Hairpin structure finder implemented with LCS

usage: lcs.py [-h] [-f FILEPATH] [-e MAXERR] [-l MINLEN] [-m MINMATCH]
[-s SAVE]

optional arguments:
-h, --help show this help message and exit
-f FILEPATH path of the file, gets seq_short on default
-e MAXERR maximum changes allowed in lcs
-l MINLEN minimum length of lcs(50~100 recommended)
-m MINMATCH minimum length of consequtive
-s SAVE store result in filepath

output example:
>./lcs -f input/seq.txt
gene length: 100586
LCS 1 : TAGATGATGATGTTATACGCGTTCTTCTGGCCGCTATTGGTGGAGGATGTAGTACTCCTCTTTTTTTAATAGTGACATAGGTCATCCTAGAGGCGGATTCGGACTCGAAGTTTGTGTTTGACGGGGGAATGTTGAGTGACCAGTCC
hairpin: CCTGGAACATGAATCACAAATGGAGAGCTAACTAATCTATATCACTTTATCTTGCTAATGCAAAGGCCAAATGCATAAGTAGTTCAAACCCGGAAAATAATCTACTTTTGG
LCS 2 : TAGATGATGATGTTATACGCGTTCTTCTGGCCGCTATTGGTGGAGGATGGGTATAGTACTCCTCTTTAATAGTGACATATTTTGGTCATCCTAGAGGCGGATTCGGACTCGAAGTTTGGACGGGGGAATGTTGAGTGACCTGTTTAGTCC
change : TAGATGATGATGTTATACGCGTTCTTCTGGCCGCTATTGGTGGAGGATGGGTATAGTACTCCTCTTTTTTTAATAGTGACATATTTTGGTCATCCTAGAGGCGGATTCGGACTCGAAGTTTGTGTTTGGACGGGGGAATGTTGAGTGACCTGTTTAGTCCC

LCS 1 : GCGCGGCGGTGCACAAGCAATTGACAACTAACCACCGTGTATTCGTTATGGCATCAGGCAGTTTAAGTCGAGACAATAGGGCTCGCAATACACAGTTTACCGCATCTTGCCCTAACTGACAAACTGTGATCGACCACTAGCCATGCCATTGCCTCTTAGACACCCGTG
hairpin: TCGATACTGAACGAATCGATGCACACTCCCTTCCTTGAAAACGCACAATCATACAAGTGGGCACATGATGG
LCS 2 : GCGCGGCGGTGCACAAGCAATTGACAACTAACCACCGTGTATTCGTTATGGCATCAGTTTAAGTCGAGACAATAGGGCTCTACACAGTTTGCAAACCGCATCTTGCCCTAACTGACAAACTGTGATCGACCACTAGCCATGCCATTGCCTCTTAGACACCCTG
change : GCGCGGCGGTGCACAAGCAATTGACAACTAACCACCGTGTATTCGTTATGGCATCAGGCAGTTTAAGTCGAGACAATAGGGCTCGCACATACACAGTTTGCAAACCGCATCTTGCCCTAACTGACAAACTGTGATCGACCACTAGCCATGCCATTGCCTCTTAGACACCCGTGT

LCS 1 : ACCCGGAAATGGCTGTATTTATTGAGGTATTATACTGTGATATGTTAAAAAAAAAAGGGGAGTAGGTGGATGATTTTCAAGAAGCTATGCCTAAGCGCGTGAGTACCATCGGCCAGACGCAGTCTTGGCCCAGTACCGACGAATCTACTGCAATCGCATGACAGGGCTAC
hairpin: CATTAGAAACTACATATGAGGAGAATACCAGACGTTATTTTTTTGAACGACCACATACATAGCATACACATAATAAATTTAAAA
LCS 2 : ACCCGGAAATGGCTGTATTTATTGAGGTATTATACAGTTGTGATATGTTAAAAAAAAAAGGGGAGTAGGTGGATGATTTTCAAGAAGCTATGCCTAAGCGCGTGAGTACCATCGGCCAGACGCAGTCTTGGCCCAGTACCGACGAATCTACTGCCCCAATCGCATGACAGGGCTAC
change : ACCCGGAAATGGCTGTATTTATTGAGGTATTATACAGTTGTGATATGTTAAAAAAAAAAGGGGAGTAGGTGGATGATTTTCAAGAAGCTATGCCTAAGCGCGTGAGTACCATCGGCCAGACGCAGTCTTGGCCCAGTACCGACGAATCTACTGCCCCAATCGCATGACAGGGCTACC

time spent:122.67