Utility to determine complementary subsequences contained into a main sequence.
For example:
- input RNA sequence:
AUGCCGAUUGCAUUUCAUACGGC - subsequence length:
5 - output:
Subsequence: CGAUU
Positions: 5-9
Set of complementary sequences: AGUUG, AGUCG, AAUUG, AAUCG, GGUUG, GGUCG, GAUUG, GAUCG
Complementary: GAUUG
Locations: 6-10
Subsequence: GAUUG
Positions: 6-10
Set of complementary sequences: CGGUU, CGGUC, CGAUU, CGAUC, CAGUU, CAGUC, CAAUU, CAAUC, UGGUU, UGGUC, UGAUU, UGAUC, UAGUU, UAGUC, UAAUU, UAAUC
Complementary: CGAUU
Locations: 5-9
NOTE: the output may contains complementary subsequences that overlap (see the example above).
usage: compl_seq_utils.py [-h] -i IN_FILE [-o OUT_FILE] -n N -t {dna,rna}
Complementary sequences utils
optional arguments:
-h, --help show this help message and exit
-i IN_FILE, --input-file IN_FILE
Input file
-o OUT_FILE, --output-file OUT_FILE
Output file
-n N, --num-chars N Number of characters in subsequence
-t {dna,rna}, --seq-type {dna,rna}
Sequence type