/
geo_mutagenesis.py
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/
geo_mutagenesis.py
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__author__ = 'Matteo'
__doc__='''This could be made into a handy mutagenesis library if I had time.'''
from Bio.Seq import Seq,MutableSeq
from Bio import SeqIO
from Bio.Alphabet import IUPAC
from difflib import Differ
def Gthg01471():
ori=Seq("ATGAGCATAAGTTTATCGGTTCCAAAATGGTTATTAACAGTTTTATCAATTTTATCTTTAGTCGTAGCATTTATTTTCGGTACCGTTTCCAATGCATCAGCAACAATTAACTATGGGGAGGAAGTCGCGGCAGTAGCAAATGACTATGTAGGAAGCCCATATAAATATGGAGGTACAACGCCAAAAGGATTTGATGCGAGTGGCTTTACTCAGTATGTGTATAAAAATGCTGCAACCAAATTGGCTATTCCGCGAACGAGTGCCGCACAGTATAAAGTCGGTAAATTTGTTAAACAAAGTGCGTTACAAAGAGGCGATTTAGTGTTTTATGCAACAGGAGCAAAAGGAAAGGTATCCTTTGTGGGAATTTATAATGGAAATGGTACGTTTATTGGTGCCACATCAAAAGGGGTAAAAGTGGTTAAAATGAGTGATAAATATTGGAAAGACCGGTATATAGGGGCTAAGCGAGTCATTAAGTAA", IUPAC.unambiguous_dna)
mut=MutableSeq("ATGAGCATAAGTTTATCGGTTCCAAAATGGTTATTAACAGTTTTATCAATTTTATCTTTAGTCGTAGCATTTATTTTCGGTACCGTTTCCAATGCATCAGCAACAATTAACTATGGGGAGGAAGTCGCGGCAGTAGCAAATGACTATGTAGGAAGCCCATATAAATATGGAGGTACAACGCCAAAAGGATTTGATGCGAGTGGCTTTACTCAGTATGTGTATAAAAATGCTGCAACCAAATTGGCTATTCCGCGAACGAGTGCCGCACAGTATAAAGTCGGTAAATTTGTTAAACAAAGTGCGTTACAAAGAGGCGATTTAGTGTTTTATGCAACAGGAGCAAAAGGAAAGGTATCCTTTGTGGGAATTTATAATGGAAATGGTACGTTTATTGGTGCCACATCAAAAGGGGTAAAAGTGGTTAAAATGAGTGATAAATATTGGAAAGACCGGTATATAGGGGCTAAGCGAGTCATTAAGTAA", IUPAC.unambiguous_dna)
a="AGTCGA"
b="GACTAG"
for i,v in enumerate([259,277,282,295,299,306]):
print(mut[v-1]+a[i])
mut[v-1]=b[i]
print(ori.translate())
print(mut.toseq().translate())
def Gthg04369():
filepath="Gthg_from_embl_pfamed.gb"
genome = list(SeqIO.parse(open(filepath, "rU"), "genbank"))
z=genome[0].seq[3583975:3585290].translate(to_stop=1)
x=genome[0].seq[3583975:3585290].tomutable()
print(x.pop(895-1))
y=x.toseq().translate(to_stop=1)
print(z)
print(y)
print(list(Differ().compare(str(z),str(y))))
print(len(z),len(y))
def Gthg01115():
filepath="Gthg_from_embl_pfamed.gb"
genome = list(SeqIO.parse(open(filepath, "rU"), "genbank"))
z=genome[0].seq[891404:892205].reverse_complement().translate(to_stop=1)
x=genome[0].seq[891404:892205].reverse_complement().tomutable()
print(x.pop(421-1))
y=x.toseq().translate(to_stop=1)
print(z)
print(y)
print(list(Differ().compare(str(z),str(y))))
print(len(z),len(y))
def Gthg03544():
filepath="Gthg_from_embl_pfamed.gb"
genome = list(SeqIO.parse(open(filepath, "rU"), "genbank"))
z=genome[0].seq[2885410:2887572].reverse_complement().translate(to_stop=1)
x=genome[0].seq[2885410:2887572].reverse_complement().tomutable()
print(x.pop(1748-1))
y=x.toseq().translate(to_stop=1)
print(z)
print(y)
print(list(Differ().compare(str(z),str(y))))
print(len(z),len(y))
if __name__ == "main":
pass