unimplemented features: – Speedup options
- run()¶
Run the MUSCLE alignment.
- Returns
Aligned sequences
- Return type