from Bio.Seq import UnknownSeq from Bio.Alphabet import IUPAC unk = UnknownSeq(20, alphabet=IUPAC.ambiguous_dna) unk.complement() unk.reverse_complement() unk_rna = unk.transcribe() print(unk_rna) unk_protein = unk.translate() print(unk_protein)
from Bio.Seq import MutableSeq
from Bio.Alphabet import IUPAC
mutable_seq = MutableSeq("GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA", IUPAC.unambiguous_dna)
mutable_seq
mutable_seq[5] = "C"
mutable_seq
mutable_seq.remove("T")
mutable_seq
mutable_seq.reverse()
mutable_seq
# UnknownSeq objects
from Bio.Seq import UnknownSeq
unk = UnknownSeq(20)
unk
print(unk)
len(unk)
from Bio.Seq import UnknownSeq
from Bio.Alphabet import IUPAC
unk_dna = UnknownSeq(20, alphabet=IUPAC.ambiguous_dna)
unk_dna
print(unk_dna)
unk_protein = unk_dna.translate()
unk_protein
# Connecting with biological databases
mutSeq.reverse() # reverse() and reverse_complement() change object itself print mutSeq #MutableSeq can't be a dictionary key, Seq and string can #UnknownSeq # Subclass of Seq when you know length but not the characters to save memory from Bio.Seq import UnknownSeq unk = UnknownSeq(25) print unk, len(unk), type(unk) unkDNA = UnknownSeq(20, alphabet=IUPAC.ambiguous_dna) print unkDNA # N = any base unkProt = UnknownSeq(10, alphabet=IUPAC.protein) print unkProt # X = any aminoacid print unkDNA.complement(), unkDNA.reverse_complement() print unkDNA.transcribe(), unkDNA.translate() unkProt = unkDNA.translate() print unkProt, len(unkProt) #Directly on strings from Bio.Seq import reverse_complement, transcribe, back_transcribe, translate noseq = 'GCTGTTATGGGTCGTTGGAAGGGTGGTCGTGCTGCTGGTTAG' print reverse_complement(noseq) # these functions print transcribe(noseq) # receive either strings print back_transcribe(noseq) # Seq, MutableSeq, UnknownSeq print translate(noseq) #SeqRecord object #.seq A Seq object #.id a string ID identifier of the sequence #.name a string common name for the sequence
