Homework 3 less the third problem which will happen later

Author: sarsees

Assignment3/assignment3_1.py

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+data = [['A1', 28], ['A2', 32], ['A3', 1], ['A4', 0],
+        ['A5', 10], ['A6', 22], ['A7', 30], ['A8', 19],
+        ['B1', 145], ['B2', 27], ['B3', 36], ['B4', 25],
+        ['B5', 9], ['B6', 38], ['B7', 21], ['B8', 12],
+        ['C1', 122], ['C2', 87], ['C3', 36], ['C4', 3],
+        ['D1', 0], ['D2', 5], ['D3', 55], ['D4', 62],
+        ['D5', 98], ['D6', 32]]
+#How many sites are there
+sites = len(data)
+#How many birds are at the 7th site
+print(data[6][1])
+#How many birds are at the last site
+print(data[25][1])
+#What is the total number of birds counted across all sites
+count = 0
+for thing in data:
+    count += thing[1]
+print(count)
+#What is the total number of birds counted on sites with codes beginning with C? 
+CountForBirdsAtC = 0
+for thing in data:
+    if thing[0].startswith('C'):
+        CountForBirdsAtC += thing[1]
+print(CountForBirdsAtC)
+    
+
+
+    
+    
+

Assignment3/assignment3_2.py

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+from __future__ import division
+import pandas
+DNAinfo = pandas.read_csv('/Users/sreehl/Documents/Advanced_Computing/Homework/Assignment3/houseelf_earlength_dna_data.csv')
+
+EarSize = []
+gc = []
+def GC_Percent(DNASequence):
+    GC = (DNASequence.count('G')+DNASequence.count('C'))/len(DNASequence)
+    return(GC)
+
+for row in DNAinfo.values:
+    gc.append(GC_Percent(row[2]))
+for row in DNAinfo.values:
+    if (row[1] > 10):
+        EarSize.append('Large')   
+    if (row[1] <= 10):
+        EarSize.append('Small')
+results = []
+results = zip(DNAinfo['id'],EarSize,gc)
+#Get the Average GC Counts by ear size
+GCBig = []
+GCSmall = []            
+for elves in results:
+    if elves[1] == ('Large'):
+        GCBig.append(elves[2]) 
+    if elves[1] == ('Small'):
+        GCSmall.append(elves[2])
+print 'Average GC Percentage for Large Eared Elves:', (sum(GCBig)/len(GCBig))
+print 'Average GC Percentage for Small Eared Elves:', (sum(GCSmall)/len(GCSmall))
+TheResults = pandas.DataFrame(results)
+TheResults.columns=['id','size','GC Percentage']
+pandas.DataFrame.to_csv(TheResults,'/Users/sreehl/Documents/Advanced_Computing/Homework/Assignment3/grangers_analysis.csv')
+

Assignment3/grangers_analysis.csv

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+,id,size,GC Percentage
+0,17A,Small,0.41
+1,24P,Small,0.39
+2,09Q,Large,0.57
+3,65Y,Small,0.4
+4,19N,Small,0.36
+5,92K,Large,0.62
+6,33W,Small,0.52
+7,98C,Large,0.63
+8,75G,Small,0.47
+9,88Q,Large,0.52

Assignment3/houseelf_earlength_dna_data.csv

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+id,earlength,dnaseq
+17A,5.1,CCGCATCTTGACTTAACTGACATATTACCATAGATGACTAGCCATGCCACTAGCTCTTAGATAACCCGATACAGTGATTATGAAAGGTTTGTGGGGTATA
+24P,7.5,GCTATGACTTGCTTAGCTACGTATGAAGGAAGAAACTTTTGTGTATTTATATGTTCACCCGTCTATTACCCATGCCCGAAGATTATGTAGGTTGTGAGAT
+09Q,12.2,CCGCCGATTGATACAGGGGACGGTGACGTCGTCATAGATTCGGCACGTTACCCTTGTAGGTGTGGAGCCACTTAGCTACGCGCCGAAGTCCCATGGCAAA
+65Y,9.9,GCAGGAGAAGTTCTTAACCTTCTCGTAGGACGTCAACCTATTCTTTAATAGAGCATTTCATTCGAGCATGACAGTAAGTACGCTTTCTCAATTGTGCTAA
+19N,10.0,TCTTCATCCTTATCAAAGTTTGGAGTCAATGATCAGGATTATTGCCTTGCAATAAATTTCTTATTCACAGTCGCTCATATTGAGCTACTCGATGGGTTAT
+92K,14.6,ACCGATGGACAATGATTCGGGTAGCACCAGGAGTCCGTAGCGCGTGCATCCCGGCGTGGCGCGCGTACAGCTTAACCACCGCTTCATGCTAGGGTGCTGG
+33W,8.2,CAGCTTGACTCGGTCTGTTAGGCCACGATTACGTGAGTTAGGGCTCTGAACTGCGCTGTATAGTCGAATCTGATTCGGCCCTCACAACTGCAAACCCCAA
+98C,17.8,CTGCATGCTAGGTTGACACGCCTGCACTGCTCGAAGAAAATATGCGAAGCGGGCGGCCTGGCCGGAGCGCTACCCCGCCGGCGCGTGCTCGAATACTGTT
+75G,9.4,CTTATTTAGATAACATGATTAGCCGAAGTTGTACGGGATATCCACCGTAAAGTCCTCCCCGGGTGTCCCTCCTTCATTTGATGATAAGCAGCCGCTACCA
+88Q,11.3,GATTGCTCGCACATGAGCAAAACGGTAGAGCGTCACTTTCAGCCCTCTTATCCCCGGCGATGTGTGTGAAATGGCGTTGATCCGGATTGACTCTATGACG