cocoatree.msa.filter_sequences¶
- cocoatree.msa.filter_sequences(sequences, sequences_id, gap_threshold=0.4, seq_threshold=0.2, verbose=False)[source]¶
Filter sequences
Remove (1) overly gapped positions; (2) overly gapped sequences.
Parameters¶
sequences : list of MSA sequences to filter
sequences_id : list of the MSA’s sequence identifiers
- gap_thresholdfloat,
maximum proportion of gaps tolerated per position (default=0.4)
- seq_thresholdfloat,
maximum proportion of gaps tolerated per sequence (default=0.2)
Returns¶
- filtered_seqslist of the remaining sequences (written as strings)
after applying the filters
- filtered_seqs_idlist of sequence identifiers that were kept after
applying the filters
- remaining_posnumpy.ndarray
remaining positions after filtering
Examples using cocoatree.msa.filter_sequences¶
Mapping original MSA, filtered MSA, PDB, and sectors
Mapping original MSA, filtered MSA, PDB, and sectors
Perform full SCA analysis on the S1A serine protease dataset
Perform full SCA analysis on the S1A serine protease dataset
