extendedMD.patterns

extendedMD.patterns.find_all_pruned_members(center_index, pattern_dic_list, r)

This function finds all the motif members assuming that the center of the motif is the BS sequence with index center_index. It returns the dictionaries related to the all the non-overlapping BS subsequences that have a distance to the center subsequence lower than R

Parameters:
  • center_index (int) – index of the center motif in the pattern_dic_list
  • pattern_dic_list (list of dic) – list of dictionaries related to all the subsequences in the pattern
  • r (float) – maximum distance to the center
Returns:

list of dictionaries of the motif members
Return type:

list of dic
extendedMD.patterns.find_pattern_center_and_members(pattern_dic_list, r)

This function finds the all the members of a motif (all non-overlapping subsequences with a distance to the motif center less than R) and and the motif’s center (the subsequence with the maximal count of members and minimal mean distance)

Parameters:
  • pattern_dic_list (list of dic) – list of dictionaries related to all the subsequences in the pattern
  • r (float) – maximum distance to the center of the motif
Returns:

  • center_dic (dic) - dictionary of the motif’s center subsequence
  • members_dic_list (list of dic) - list of dictionaries related to all the motif’s members
  • min_mean_dist (float) - mean distance between the motif’s center and all the motif’s members
extendedMD.patterns.lists_overlap(l1, l2)

This functions return whether two lists overlap

Parameters:
  • l1 (list) – list 1
  • l2 (list) – list 2
Returns:

whether the list overlap. If TRUE, then the list overlap
Return type:

bool