Goal: Introduction to pairwise sequence alignment

!curl 'http://histo.ucsf.edu/BMS270/BMS270_2018/code/geneticCode.py' > geneticCode.py

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from geneticCode import geneticCode

geneticCode["ATG"]

'M'

geneticCode["NNN"]

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-4-b70f9a2c6a01> in <module>()
----> 1 geneticCode["NNN"]

KeyError: 'NNN'

geneticCode["aaa"]

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-5-d6f92b870578> in <module>()
----> 1 geneticCode["aaa"]

KeyError: 'aaa'

geneticCode["aaa".upper()]

'K'

"asdf".upper()

'ASDF'

"this has spaces".replace(" ","")

'thishasspaces'

"".join(i for i in "ATGCNNFGCTAGN  NttgC".upper() if(i in "ATGC"))

'ATGCGCTAGTTGC'

"hi" in {"hi":"there"}

True

for (key,val) in geneticCode.items():
    print(key,"->",val)

CTT -> L
TGG -> W
TCG -> S
GTT -> V
GTG -> V
GCG -> A
ACT -> T
TTG -> L
GAC -> D
TAC -> Y
TTC -> F
ACC -> T
GCT -> A
CGG -> R
CCC -> P
CGA -> R
CTA -> L
GGG -> G
TAA -> *
TCC -> S
GTC -> V
CAT -> H
AAA -> K
GTA -> V
CCA -> P
CAG -> Q
AGG -> R
AGC -> S
AGA -> R
CCG -> P
AAC -> N
CGC -> R
GGT -> G
GAG -> E
TAT -> Y
ACG -> T
AAT -> N
ACA -> T
TTA -> L
ATC -> I
CCT -> P
GAT -> D
TGT -> C
TCT -> S
AAG -> K
CGT -> R
CTC -> L
GGC -> G
GCC -> A
TCA -> S
TGC -> C
GCA -> A
ATA -> I
TTT -> F
CAC -> H
TAG -> *
ATG -> M
AGT -> S
CAA -> Q
ATT -> I
TGA -> *
CTG -> L
GGA -> G
GAA -> E

def identity_matrix(alphabet):
    d = {}
    for i in alphabet:
        d[i] = {}
        for j in alphabet:
            if(i == j):
                d[i][j] = 1
            else:
                d[i][j] = -1
    return d

identity_matrix("ATGC")

{'A': {'A': 1, 'C': -1, 'G': -1, 'T': -1},
 'C': {'A': -1, 'C': 1, 'G': -1, 'T': -1},
 'G': {'A': -1, 'C': -1, 'G': 1, 'T': -1},
 'T': {'A': -1, 'C': -1, 'G': -1, 'T': 1}}

score = identity_matrix("ATGC")

seq1 = "TGTGGT"
seq2 = "TGAGGT"

score["A"]["T"]

-1