def find_in_sequences(fragment, sequences):
"""
Find the position of the fragment in the specified sequences.
@param the fragment (sequence of base pairs)
@param sequences SimpleGenomeSequence[]
"""
regex = base_regexp_expand(fragment, overlap=True)
matches = []
for seq in sequences:
seq_matches = __find_in_sequence_regex(regex, seq, overlapped=True)
if seq_matches:
matches.append((seq, seq_matches))
return matches
def find_in_sequence_map(fragment, sequences):
"""
Like find_in_sequences, but returns only the matches
themselves, essentially a mapping operation. Returns empty
lists for a sequence slot if there are no matches. The
length of the return value should always equal
the length of the sequence array; this is
a shortcut to [find_in_sequence(fragment, sequence) for sequence in sequences]
"""
regex = base_regexp_expand(fragment, overlap=True)
return_list = []
for seq in sequences:
return_list.append(__find_in_sequence_regex(regex, seq, overlapped=True))
return return_list
def find_in_sequence(fragment, sequence):
regex = base_regexp_expand(fragment, overlap=True)
return __find_in_sequence_regex(regex, sequence, overlapped=True)
