User talk:Hossein Azari Soufiani: Difference between revisions
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==Code for Third Homework== | |||
import random | |||
import numpy as np | |||
print | |||
print | |||
Code='cggagcagctcactattcacccgatgagaggggaggagagagagagaaaatgtcctttaggccggttcctcttacttggcagagggaggctgctattctccgcctgcatttctttttctggattacttagttatggcctttgcaaaggcaggggtatttgttttgatgcaaacctcaatccctccccttctttgaatggtgtgccccaccccccgggtcgcctgcaacctaggcggacgctaccatggcgtagacagggagggaaagaagtgtgcagaaggcaagcccggaggcactttcaagaatgagcatatctcatcttcccggagaaaaaaaaaaaagaatggtacgtctgagaatgaaattttgaaagagtgcaatgatgggtcgtttgataatttgtcgggaaaaacaatctacctgttatctagctttgggctaggccattccagttccagacgcaggctgaacgtcgtgaagcggaaggggcgggcccgcaggcgtccgtgtggtcctccgtgcagccctcggcccgagccggttcttcctggtaggaggcggaactcgaattcatttctcccgctgccccatctcttagctcgcggttgtttcattccgcagtttcttcccatgcacctgccgcgtaccggccactttgtgccgtacttacgtcatctttttcctaaatcgaggtggcatttacacacagcgccagtgcacacagcaagtgcacaggaagatgagttttggcccctaaccgctccgtgatgcctaccaagtcacagacccttttcatcgtcccagaaacgtttcatcacgtctcttcccagtcgattcccgaccccacctttattttgatctccataaccattttgcctgttggagaacttcatatagaatggaatcaggatgggcgctgtggctcacgcctgcactttggctcacgcctgcactttgggaggccgaggcgggcggattacttgaggataggagttccagaccagcgtggccaacgtggtg' | |||
RCCode=Code | |||
TempCode=Code | |||
print 'Code=',Code | |||
print | |||
print | |||
pro1=range(1,339) | |||
pro2=range(1,339) | |||
pro3=range(1,339) | |||
prom1=range(1,339) | |||
prom2=range(1,339) | |||
prom3=range(1,339) | |||
#----------------------Problem one -------------------------------------------- | |||
GCcontent=0 | |||
for i in range(0,len(Code)-1): | |||
if Code[i]=='c': | |||
GCcontent=GCcontent+1 | |||
elif Code[i]=='g': | |||
GCcontent=GCcontent+1 | |||
print 'GC Content=',GCcontent | |||
print | |||
print | |||
print | |||
print | |||
#----------------------Problem two--------------------------------------------- | |||
for i in range(0,len(Code)-1): | |||
if Code[len(Code)-1-i]=='c': | |||
RCCode=RCCode[:i]+'g'+RCCode[i+1:] | |||
if Code[len(Code)-1-i]=='g': | |||
RCCode=RCCode[:i]+'c'+RCCode[i+1:] | |||
if Code[len(Code)-1-i]=='t': | |||
RCCode=RCCode[:i]+'a'+RCCode[i+1:] | |||
if Code[len(Code)-1-i]=='a': | |||
RCCode=RCCode[:i]+'t'+RCCode[i+1:] | |||
print 'Recerse Complement=:', RCCode | |||
print | |||
print | |||
#----------------------Problem Three--------------------------------------------- | |||
standard = { 'ttt': 'F', 'tct': 'S', 'tat': 'Y', 'tgt': 'C', | |||
'ttc': 'F', 'tcc': 'S', 'tac': 'Y', 'tgc': 'C', | |||
'tta': 'L', 'tca': 'S', 'taa': '*', 'tga': '*', | |||
'ttg': 'L', 'tcg': 'S', 'tag': '*', 'tgg': 'W', | |||
'ctt': 'L', 'cct': 'P', 'cat': 'H', 'cgt': 'R', | |||
'ctc': 'L', 'ccc': 'P', 'cac': 'H', 'cgc': 'R', | |||
'cta': 'L', 'cca': 'P', 'caa': 'Q', 'cga': 'R', | |||
'ctg': 'L', 'ccg': 'P', 'cag': 'Q', 'cgg': 'R', | |||
'att': 'I', 'act': 'T', 'aat': 'N', 'agt': 'S', | |||
'atc': 'I', 'acc': 'T', 'aac': 'N', 'agc': 'S', | |||
'ata': 'I', 'aca': 'T', 'aaa': 'K', 'aga': 'R', | |||
'atg': 'M', 'acg': 'T', 'aag': 'K', 'agg': 'R', | |||
'gtt': 'V', 'gct': 'A', 'gat': 'D', 'ggt': 'G', | |||
'gtc': 'V', 'gcc': 'A', 'gac': 'D', 'ggc': 'G', | |||
'gta': 'V', 'gca': 'A', 'gaa': 'E', 'gga': 'G', | |||
'gtg': 'V', 'gcg': 'A', 'gag': 'E', 'ggg': 'G' | |||
} | |||
for i in range(0,338): | |||
Temp1=Code[3*i]+Code[3*i+1]+Code[3*i+2] | |||
Temp2=Code[3*i+1]+Code[3*i+2]+Code[3*i+3] | |||
Temp3=Code[3*i+2]+Code[3*i+3]+Code[3*i+4] | |||
pro1[i]=standard[Temp1] | |||
pro2[i]=standard[Temp2] | |||
pro3[i]=standard[Temp3] | |||
Temp1=RCCode[3*i]+RCCode[3*i+1]+RCCode[3*i+2] | |||
Temp2=RCCode[3*i+1]+RCCode[3*i+2]+RCCode[3*i+3] | |||
Temp3=RCCode[3*i+2]+RCCode[3*i+3]+RCCode[3*i+4] | |||
prom1[i]=standard[Temp1] | |||
prom2[i]=standard[Temp2] | |||
prom3[i]=standard[Temp3] | |||
print 'Sequence of (+1) frame' | |||
print pro1 | |||
print 'Sequence of (+2) frame' | |||
print pro2 | |||
print 'Sequence of (+3) frame' | |||
print pro3 | |||
print 'Sequence of (-1) frame' | |||
print prom1 | |||
print 'Sequence of (-2) frame' | |||
print prom2 | |||
print 'Sequence of (-3) frame' | |||
print prom3 | |||
#-----------------------------Problem Four--------------------------- | |||
counter=0 | |||
for j in range(0,1000): | |||
Code=TempCode | |||
for i in range(0,10): | |||
Te=random.random() | |||
Te=np.fix(100*Te) | |||
Te2=random.random() | |||
Te2=int(np.fix(10*Te2))%3 | |||
if (Code[100*i+int(Te)]=='c') and (Te2==1): | |||
Code=Code[:100*i+int(Te)]+'g'+Code[100*i+int(Te)+1:] | |||
elif (Code[100*i+int(Te)]=='c') and (Te2==2): | |||
Code=Code[:100*i+int(Te)]+'t'+Code[100*i+int(Te)+1:] | |||
elif (Code[100*i+int(Te)]=='c') and (Te2==0): | |||
Code=Code[:100*i+int(Te)]+'a'+Code[100*i+int(Te)+1:] | |||
elif (Code[100*i+int(Te)]=='t') and (Te2==1): | |||
Code=Code[:100*i+int(Te)]+'g'+Code[100*i+int(Te)+1:] | |||
elif (Code[100*i+int(Te)]=='t') and (Te2==2): | |||
Code=Code[:100*i+int(Te)]+'c'+Code[100*i+int(Te)+1:] | |||
elif (Code[100*i+int(Te)]=='t') and (Te2==0): | |||
Code=Code[:100*i+int(Te)]+'a'+Code[100*i+int(Te)+1:] | |||
elif (Code[100*i+int(Te)]=='g') and (Te2==1): | |||
Code=Code[:100*i+int(Te)]+'c'+Code[100*i+int(Te)+1:] | |||
elif (Code[100*i+int(Te)]=='g') and (Te2==2): | |||
Code=Code[:100*i+int(Te)]+'t'+Code[100*i+int(Te)+1:] | |||
elif (Code[100*i+int(Te)]=='g') and (Te2==0): | |||
Code=Code[:100*i+int(Te)]+'a'+Code[100*i+int(Te)+1:] | |||
elif (Code[100*i+int(Te)]=='a') and (Te2==1): | |||
Code=Code[:100*i+int(Te)]+'g'+Code[100*i+int(Te)+1:] | |||
elif (Code[100*i+int(Te)]=='a') and (Te2==2): | |||
Code=Code[:100*i+int(Te)]+'t'+Code[100*i+int(Te)+1:] | |||
elif (Code[100*i+int(Te)]=='a') and (Te2==0): | |||
Code=Code[:100*i+int(Te)]+'c'+Code[100*i+int(Te)+1:] | |||
pro21=range(1,339) | |||
pro22=range(1,339) | |||
pro23=range(1,339) | |||
for i in range(0,338): | |||
Temp1=Code[3*i]+Code[3*i+1]+Code[3*i+2] | |||
Temp2=Code[3*i+1]+Code[3*i+2]+Code[3*i+3] | |||
Temp3=Code[3*i+2]+Code[3*i+3]+Code[3*i+4] | |||
pro21[i]=standard[Temp1] | |||
pro22[i]=standard[Temp2] | |||
pro23[i]=standard[Temp3] | |||
for i in range(0,len(pro21)-1): | |||
if pro21[i]=='*' and pro1[i]!='*': | |||
counter=counter+1 | |||
print 'Percent of Premature Termination=',counter,'/1000' | |||
print | |||
print | |||
print 'Before Mutation:', pro1 | |||
print | |||
print | |||
print 'After Mutation:', pro21 | |||
input() | |||
== Personal/Lab Info == | == Personal/Lab Info == |
Revision as of 14:16, 25 September 2009
Hello, Hossein Azari Soufiani! This is a welcome message from OpenWetWare. By the way, we've announced you on the home page! You can leave messages to any OWW member by editing their User_talk pages like this one. And don't forget to personalize your User Page so that we can get to know you better! We've included some tips below to get you started.
Report of Second Homework
The paper "Foundations for the Engineering Biology" was really interesting for me because I am an engineer and I like to see the problems from engineering point of view. The paper was written in a very classic engineering manner and it made understanding of our position in Bioengineering more clear for me.
Installing and preparing Python was very different than the other programs which I used before like Matlab, C++. I enjoyed using it, specially the object oriented programing ability makes it really powerful. Plot for Python is very similar to Matlab and we have same commands with a little bit difference. Here you see a plot for three different growth rates for exponential function plotted with different colors.
Code for Third Homework
import random import numpy as np
print print
Code='cggagcagctcactattcacccgatgagaggggaggagagagagagaaaatgtcctttaggccggttcctcttacttggcagagggaggctgctattctccgcctgcatttctttttctggattacttagttatggcctttgcaaaggcaggggtatttgttttgatgcaaacctcaatccctccccttctttgaatggtgtgccccaccccccgggtcgcctgcaacctaggcggacgctaccatggcgtagacagggagggaaagaagtgtgcagaaggcaagcccggaggcactttcaagaatgagcatatctcatcttcccggagaaaaaaaaaaaagaatggtacgtctgagaatgaaattttgaaagagtgcaatgatgggtcgtttgataatttgtcgggaaaaacaatctacctgttatctagctttgggctaggccattccagttccagacgcaggctgaacgtcgtgaagcggaaggggcgggcccgcaggcgtccgtgtggtcctccgtgcagccctcggcccgagccggttcttcctggtaggaggcggaactcgaattcatttctcccgctgccccatctcttagctcgcggttgtttcattccgcagtttcttcccatgcacctgccgcgtaccggccactttgtgccgtacttacgtcatctttttcctaaatcgaggtggcatttacacacagcgccagtgcacacagcaagtgcacaggaagatgagttttggcccctaaccgctccgtgatgcctaccaagtcacagacccttttcatcgtcccagaaacgtttcatcacgtctcttcccagtcgattcccgaccccacctttattttgatctccataaccattttgcctgttggagaacttcatatagaatggaatcaggatgggcgctgtggctcacgcctgcactttggctcacgcctgcactttgggaggccgaggcgggcggattacttgaggataggagttccagaccagcgtggccaacgtggtg' RCCode=Code TempCode=Code
print 'Code=',Code print print
pro1=range(1,339)
pro2=range(1,339)
pro3=range(1,339)
prom1=range(1,339)
prom2=range(1,339)
prom3=range(1,339)
- ----------------------Problem one --------------------------------------------
GCcontent=0
for i in range(0,len(Code)-1):
if Code[i]=='c': GCcontent=GCcontent+1 elif Code[i]=='g': GCcontent=GCcontent+1
print 'GC Content=',GCcontent
print
print
print
print
- ----------------------Problem two---------------------------------------------
for i in range(0,len(Code)-1):
if Code[len(Code)-1-i]=='c': RCCode=RCCode[:i]+'g'+RCCode[i+1:] if Code[len(Code)-1-i]=='g': RCCode=RCCode[:i]+'c'+RCCode[i+1:] if Code[len(Code)-1-i]=='t': RCCode=RCCode[:i]+'a'+RCCode[i+1:] if Code[len(Code)-1-i]=='a': RCCode=RCCode[:i]+'t'+RCCode[i+1:]
print 'Recerse Complement=:', RCCode print print
- ----------------------Problem Three---------------------------------------------
standard = { 'ttt': 'F', 'tct': 'S', 'tat': 'Y', 'tgt': 'C', 'ttc': 'F', 'tcc': 'S', 'tac': 'Y', 'tgc': 'C', 'tta': 'L', 'tca': 'S', 'taa': '*', 'tga': '*', 'ttg': 'L', 'tcg': 'S', 'tag': '*', 'tgg': 'W',
'ctt': 'L', 'cct': 'P', 'cat': 'H', 'cgt': 'R', 'ctc': 'L', 'ccc': 'P', 'cac': 'H', 'cgc': 'R', 'cta': 'L', 'cca': 'P', 'caa': 'Q', 'cga': 'R', 'ctg': 'L', 'ccg': 'P', 'cag': 'Q', 'cgg': 'R',
'att': 'I', 'act': 'T', 'aat': 'N', 'agt': 'S', 'atc': 'I', 'acc': 'T', 'aac': 'N', 'agc': 'S',
'ata': 'I', 'aca': 'T', 'aaa': 'K', 'aga': 'R',
'atg': 'M', 'acg': 'T', 'aag': 'K', 'agg': 'R',
'gtt': 'V', 'gct': 'A', 'gat': 'D', 'ggt': 'G', 'gtc': 'V', 'gcc': 'A', 'gac': 'D', 'ggc': 'G', 'gta': 'V', 'gca': 'A', 'gaa': 'E', 'gga': 'G', 'gtg': 'V', 'gcg': 'A', 'gag': 'E', 'ggg': 'G' }
for i in range(0,338):
Temp1=Code[3*i]+Code[3*i+1]+Code[3*i+2] Temp2=Code[3*i+1]+Code[3*i+2]+Code[3*i+3] Temp3=Code[3*i+2]+Code[3*i+3]+Code[3*i+4]
pro1[i]=standard[Temp1] pro2[i]=standard[Temp2] pro3[i]=standard[Temp3]
Temp1=RCCode[3*i]+RCCode[3*i+1]+RCCode[3*i+2] Temp2=RCCode[3*i+1]+RCCode[3*i+2]+RCCode[3*i+3] Temp3=RCCode[3*i+2]+RCCode[3*i+3]+RCCode[3*i+4]
prom1[i]=standard[Temp1] prom2[i]=standard[Temp2] prom3[i]=standard[Temp3]
print 'Sequence of (+1) frame' print pro1
print 'Sequence of (+2) frame' print pro2
print 'Sequence of (+3) frame' print pro3
print 'Sequence of (-1) frame' print prom1
print 'Sequence of (-2) frame' print prom2
print 'Sequence of (-3) frame' print prom3
- -----------------------------Problem Four---------------------------
counter=0 for j in range(0,1000):
Code=TempCode for i in range(0,10):
Te=random.random() Te=np.fix(100*Te) Te2=random.random() Te2=int(np.fix(10*Te2))%3
if (Code[100*i+int(Te)]=='c') and (Te2==1): Code=Code[:100*i+int(Te)]+'g'+Code[100*i+int(Te)+1:] elif (Code[100*i+int(Te)]=='c') and (Te2==2): Code=Code[:100*i+int(Te)]+'t'+Code[100*i+int(Te)+1:]
elif (Code[100*i+int(Te)]=='c') and (Te2==0): Code=Code[:100*i+int(Te)]+'a'+Code[100*i+int(Te)+1:]
elif (Code[100*i+int(Te)]=='t') and (Te2==1): Code=Code[:100*i+int(Te)]+'g'+Code[100*i+int(Te)+1:] elif (Code[100*i+int(Te)]=='t') and (Te2==2): Code=Code[:100*i+int(Te)]+'c'+Code[100*i+int(Te)+1:]
elif (Code[100*i+int(Te)]=='t') and (Te2==0): Code=Code[:100*i+int(Te)]+'a'+Code[100*i+int(Te)+1:]
elif (Code[100*i+int(Te)]=='g') and (Te2==1): Code=Code[:100*i+int(Te)]+'c'+Code[100*i+int(Te)+1:] elif (Code[100*i+int(Te)]=='g') and (Te2==2): Code=Code[:100*i+int(Te)]+'t'+Code[100*i+int(Te)+1:]
elif (Code[100*i+int(Te)]=='g') and (Te2==0): Code=Code[:100*i+int(Te)]+'a'+Code[100*i+int(Te)+1:]
elif (Code[100*i+int(Te)]=='a') and (Te2==1): Code=Code[:100*i+int(Te)]+'g'+Code[100*i+int(Te)+1:] elif (Code[100*i+int(Te)]=='a') and (Te2==2): Code=Code[:100*i+int(Te)]+'t'+Code[100*i+int(Te)+1:]
elif (Code[100*i+int(Te)]=='a') and (Te2==0): Code=Code[:100*i+int(Te)]+'c'+Code[100*i+int(Te)+1:]
pro21=range(1,339) pro22=range(1,339) pro23=range(1,339)
for i in range(0,338):
Temp1=Code[3*i]+Code[3*i+1]+Code[3*i+2] Temp2=Code[3*i+1]+Code[3*i+2]+Code[3*i+3] Temp3=Code[3*i+2]+Code[3*i+3]+Code[3*i+4]
pro21[i]=standard[Temp1] pro22[i]=standard[Temp2] pro23[i]=standard[Temp3]
for i in range(0,len(pro21)-1):
if pro21[i]=='*' and pro1[i]!='*': counter=counter+1
print 'Percent of Premature Termination=',counter,'/1000' print print
print 'Before Mutation:', pro1 print print
print 'After Mutation:', pro21
input()
Personal/Lab Info
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