Mercurial > repos > abims-sbr > mutcount

comparison scripts/S02b_study_seq_composition_nuc.py @ 5:0ba551449008 draft

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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
author abims-sbr
date Tue, 27 Feb 2018 08:48:34 -0500
parents 5766f80370e7
children f1e24200e5ae
comparison
equal deleted inserted replaced
4:5766f80370e7 5:0ba551449008
120 120
121 ## 3 ## PathOUT 121 ## 3 ## PathOUT
122 ## 3.1 ## NUC composition 122 ## 3.1 ## NUC composition
123 fileOUT_NUC=open("./OUT/nuc_compositions.csv","w") 123 fileOUT_NUC=open("./OUT/nuc_compositions.csv","w")
124 fileOUT_NUC.write("LOCUS,") 124 fileOUT_NUC.write("LOCUS,")
125 for taxa in LT: 125 for taxa in LT[0:-1]:
126 fileOUT_NUC.write("%s_prop_A,%s_prop_T,%s_prop_C,%s_prop_G," %(taxa,taxa,taxa,taxa)) 126 fileOUT_NUC.write("%s_prop_A,%s_prop_T,%s_prop_C,%s_prop_G," %(taxa,taxa,taxa,taxa))
127 fileOUT_NUC.write("%s_prop_A,%s_prop_T,%s_prop_C,%s_prop_G" %(LT[-1],LT[-1],LT[-1],LT[-1]))
127 fileOUT_NUC.write("\n") 128 fileOUT_NUC.write("\n")
128 129
129 ## 3.2 ## NUC percent_GC 130 ## 3.2 ## NUC percent_GC
130 fileOUT_percent_GC=open("./OUT/percent_GC.csv","w") 131 fileOUT_percent_GC=open("./OUT/percent_GC.csv","w")
131 fileOUT_percent_GC.write("LOCUS,") 132 fileOUT_percent_GC.write("LOCUS,")
132 for taxa in LT: 133 for taxa in LT[0:-1]:
133 fileOUT_percent_GC.write("%s_percent_GC," %(taxa)) 134 fileOUT_percent_GC.write("%s_percent_GC," %(taxa))
135 fileOUT_percent_GC.write("%s_percentGC" %(LT[-1]))
134 fileOUT_percent_GC.write("\n") 136 fileOUT_percent_GC.write("\n")
135 137
136 ## 3.3 ## NUC percent_purine 138 ## 3.3 ## NUC percent_purine
137 fileOUT_percent_purine=open("./OUT/percent_purine.csv","w") 139 fileOUT_percent_purine=open("./OUT/percent_purine.csv","w")
138 fileOUT_percent_purine.write("LOCUS,") 140 fileOUT_percent_purine.write("LOCUS,")
139 for taxa in LT: 141 for taxa in LT[0:-1]:
140 fileOUT_percent_purine.write("%s_percent_purine," %(taxa)) 142 fileOUT_percent_purine.write("%s_percent_purine," %(taxa))
143 fileOUT_percent_purine.write("%s_percent_purine" %(LT[-1]))
141 fileOUT_percent_purine.write("\n") 144 fileOUT_percent_purine.write("\n")
142 145
143 ## 3.4 ## Purine Load 146 ## 3.4 ## Purine Load
144 fileOUT_Purine_Load=open("./OUT/Purine_Load_Indice.csv", "w") 147 fileOUT_Purine_Load=open("./OUT/Purine_Load_Indice.csv", "w")
145 fileOUT_Purine_Load.write("LOCUS,") 148 fileOUT_Purine_Load.write("LOCUS,")
146 for taxa in LT: 149 for taxa in LT[0:-1]:
147 fileOUT_Purine_Load.write("%s_TOTAL,%s_DIFF_GC,%s_DIFF_AT,%s_PLI_GC1000,%s_PLI_AT1000," %(taxa,taxa,taxa,taxa,taxa)) 150 fileOUT_Purine_Load.write("%s_TOTAL,%s_DIFF_GC,%s_DIFF_AT,%s_PLI_GC1000,%s_PLI_AT1000," %(taxa,taxa,taxa,taxa,taxa))
151 fileOUT_Purine_Load.write("%s_TOTAL,%s_DIFF_GC,%s_DIFF_AT,%s_PLI_GC1000,%s_PLI_AT1000" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1]))
148 fileOUT_Purine_Load.write("\n") 152 fileOUT_Purine_Load.write("\n")
149 153
150 ##################### 154 #####################
151 ## 4 ## Process Loci 155 ## 4 ## Process Loci
152 ##################### 156 #####################
158 fileOUT_NUC.write("%s," %locus) 162 fileOUT_NUC.write("%s," %locus)
159 fileOUT_percent_GC.write("%s," %locus) 163 fileOUT_percent_GC.write("%s," %locus)
160 fileOUT_percent_purine.write("%s," %locus) 164 fileOUT_percent_purine.write("%s," %locus)
161 fileOUT_Purine_Load.write("%s," %locus) 165 fileOUT_Purine_Load.write("%s," %locus)
162 166
163 for taxa in LT: 167 for taxa in LT[0:-1]:
164 if taxa in bash.keys(): 168 if taxa in bash.keys():
165 seq = bash[taxa] 169 seq = bash[taxa]
166 percent_GC, percent_purine,prop_A, prop_T, prop_C, prop_G = base_composition(seq) ### DEF2 ### 170 percent_GC, percent_purine,prop_A, prop_T, prop_C, prop_G = base_composition(seq) ### DEF2 ###
167 TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000 = purine_loading(seq) ### DEF3 ### 171 TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000 = purine_loading(seq) ### DEF3 ###
168 fileOUT_NUC.write("%.5f,%.5f,%.5f,%.5f," %(prop_A,prop_T,prop_C,prop_G)) 172 fileOUT_NUC.write("%.5f,%.5f,%.5f,%.5f," %(prop_A,prop_T,prop_C,prop_G))
173 fileOUT_NUC.write("%s,%s,%s,%s," %("NA","NA","NA","NA")) 177 fileOUT_NUC.write("%s,%s,%s,%s," %("NA","NA","NA","NA"))
174 fileOUT_percent_GC.write("%s," %"NA") 178 fileOUT_percent_GC.write("%s," %"NA")
175 fileOUT_percent_purine.write("%s," %"NA") 179 fileOUT_percent_purine.write("%s," %"NA")
176 fileOUT_Purine_Load.write("%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA")) 180 fileOUT_Purine_Load.write("%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA"))
177 181
182 if LT[-1] in bash.keys():
183 seq = bash[LT[-1]]
184 percent_GC, percent_purine,prop_A, prop_T, prop_C, prop_G = base_composition(seq) ### DEF2 ###
185 TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000 = purine_loading(seq) ### DEF3 ###
186 fileOUT_NUC.write("%.5f,%.5f,%.5f,%.5f" %(prop_A,prop_T,prop_C,prop_G))
187 fileOUT_percent_GC.write("%.5f" %percent_GC)
188 fileOUT_percent_purine.write("%.5f" %percent_purine)
189 fileOUT_Purine_Load.write("%d,%d,%d,%.5f,%.5f" %(TOTAL, DIFF_GC, DIFF_AT,PLI_GC_1000, PLI_AT_1000))
190 else:
191 fileOUT_NUC.write("%s,%s,%s,%s" %("NA","NA","NA","NA"))
192 fileOUT_percent_GC.write("%s" %"NA")
193 fileOUT_percent_purine.write("%s" %"NA")
194 fileOUT_Purine_Load.write("%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA"))
195
196
178 fileOUT_NUC.write("\n") 197 fileOUT_NUC.write("\n")
179 fileOUT_percent_GC.write("\n") 198 fileOUT_percent_GC.write("\n")
180 fileOUT_percent_purine.write("\n") 199 fileOUT_percent_purine.write("\n")
181 fileOUT_Purine_Load.write("\n") 200 fileOUT_Purine_Load.write("\n")
182 fileOUT_NUC.close() 201 fileOUT_NUC.close()