cocoatree.msa.map_msa_positions

cocoatree.msa.map_msa_positions(n_loaded_pos, remaining_pos)

Maps positions between the original and the filtered MSA

Parameters

n_loaded_posint,

Number of positions in the original unfiltered MSA

remaining_posnp.ndarray,

array containing the indexes of positions that have been conserved after filtering the MSA (output from cocoatree.msa.filter_sequences)

Returns

original2filtereddictionnary,

the keys are the positions in the original MSA and the values are the corresponding positions in the filtered MSA. When the original position has been filtered, the value is set to ‘None’.

filtered2originaldictionnary,

the keys are the positions in the filtered MSA and the values are the corresponding positions in the original MSA.

Examples using cocoatree.msa.map_msa_positions

Mapping original MSA, filtered MSA, PDB, and sectors

Mapping original MSA, filtered MSA, PDB, and sectors