Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.py @ 107:01c9993865af draft

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Uploaded
author davidvanzessen
date Wed, 13 Jul 2016 08:04:13 -0400
parents 603a10976e9c
children 6add3e66f4fa
comparison
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106:074ae1e30e8f 107:01c9993865af
84 AA_mutation_dic = {"ca": AA_mutation[:], "cg": AA_mutation[:], "cm": AA_mutation[:], "un": AA_mutation[:]} 84 AA_mutation_dic = {"ca": AA_mutation[:], "cg": AA_mutation[:], "cm": AA_mutation[:], "un": AA_mutation[:]}
85 AA_mutation_empty = AA_mutation[:] 85 AA_mutation_empty = AA_mutation[:]
86 86
87 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt" 87 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt"
88 with open(aa_mutations_by_id_file, 'w') as o: 88 with open(aa_mutations_by_id_file, 'w') as o:
89 o.write("ID\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n")
89 for ID in mutationListByID.keys(): 90 for ID in mutationListByID.keys():
90 AA_mutation_for_ID = AA_mutation_empty[:] 91 AA_mutation_for_ID = AA_mutation_empty[:]
91 for mutation in mutationListByID[ID]: 92 for mutation in mutationListByID[ID]:
92 if mutation[4]: 93 if mutation[4]:
93 AA_mutation_position = int(mutation[4]) 94 AA_mutation_position = int(mutation[4])
94 AA_mutation[AA_mutation_position] += 1 95 AA_mutation[AA_mutation_position] += 1
95 AA_mutation_for_ID[AA_mutation_position] += 1 96 AA_mutation_for_ID[AA_mutation_position] += 1
96 clss = genedic[ID][:2] 97 clss = genedic[ID][:2]
97 AA_mutation_dic[clss][AA_mutation_position] += 1 98 AA_mutation_dic[clss][AA_mutation_position] += 1
98 o.write(ID + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n") 99 o.write(ID + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n")
99 100
100 101
101 102
102 #absent AA stuff 103 #absent AA stuff
103 absentAACDR1Dic = defaultdict(list) 104 absentAACDR1Dic = defaultdict(list)
131 absentAA[c] -= 1 132 absentAA[c] -= 1
132 133
133 134
134 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/absent_aa_id.txt" 135 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/absent_aa_id.txt"
135 with open(aa_mutations_by_id_file, 'w') as o: 136 with open(aa_mutations_by_id_file, 'w') as o:
136 o.write("ID\tcdr1length\tcdr2length\t" + "\t".join([str(x) for x in range(1,AALength-1)]) + "\n") 137 o.write("ID\tcdr1length\tcdr2length\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n")
137 for ID in IDlist: 138 for ID in IDlist:
138 absentAAbyID = [1] * (AALength-1) 139 absentAAbyID = [1] * (AALength-1)
139 cdr1Length = cdr1LengthDic[ID] 140 cdr1Length = cdr1LengthDic[ID]
140 for c in absentAACDR1Dic[cdr1Length]: 141 for c in absentAACDR1Dic[cdr1Length]:
141 absentAAbyID[c] -= 1 142 absentAAbyID[c] -= 1
142 143
143 cdr2Length = cdr2LengthDic[ID] 144 cdr2Length = cdr2LengthDic[ID]
144 for c in absentAACDR2Dic[cdr2Length]: 145 for c in absentAACDR2Dic[cdr2Length]:
145 absentAAbyID[c] -= 1 146 absentAAbyID[c] -= 1
146 o.write(ID + "\t" + str(cdr1Length) + "\t" + str(cdr2Length) + "\t" + "\t".join([str(x) for x in absentAAbyID]) + "\n") 147 o.write(ID + "\t" + str(cdr1Length) + "\t" + str(cdr2Length) + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in absentAAbyID]) + "\n")
147 148
148 149
149 150
150 aa_mutations_file = outfile[:outfile.rindex("/")] + "/aa_mutations.txt" 151 aa_mutations_file = outfile[:outfile.rindex("/")] + "/aa_mutations.txt"
151 with open(aa_mutations_file, 'w') as o: 152 with open(aa_mutations_file, 'w') as o: