def __repr__(self):
content = Seq.__str__(self)
if len(content) > 15:
content = (content[:5].lower() + ("(%d)" % len(content)) +
content[-5:].lower())
return "(%s-%s-%s)" % (repr(
self.left_end), content, repr(self.right_end))
def createAmbiguousProteinList(nucRecord, firstNucPosition):
print "%s"%(nucRecord[firstNucPosition]+nucRecord[firstNucPosition + 1]
+nucRecord[firstNucPosition + 2])
nucleotideSequence = Seq("%s"%(nucRecord[firstNucPosition]+nucRecord[firstNucPosition + 1]
+nucRecord[firstNucPosition + 2]))
nucleotideSequence = Seq("AAK")
altNucleotideSeqs = []
altNucleotideString = ""
for nucleotide in nucleotideSequence:
if nucleotide.lower() in NUCLEOTIDE_AMBIGUITY_MAPPING.keys():
print "ambiguous nucleotide:", nucleotide
#if there are no alternate nucleotide sequences yet, make them
if altNucleotideSeqs == []:
for ambiguousNucleotide in NUCLEOTIDE_AMBIGUITY_MAPPING.get(nucleotide.lower()):
altNucleotideString = nucleotideSequence.__str__()
altNucleotideString = altNucleotideString.replace(nucleotide, ambiguousNucleotide.upper())
altNucleotideSeqs.append(Seq(altNucleotideString))
print altNucleotideString
else: #this is not hte first ambiguous nucleotide
tempAltNucleotideSeqs = []
for altNucleotideSeq in altNucleotideSeqs:
print "Existing seq:" + altNucleotideSeq.__str__()
for ambiguousNucleotide in NUCLEOTIDE_AMBIGUITY_MAPPING.get(nucleotide.lower()):
altNucleotideString = altNucleotideSeq.__str__()
altNucleotideString = altNucleotideString.replace(nucleotide, ambiguousNucleotide.upper())
tempAltNucleotideSeqs.append(Seq(altNucleotideString))
print altNucleotideString
#remove the original altNucleotideSeq which has been replaced now
#replace the existing list with the new list
altNucleotideSeqs = tempAltNucleotideSeqs
for altNucleotideSeq in altNucleotideSeqs:
print altNucleotideSeq.translate() + "/",
def __repr__(self):
return "%s(%s)" % (Seq.__str__(self), {1: "+", -1: "-"}[self.strand])
from Bio.Seq import Seq
import re
f = open('file9.txt', 'r')
seq = Seq(f.read())
rev = seq.reverse_complement()
str = seq.__str__() + " " + rev.__str__()
l = [[0], [-3]]
for i in range(0, len(str) + 1):
a = str[(i):(i + 3)]
if (a == 'TGA' or a == 'TAG' or a == 'TAA' or i == (len(str))):
for j in range(i - 3, -1, -3):
if (str[j:(j + 3)] == 'ATG'):
l[0].append(j)
l[1].append(i)
if (str[j:(j + 3)] == 'TGA' or str[j:(j + 3)] == 'TAG'
or str[j:(j + 3)] == 'TAA' or str[j:(j + 3)] == ' '):
break
m = [b - a for a, b in zip(l[0], l[1])]
m.__delitem__(0)
idx = m.index(max(m))
print(Seq(str[(l[0][idx + 1]):l[1][idx + 1]]).translate())
