shmir.designer package¶
Submodules¶
shmir.designer.design module¶
shmir.designer.errors module¶
- exception shmir.designer.errors.BaseException(message=None)¶
Bases: exceptions.Exception
Base exception class.
- exception shmir.designer.errors.IncorrectDataError(message=None)¶
Bases: shmir.designer.errors.BaseException
Exception error class for incorrect data input
- exception shmir.designer.errors.NoResultError(message=None)¶
Bases: shmir.designer.errors.BaseException
Exception error class for no results
- exception shmir.designer.errors.ValidationError(message=None)¶
Bases: shmir.designer.errors.BaseException
Exception error class for incorrect input
shmir.designer.offtarget module¶
shmir.designer.score module¶
shmir.designer.search module¶
shmir.designer.ss module¶
shmir.designer.utils module¶
- shmir.designer.utils.adjusted_frames(seq1, seq2, shift_left, shift_right, all_frames)¶
Take output of parse_input function and insert into flanking sequences. take from database all miRNA results and check if ends of input is suitable for flanking sequences. If first value == and miRNA_end_5 second value == miRNA_end_3 then simply concatenate sequences flanks5_s + first_sequence + loop_s + second_sequence + flanks3_s. If any end is different function has to modify end of the insert: Right end: if miRNA_end_5 < first_end add to right site of second sequence additional nucleotides (as many as |miRNA_end_5 - first_end|) like (dots are nucleotides to add, big letter are flanking sequences, small are input):
AAAGGGGCTTTTagtcttaga TTTCCCCGAA....agaatct
if miRNA_end_5 > first_end cut nucleotides from rigth site of flanks3_s and/or from right site of second sequence
before cut: AAAGGGGCTTTTagtcttaga TTTCCCCGAAAATTcctcagaatct (-2, +2)
After AAAGGGGCTTTTagtcttaga TTTCCCCGAAAAtcagaatct
Nucleotides are always added to the right side of sequences. We cut off nucleotides only from flanking sequences or loop.
- Args:
- seq1(str) first sequence. seq2(str) second sequence. shift_left(int) - shift on sequence from left side. shift_right(int) - shift on sequence from right side. all_frames(pri-miRNA objects) frames from which we create sh-miRs.
- Returns:
- list of tuples (changed frame, first sequence, second sequence).
- shmir.designer.utils.reverse_complement(sequence)¶
Generates reverse complement sequence to given
- Args:
- sequence(str).
- Returns:
- revese complement sequence(str) to given.