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test_seq
Testing Seq
===========
TCAAAAGGATGCATCATG
18
T
G
AA
Reverse using -1 stride: Seq('GTACTACGTAGGAAAACT', IUPACUnambiguousDNA())
Extract every third nucleotide (slicing with stride 3):
Seq('TAGTAA', IUPACUnambiguousDNA())
Seq('CAGGTT', IUPACUnambiguousDNA())
Seq('AAACCG', IUPACUnambiguousDNA())
GATC
IUPACUnambiguousDNA()
19
expected error, and got it
IUPACAmbiguousDNA()
Testing MutableSeq
==================
Testing creating MutableSeqs in multiple ways
MutableSeq('TCAAAAGGATGCATCATG', IUPACAmbiguousDNA())
TCAAAAGGATGCATCATG
18
Seq('TCAAAAGGATGCATCATG', IUPACAmbiguousDNA())
T
MutableSeq('CAAA', IUPACAmbiguousDNA())
Set slice with string: MutableSeq('TGATAAAGGATGCATCATG', IUPACAmbiguousDNA())
Set slice with MutableSeq: MutableSeq('TAATAAAGGATGCATCATG', IUPACAmbiguousDNA())
Set slice with array: MutableSeq('TGATTAAAGGATGCATCATG', IUPACAmbiguousDNA())
Set item: MutableSeq('TGAGTAAAGGATGCATCATG', IUPACAmbiguousDNA())
Delete slice: MutableSeq('TGAGAAAGGATGCATCATG', IUPACAmbiguousDNA())
Delete item: MutableSeq('TGAAAAGGATGCATCATG', IUPACAmbiguousDNA())
Append: MutableSeq('TGAAAAGGATGCATCATGC', IUPACAmbiguousDNA())
Insert: MutableSeq('TGAAGAAGGATGCATCATGC', IUPACAmbiguousDNA())
Pop off the last item: C
Removed Gs: MutableSeq('TAAGAAGGATGCATCATG', IUPACAmbiguousDNA())
Expected value error and got it
A count: 7
A index: 1
Reversed Seq: MutableSeq('GTACTACGTAGGAAGAAT', IUPACAmbiguousDNA())
Reverse using -1 stride: MutableSeq('TAAGAAGGATGCATCATG', IUPACAmbiguousDNA())
Extended Seq: MutableSeq('GTACTACGTAGGAAGAATGATTTT', IUPACAmbiguousDNA())
Delete stride slice: MutableSeq('GTACTACGTAGGAAGAATGATTTT', IUPACAmbiguousDNA())
Extract every third nucleotide (slicing with stride 3):
MutableSeq('GCCAAAGT', IUPACAmbiguousDNA())
MutableSeq('TTGGAAAT', IUPACAmbiguousDNA())
MutableSeq('AATGGTTT', IUPACAmbiguousDNA())
Setting wobble codon to N (set slice with stride 3):
MutableSeq('GTNCTNCGNAGNAANAANGANTTN', IUPACAmbiguousDNA())
Checking ambiguous complements
==============================
DNA Ambiguity mapping: {'A': 'A', 'C': 'C', 'B': 'CGT', 'D': 'AGT', 'G': 'G', 'H': 'ACT', 'K': 'GT', 'M': 'AC', 'N': 'GATC', 'S': 'CG', 'R': 'AG', 'T': 'T', 'W': 'AT', 'V': 'ACG', 'Y': 'CT', 'X': 'GATC'}
DNA Complement mapping: {'A': 'T', 'C': 'G', 'B': 'V', 'D': 'H', 'G': 'C', 'H': 'D', 'K': 'M', 'M': 'K', 'N': 'N', 'S': 'S', 'R': 'Y', 'T': 'A', 'W': 'W', 'V': 'B', 'Y': 'R', 'X': 'X'}
A={A} --> {T}=T
C={C} --> {G}=G
B={CGT} --> {GCA}=V
D={AGT} --> {TCA}=H
G={G} --> {C}=C
H={ACT} --> {TGA}=D
K={GT} --> {CA}=M
M={AC} --> {TG}=K
N={GATC} --> {CTAG}=N
S={CG} --> {GC}=S
R={AG} --> {TC}=Y
T={T} --> {A}=A
W={AT} --> {TA}=W
V={ACG} --> {TGC}=B
Y={CT} --> {GA}=R
X={GATC} --> {CTAG}=X
RNA Ambiguity mapping: {'A': 'A', 'C': 'C', 'B': 'CGU', 'D': 'AGU', 'G': 'G', 'H': 'ACU', 'K': 'GU', 'M': 'AC', 'N': 'GAUC', 'S': 'CG', 'R': 'AG', 'U': 'U', 'W': 'AU', 'V': 'ACG', 'Y': 'CU', 'X': 'GAUC'}
RNA Complement mapping: {'A': 'U', 'C': 'G', 'B': 'V', 'D': 'H', 'G': 'C', 'H': 'D', 'K': 'M', 'M': 'K', 'N': 'N', 'S': 'S', 'R': 'Y', 'U': 'A', 'W': 'W', 'V': 'B', 'Y': 'R', 'X': 'X'}
A={A} --> {U}=U
C={C} --> {G}=G
B={CGU} --> {GCA}=V
D={AGU} --> {UCA}=H
G={G} --> {C}=C
H={ACU} --> {UGA}=D
K={GU} --> {CA}=M
M={AC} --> {UG}=K
N={GAUC} --> {CUAG}=N
S={CG} --> {GC}=S
R={AG} --> {UC}=Y
U={U} --> {A}=A
W={AU} --> {UA}=W
V={ACG} --> {UGC}=B
Y={CU} --> {GA}=R
X={GAUC} --> {CUAG}=X
Reverse complements:
Seq('ACBDGHKMNSRUWVYX', Alphabet()) -> Seq('XRBWAYSNKMDCHVGU', Alphabet())
Seq('ACBDGHKMNSRTWVYX', Alphabet()) -> Seq('XRBWAYSNKMDCHVGT', Alphabet())
Seq('ACBDGHKMNSRUWVYX', RNAAlphabet()) -> Seq('XRBWAYSNKMDCHVGU', RNAAlphabet())
Seq('ACBDGHKMNSRTWVYX', DNAAlphabet()) -> Seq('XRBWAYSNKMDCHVGT', DNAAlphabet())
Seq('ACBDGHKMNSRUWVYX', IUPACAmbiguousRNA()) -> Seq('XRBWAYSNKMDCHVGU', IUPACAmbiguousRNA())
Seq('ACBDGHKMNSRTWVYX', IUPACAmbiguousDNA()) -> Seq('XRBWAYSNKMDCHVGT', IUPACAmbiguousDNA())
Seq('AWGAARCKG', Alphabet()) -> Seq('CMGYTTCWT', Alphabet())
Transcribe DNA into RNA
=======================
Seq('TCAAAAGGATGCATCATG', IUPACUnambiguousDNA()) -> Seq('UCAAAAGGAUGCAUCAUG', IUPACUnambiguousRNA())
Seq('T', IUPACAmbiguousDNA()) -> Seq('U', IUPACAmbiguousRNA())
Seq('TCAAAAGGATGCATCATGT', IUPACAmbiguousDNA()) -> Seq('UCAAAAGGAUGCAUCAUGU', IUPACAmbiguousRNA())
Seq('ATGAAACTG', Alphabet()) -> Seq('AUGAAACUG', RNAAlphabet())
Seq('AUGAAACUG', DNAAlphabet()) -> Seq('AUGAAACUG', RNAAlphabet())
Seq('ATGAAACTG', RNAAlphabet()) -> Seq('AUGAAACUG', RNAAlphabet())
Seq('ATGAAACTG', NucleotideAlphabet()) -> Seq('AUGAAACUG', RNAAlphabet())
Seq('AUGAAACTG', NucleotideAlphabet()) -> Seq('AUGAAACUG', RNAAlphabet())
MutableSeq('ATGAAACTG', RNAAlphabet()) -> Seq('AUGAAACUG', RNAAlphabet())
Seq('ACTGTCGTCT', ProteinAlphabet()) -> Proteins cannot be transcribed!
Back-transcribe RNA into DNA
============================
Seq('TCAAAAGGATGCATCATG', IUPACUnambiguousDNA()) -> Seq('UCAAAAGGAUGCAUCAUG', IUPACUnambiguousRNA())
Seq('T', IUPACAmbiguousDNA()) -> Seq('U', IUPACAmbiguousRNA())
Seq('TCAAAAGGATGCATCATGT', IUPACAmbiguousDNA()) -> Seq('UCAAAAGGAUGCAUCAUGU', IUPACAmbiguousRNA())
Seq('ATGAAACTG', Alphabet()) -> Seq('AUGAAACUG', RNAAlphabet())
Seq('AUGAAACUG', DNAAlphabet()) -> Seq('AUGAAACUG', RNAAlphabet())
Seq('ATGAAACTG', RNAAlphabet()) -> Seq('AUGAAACUG', RNAAlphabet())
Seq('ATGAAACTG', NucleotideAlphabet()) -> Seq('AUGAAACUG', RNAAlphabet())
Seq('AUGAAACTG', NucleotideAlphabet()) -> Seq('AUGAAACUG', RNAAlphabet())
MutableSeq('ATGAAACTG', RNAAlphabet()) -> Seq('AUGAAACUG', RNAAlphabet())
Seq('ACTGTCGTCT', ProteinAlphabet()) -> Proteins cannot be transcribed!
Reverse Complement
==================
Seq('TCAAAAGGATGCATCATG', IUPACUnambiguousDNA())
-> Seq('CATGATGCATCCTTTTGA', IUPACUnambiguousDNA())
Seq('T', IUPACAmbiguousDNA())
-> Seq('A', IUPACAmbiguousDNA())
Seq('TCAAAAGGATGCATCATGT', IUPACAmbiguousDNA())
-> Seq('ACATGATGCATCCTTTTGA', IUPACAmbiguousDNA())
Seq('ATGAAACTG', Alphabet())
-> Seq('CAGTTTCAT', Alphabet())
Seq('AUGAAACUG', DNAAlphabet())
-> Seq('CUGTTTCUT', DNAAlphabet())
Seq('ATGAAACTG', RNAAlphabet())
-> Seq('CTGUUUCTU', RNAAlphabet())
Seq('ATGAAACTG', NucleotideAlphabet())
-> Seq('CAGTTTCAT', NucleotideAlphabet())
Seq('AUGAAACTG', NucleotideAlphabet())
-> Seq('CTGUUUCAU', NucleotideAlphabet())
MutableSeq('ATGAAACTG', RNAAlphabet())
-> Seq('CTGUUUCTU', RNAAlphabet())
Seq('ACTGTCGTCT', ProteinAlphabet())
-> Proteins do not have complements!
Translating
===========
Seq('TCAAAAGGATGCATCATG', IUPACUnambiguousDNA())
-> Seq('SKGCIM', HasStopCodon(IUPACProtein(), '*'))
Seq('T', IUPACAmbiguousDNA())
-> Seq('', HasStopCodon(ExtendedIUPACProtein(), '*'))
Seq('TCAAAAGGATGCATCATGT', IUPACAmbiguousDNA())
-> Seq('SKGCIM', HasStopCodon(ExtendedIUPACProtein(), '*'))
Seq('ATGAAACTG', Alphabet())
-> Seq('MKL', HasStopCodon(IUPACProtein(), '*'))
Seq('AUGAAACUG', DNAAlphabet())
-> Seq('MKL', HasStopCodon(IUPACProtein(), '*'))
Seq('ATGAAACTG', RNAAlphabet())
-> Seq('MKL', HasStopCodon(IUPACProtein(), '*'))
Seq('ATGAAACTG', NucleotideAlphabet())
-> Seq('MKL', HasStopCodon(IUPACProtein(), '*'))
Seq('AUGAAACTG', NucleotideAlphabet())
-> Seq('MKL', HasStopCodon(IUPACProtein(), '*'))
MutableSeq('ATGAAACTG', RNAAlphabet())
-> Seq('MKL', HasStopCodon(IUPACProtein(), '*'))
Seq('ACTGTCGTCT', ProteinAlphabet())
-> Proteins cannot be translated!
Seq's .complement() method
==========================
Seq('TCAAAAGGATGCATCATG', IUPACUnambiguousDNA()) -> Seq('AGTTTTCCTACGTAGTAC', IUPACUnambiguousDNA())
Seq('T', IUPACAmbiguousDNA()) -> Seq('A', IUPACAmbiguousDNA())
Seq('TCAAAAGGATGCATCATGT', IUPACAmbiguousDNA()) -> Seq('AGTTTTCCTACGTAGTACA', IUPACAmbiguousDNA())
Seq('ATGAAACTG', Alphabet()) -> Seq('TACTTTGAC', Alphabet())
Seq('AUGAAACUG', DNAAlphabet()) -> Seq('TUCTTTGUC', DNAAlphabet())
Seq('ATGAAACTG', RNAAlphabet()) -> Seq('UTCUUUGTC', RNAAlphabet())
Seq('ATGAAACTG', NucleotideAlphabet()) -> Seq('TACTTTGAC', NucleotideAlphabet())
Seq('AUGAAACTG', NucleotideAlphabet()) -> Seq('UACUUUGTC', NucleotideAlphabet())
Seq('ACTGTCGTCT', ProteinAlphabet()) -> Proteins do not have complements!
Seq's .reverse_complement() method
==================================
Seq('TCAAAAGGATGCATCATG', IUPACUnambiguousDNA()) -> Seq('CATGATGCATCCTTTTGA', IUPACUnambiguousDNA())
Seq('T', IUPACAmbiguousDNA()) -> Seq('A', IUPACAmbiguousDNA())
Seq('TCAAAAGGATGCATCATGT', IUPACAmbiguousDNA()) -> Seq('ACATGATGCATCCTTTTGA', IUPACAmbiguousDNA())
Seq('ATGAAACTG', Alphabet()) -> Seq('CAGTTTCAT', Alphabet())
Seq('AUGAAACUG', DNAAlphabet()) -> Seq('CUGTTTCUT', DNAAlphabet())
Seq('ATGAAACTG', RNAAlphabet()) -> Seq('CTGUUUCTU', RNAAlphabet())
Seq('ATGAAACTG', NucleotideAlphabet()) -> Seq('CAGTTTCAT', NucleotideAlphabet())
Seq('AUGAAACTG', NucleotideAlphabet()) -> Seq('CTGUUUCAU', NucleotideAlphabet())
Seq('ACTGTCGTCT', ProteinAlphabet()) -> Proteins do not have complements!
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