Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.py @ 108:6add3e66f4fa draft

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Uploaded
author davidvanzessen
date Wed, 13 Jul 2016 09:04:15 -0400
parents 01c9993865af
children ade5cf6fd2dc
comparison
equal deleted inserted replaced
107:01c9993865af 108:6add3e66f4fa
144 cdr2Length = cdr2LengthDic[ID] 144 cdr2Length = cdr2LengthDic[ID]
145 for c in absentAACDR2Dic[cdr2Length]: 145 for c in absentAACDR2Dic[cdr2Length]:
146 absentAAbyID[c] -= 1 146 absentAAbyID[c] -= 1
147 o.write(ID + "\t" + str(cdr1Length) + "\t" + str(cdr2Length) + "\t" + genedic[ID] + "\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")
148 148
149
150
151 aa_mutations_file = outfile[:outfile.rindex("/")] + "/aa_mutations.txt"
152 with open(aa_mutations_file, 'w') as o:
153 o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
154 o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation[1:]]) + "\n")
155 o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")
156
157
158 aa_mutations_file_ca = outfile[:outfile.rindex("/")] + "/aa_mutations_ca.txt"
159 with open(aa_mutations_file_ca, 'w') as o:
160 o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
161 o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation_dic["ca"][1:]]) + "\n")
162 o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")
163
164
165 aa_mutations_file_cg = outfile[:outfile.rindex("/")] + "/aa_mutations_cg.txt"
166 with open(aa_mutations_file_cg, 'w') as o:
167 o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
168 o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation_dic["cg"][1:]]) + "\n")
169 o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")
170
171
172 aa_mutations_file_cm = outfile[:outfile.rindex("/")] + "/aa_mutations_cm.txt"
173 with open(aa_mutations_file_cm, 'w') as o:
174 o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
175 o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation_dic["cg"][1:]]) + "\n")
176 o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")
177
178 if linecount == 0: 149 if linecount == 0:
179 print "No data, exiting" 150 print "No data, exiting"
180 with open(outfile, 'w') as o: 151 with open(outfile, 'w') as o:
181 o.write("RGYW (%)," + ("0,0,0\n" * len(genes))) 152 o.write("RGYW (%)," + ("0,0,0\n" * len(genes)))
182 o.write("WRCY (%)," + ("0,0,0\n" * len(genes))) 153 o.write("WRCY (%)," + ("0,0,0\n" * len(genes)))