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| # -*- coding: utf-8 -*- | |
| #import math | |
| import logging | |
| def find_aprox_match_iter(needle, hstack, missmatch_level, hs_start_pos = 0): | |
| i = hs_start_pos # start iterate from start position | |
| start = hs_start_pos # start of founded region at begining start of search | |
| mmatch_count = 0 # missmatch counter | |
| needle_len = len(needle) | |
| j = 0 # needle iterator | |
| while i < len(hstack): | |
| if hstack[i] != needle[j]: | |
| mmatch_count += 1 | |
| if mmatch_count > missmatch_level: | |
| # if missmatch level oversized back to strat + 1 and start again | |
| i -= j | |
| # needle iterator restart (-1) because it will be increased in a moment | |
| j = -1 | |
| # new start = start + 1 | |
| start = i+1 | |
| #print 'start = '+str(start) | |
| # reset mmatch_count | |
| mmatch_count = 0 | |
| i += 1 | |
| j += 1 | |
| # if needle iterator = len of needle match found return it. | |
| if j >= needle_len: | |
| return (start,i,mmatch_count) | |
| def find_all_aprox_matches(needle, hstack, missmatch_level, hs_start_pos): | |
| ret_list = [] # list of matches to return | |
| i = hs_start_pos # start iteration from start position | |
| needle_len = len(needle) | |
| while i+needle_len <= len(hstack): | |
| r = find_aprox_match_iter(needle, hstack, missmatch_level, i) | |
| # match found append to list strat new look in start + 1 position | |
| if r: | |
| ret_list.append(r) | |
| i = r[0]+1 | |
| # match not found - no more maches in hstack | |
| else: | |
| break | |
| return ret_list | |
| # return string from between two aproximated motifs | |
| def find_motif_in_aprox_range(start_motif, stop_motif, hstack, missmatch_level, hs_start_pos = 0): | |
| start = 0 | |
| stop = 0 | |
| start = find_aprox_match_iter(start_motif, hstack, missmatch_level, hs_start_pos = 0) | |
| stop = find_aprox_match_iter(stop_motif, hstack, missmatch_level, start[1]) | |
| if start and stop: | |
| return hstack[start[1]:stop[0]] | |
| def find_all_motifs_in_aprox_range(start_motif, stop_motif, hstack, missmatch_level, hs_start_pos = 0, len_min = 0, len_max = float('inf')): | |
| i = hs_start_pos | |
| start = 0 | |
| stop = 0 | |
| ret_list = [] | |
| logger = logging.getLogger(__name__) | |
| #logger.setLevel(logging.DEBUG) | |
| logger.debug([start_motif, stop_motif, hstack, missmatch_level, hs_start_pos, len_min, len_max]) | |
| logger.debug(hstack) | |
| while i <= len(hstack): | |
| start = find_aprox_match_iter(start_motif, hstack, missmatch_level, i) | |
| stop = find_aprox_match_iter(stop_motif, hstack, missmatch_level, start[1]) | |
| if start and stop: | |
| if stop[1] - start[0] >= len_min and stop[1] - start[0] <= len_max: | |
| ret_list.append(hstack[start[0]:stop[1]]) | |
| i = start[0]+1 | |
| else: | |
| break | |
| logger.debug(ret_list) | |
| return ret_list | |
| def find_motif(needle, hstack, missmatch_level, hs_start_pos = 0): | |
| r = 0 | |
| r = find_aprox_match_iter(needle, hstack, missmatch_level, hs_start_pos = 0) | |
| if r: | |
| return hstack[r[0]:r[1]] | |
| def find_all_motifs(needle, hstack, missmatch_level, hs_start_pos = 0): | |
| i = hs_start_pos | |
| ret_list = [] | |
| while i <= len(hstack): | |
| r = find_aprox_match_iter(needle, hstack, missmatch_level, i ) | |
| if r: | |
| ret_list.append(hstack[r[0]:r[1]]) | |
| i = r[0]+1 | |
| else: | |
| break | |
| return ret_list |