Example #1
0
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)
Example #2
0
mutSeq[2:-5]='TTTT'
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