Carlos-Francisco Méndez-Cruz / automatic-extraction-growth-conditions

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Carlos-Francisco Méndez-Cruz
4e4ff446 1 parent 3f696776

Conditions tagged per XML file - csv format

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Showing 26 changed files with 320 additions and 4 deletions
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
3 +"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
4 +"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
5 +"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
2 "GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 6 "GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
3 "GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 7 "GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
4 "GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 8 "GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
...@@ -14,10 +18,6 @@ ...@@ -14,10 +18,6 @@
14 "GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 18 "GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
15 "GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 19 "GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
16 "GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 20 "GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
17 -"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
18 -"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
19 -"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
20 -"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
21 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 21 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
22 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 22 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
23 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 23 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
......
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1 +Serie Sample
2 +GSE11230 GSM282644
3 +GSE11230 GSM282645
4 +GSE11230 GSM283059
5 +GSE19053 GSM471482
6 +GSE19053 GSM471483
7 +GSE19053 GSM471484
8 +GSE19053 GSM471485
9 +GSE19053 GSM471486
10 +GSE19053 GSM471487
11 +GSE19053 GSM471488
12 +GSE19053 GSM471489
13 +GSE19053 GSM471490
14 +GSE19053 GSM471491
15 +GSE19053 GSM471492
16 +GSE19053 GSM471493
17 +GSE19053 GSM471494
18 +GSE19053 GSM471495
19 +GSE19053 GSM476145
20 +GSE26054 GSM639826
21 +GSE26054 GSM639827
22 +GSE26054 GSM639828
23 +GSE26054 GSM639829
24 +GSE26054 GSM639830
25 +GSE26054 GSM639831
26 +GSE26054 GSM639832
27 +GSE26054 GSM639833
28 +GSE26054 GSM639834
29 +GSE26054 GSM639835
30 +GSE26054 GSM639836
31 +GSE26054 GSM639837
32 +GSE26589 GSM654485
33 +GSE26589 GSM654486
34 +GSE26589 GSM654487
35 +GSE26589 GSM654488
36 +GSE41186 GSM1010199
37 +GSE41186 GSM1010200
38 +GSE41186 GSM1010201
39 +GSE41186 GSM1010202
40 +GSE41186 GSM1010203
41 +GSE41186 GSM1010204
42 +GSE41186 GSM1010205
43 +GSE41186 GSM1010206
44 +GSE41186 GSM1010207
45 +GSE41186 GSM1010208
46 +GSE41186 GSM1010209
47 +GSE41186 GSM1010210
48 +GSE41186 GSM1010211
49 +GSE41186 GSM1010212
50 +GSE41186 GSM1010213
51 +GSE41186 GSM1010214
52 +GSE41186 GSM1010215
53 +GSE41186 GSM1010216
54 +GSE41186 GSM1010217
55 +GSE41186 GSM1010218
56 +GSE41186 GSM1054383
57 +GSE41186 GSM1054384
58 +GSE41186 GSM1143890
59 +GSE41186 GSM1143891
60 +GSE41186 GSM1143892
61 +GSE41190 GSM1010244
62 +GSE41190 GSM1010245
63 +GSE41190 GSM1010246
64 +GSE41190 GSM1010247
65 +GSE41195 GSM1010199
66 +GSE41195 GSM1010200
67 +GSE41195 GSM1010201
68 +GSE41195 GSM1010202
69 +GSE41195 GSM1010203
70 +GSE41195 GSM1010204
71 +GSE41195 GSM1010205
72 +GSE41195 GSM1010206
73 +GSE41195 GSM1010207
74 +GSE41195 GSM1010208
75 +GSE41195 GSM1010209
76 +GSE41195 GSM1010210
77 +GSE41195 GSM1010211
78 +GSE41195 GSM1010212
79 +GSE41195 GSM1010213
80 +GSE41195 GSM1010214
81 +GSE41195 GSM1010215
82 +GSE41195 GSM1010216
83 +GSE41195 GSM1010217
84 +GSE41195 GSM1010218
85 +GSE41195 GSM1010219
86 +GSE41195 GSM1010220
87 +GSE41195 GSM1010221
88 +GSE41195 GSM1010222
89 +GSE41195 GSM1010223
90 +GSE41195 GSM1010224
91 +GSE41195 GSM1010240
92 +GSE41195 GSM1010241
93 +GSE41195 GSM1010242
94 +GSE41195 GSM1010243
95 +GSE41195 GSM1010244
96 +GSE41195 GSM1010245
97 +GSE41195 GSM1010246
98 +GSE41195 GSM1010247
99 +GSE41195 GSM1054383
100 +GSE41195 GSM1054384
101 +GSE41195 GSM1072326
102 +GSE41195 GSM1072327
103 +GSE41195 GSM1072328
104 +GSE41195 GSM1124977
105 +GSE41195 GSM1124978
106 +GSE41195 GSM1124979
107 +GSE41195 GSM1124980
108 +GSE41195 GSM1126445
109 +GSE41195 GSM1126446
110 +GSE41195 GSM1143890
111 +GSE41195 GSM1143891
112 +GSE41195 GSM1143892
113 +GSE4321 GSM98717
114 +GSE4321 GSM98718
115 +GSE4321 GSM98719
116 +GSE4321 GSM98720
117 +GSE4321 GSM98721
118 +GSE4321 GSM98722
119 +GSE4321 GSM98723
120 +GSE4321 GSM98724
121 +GSE4321 GSM98725
122 +GSE4321 GSM98726
123 +GSE4321 GSM98727
124 +GSE4321 GSM98728
125 +GSE4321 GSM98729
126 +GSE4321 GSM98730
127 +GSE4321 GSM98731
128 +GSE4321 GSM98732
129 +GSE54899 GSM1326335
130 +GSE54899 GSM1326336
131 +GSE54899 GSM1326337
132 +GSE54899 GSM1326338
133 +GSE54899 GSM1326339
134 +GSE54899 GSM1326340
135 +GSE54899 GSM1326341
136 +GSE54899 GSM1326342
137 +GSE54899 GSM1326343
138 +GSE54899 GSM1326344
139 +GSE54899 GSM1326345
140 +GSE54899 GSM1326346
141 +GSE54901 GSM1326335
142 +GSE54901 GSM1326336
143 +GSE54901 GSM1326337
144 +GSE54901 GSM1326338
145 +GSE54901 GSM1326339
146 +GSE54901 GSM1326340
147 +GSE54901 GSM1326341
148 +GSE54901 GSM1326342
149 +GSE54901 GSM1326343
150 +GSE54901 GSM1326344
151 +GSE54901 GSM1326345
152 +GSE54901 GSM1326346
153 +GSE54901 GSM1326347
154 +GSE54901 GSM1326348
155 +GSE54901 GSM1326349
156 +GSE54901 GSM1326350
157 +GSE54901 GSM1326351
158 +GSE54901 GSM1326352
159 +GSE54901 GSM1326353
160 +GSE54901 GSM1326354
161 +GSE55199 GSM1331409
162 +GSE55199 GSM1331410
163 +GSE55199 GSM1331411
164 +GSE55199 GSM1331412
165 +GSE55199 GSM1331413
166 +GSE55199 GSM1331414
167 +GSE55199 GSM1331415
168 +GSE55199 GSM1331416
169 +GSE55199 GSM1331417
170 +GSE55199 GSM1331418
171 +GSE55199 GSM1331419
172 +GSE55199 GSM1331420
173 +GSE55199 GSM1331421
174 +GSE55199 GSM1331422
175 +GSE55199 GSM1331423
176 +GSE55199 GSM1331424
177 +GSE55199 GSM1331425
178 +GSE55199 GSM1331426
179 +GSE55199 GSM1331427
180 +GSE55199 GSM1331428
181 +GSE55199 GSM1331429
182 +GSE55199 GSM1331430
183 +GSE55365 GSM1334746
184 +GSE55365 GSM1334747
185 +GSE55365 GSM1334748
186 +GSE55365 GSM1334749
187 +GSE55365 GSM1334750
188 +GSE55365 GSM1334751
189 +GSE55365 GSM1334752
190 +GSE55365 GSM1334753
191 +GSE55365 GSM1334754
192 +GSE55365 GSM1334755
193 +GSE55365 GSM1334756
194 +GSE55365 GSM1334757
195 +GSE55365 GSM1334758
196 +GSE55365 GSM1334759
197 +GSE55365 GSM1334760
198 +GSE55365 GSM1334761
199 +GSE55365 GSM1334762
200 +GSE55365 GSM1334763
201 +GSE55366 GSM1334764
202 +GSE55366 GSM1334765
203 +GSE55366 GSM1334766
204 +GSE55366 GSM1334767
205 +GSE55366 GSM1334768
206 +GSE55366 GSM1334769
207 +GSE55366 GSM1334770
208 +GSE55366 GSM1334771
209 +GSE55366 GSM1334772
210 +GSE55366 GSM1334773
211 +GSE55366 GSM1334774
212 +GSE55366 GSM1334775
213 +GSE60546 GSM1482120
214 +GSE60546 GSM1482121
215 +GSE65641 GSM1602341
216 +GSE65641 GSM1602342
217 +GSE65641 GSM1602343
218 +GSE65641 GSM1602344
219 +GSE65641 GSM1602345
220 +GSE65641 GSM1602346
221 +GSE65641 GSM2829281
222 +GSE65641 GSM2829282
223 +GSE65641 GSM2829283
224 +GSE65641 GSM2829284
225 +GSE65641 GSM2829285
226 +GSE65641 GSM2829286
227 +GSE65642 GSM1602347
228 +GSE65642 GSM1602348
229 +GSE65642 GSM1602349
230 +GSE65642 GSM1602350
231 +GSE65642 GSM1602351
232 +GSE65642 GSM1602352
233 +GSE65642 GSM1602353
234 +GSE65642 GSM1602354
235 +GSE65642 GSM1602355
236 +GSE65642 GSM1602356
237 +GSE65642 GSM1602357
238 +GSE65642 GSM1602358
239 +GSE65710 GSM1603380
240 +GSE65710 GSM1603381
241 +GSE65710 GSM1603382
242 +GSE65710 GSM1603383
243 +GSE65710 GSM1603384
244 +GSE65710 GSM1603385
245 +GSE65711 GSM1603386
246 +GSE65711 GSM1603387
247 +GSE65711 GSM1603388
248 +GSE65711 GSM1603389
249 +GSE65711 GSM1603390
250 +GSE65711 GSM1603391
251 +GSE65711 GSM1603392
252 +GSE65711 GSM1603393
253 +GSE66441 GSM1622463
254 +GSE66441 GSM1622464
255 +GSE66441 GSM1622465
256 +GSE66441 GSM1622466
257 +GSE66441 GSM1622467
258 +GSE66441 GSM1622468
259 +GSE66441 GSM1633277
260 +GSE66441 GSM1633278
261 +GSE66481 GSM1623160
262 +GSE66481 GSM1623161
263 +GSE66481 GSM1623162
264 +GSE66481 GSM1623163
265 +GSE66481 GSM1623164
266 +GSE66481 GSM1623165
267 +GSE66481 GSM1623166
268 +GSE66481 GSM1623167
269 +GSE74930 GSM1937949
270 +GSE74930 GSM1937950
271 +GSE74930 GSM1937951
272 +GSE74930 GSM1937952
273 +GSE74930 GSM1937953
274 +GSE74930 GSM1937954
275 +GSE74930 GSM1937955
276 +GSE74930 GSM1937956
277 +GSE74930 GSM1937957
278 +GSE74930 GSM1937958
279 +GSE74930 GSM1937959
280 +GSE74930 GSM1937960
281 +GSE74930 GSM1937961
282 +GSE74930 GSM1937962
283 +GSE74931 GSM1937963
284 +GSE74932 GSM1937964
285 +GSE74932 GSM1937965
286 +GSE74932 GSM1937966
287 +GSE74932 GSM1937967
288 +GSE74932 GSM1937968
289 +GSE74932 GSM1937969
290 +GSE74932 GSM1937970
291 +GSE74932 GSM1937971
292 +GSE74932 GSM1937972
293 +GSE88979 GSM2356685
294 +GSE88979 GSM2356686
295 +GSE88980 GSM2356687
296 +GSE88980 GSM2356688
297 +GSE88980 GSM2356689
298 +GSE88980 GSM2356690
299 +GSE93506 GSM2453482
300 +GSE93506 GSM2453483
301 +GSE93506 GSM2453484
302 +GSE93506 GSM2453485
303 +GSE93506 GSM2453486
304 +GSE93506 GSM2453487
305 +GSE93506 GSM2667742
306 +GSE93506 GSM2667743
307 +GSE93506 GSM2667744
308 +GSE93506 GSM2667745
309 +GSE93506 GSM2667746
...@@ -57,6 +57,7 @@ if __name__ == "__main__": ...@@ -57,6 +57,7 @@ if __name__ == "__main__":
57 tags = ["Name", "Anti", "Orgn", "Strain", "Substrain", "Gtype", "Gversion", "Med", "Technique", "Supp", "Air", "Temp", "pH", "Press", "OD", "Phase", "Rate", "Vess", "Agit", ] 57 tags = ["Name", "Anti", "Orgn", "Strain", "Substrain", "Gtype", "Gversion", "Med", "Technique", "Supp", "Air", "Temp", "pH", "Press", "OD", "Phase", "Rate", "Vess", "Agit", ]
58 processed_files = 0 58 processed_files = 0
59 saved_files = 0 59 saved_files = 0
60 + complete_report = []
60 # Walk directory to read files 61 # Walk directory to read files
61 for path, dirs, files in os.walk(options.inputPath): 62 for path, dirs, files in os.walk(options.inputPath):
62 for f in files: 63 for f in files:
...@@ -119,6 +120,7 @@ if __name__ == "__main__": ...@@ -119,6 +120,7 @@ if __name__ == "__main__":
119 output = output + '"' + tag + '",' 120 output = output + '"' + tag + '",'
120 output = output.rstrip(',') 121 output = output.rstrip(',')
121 oFile.write(output + "\n") 122 oFile.write(output + "\n")
123 + complete_report.append(output)
122 for serie, hashSample in hashGcs.items(): 124 for serie, hashSample in hashGcs.items():
123 print("Serie: {}".format(serie)) 125 print("Serie: {}".format(serie))
124 for sample, hashTag in sorted(hashSample.items()): 126 for sample, hashTag in sorted(hashSample.items()):
...@@ -135,6 +137,7 @@ if __name__ == "__main__": ...@@ -135,6 +137,7 @@ if __name__ == "__main__":
135 output = output + '"' + tag + '",' 137 output = output + '"' + tag + '",'
136 output = output.rstrip(',') 138 output = output.rstrip(',')
137 oFile.write(output + "\n") 139 oFile.write(output + "\n")
140 + complete_report.append(output)
138 # oFile.write("{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(sample, serie, Technique, Orgn, Strain, Substrain, Gversion, Gtype, Phase, Air, Med, Temp, Supp)) 141 # oFile.write("{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(sample, serie, Technique, Orgn, Strain, Substrain, Gversion, Gtype, Phase, Air, Med, Temp, Supp))
139 # for tag, listContent in sorted(hashTag.items()): 142 # for tag, listContent in sorted(hashTag.items()):
140 # print("\t\tTag: {}".format(tag)) 143 # print("\t\tTag: {}".format(tag))
...@@ -144,6 +147,10 @@ if __name__ == "__main__": ...@@ -144,6 +147,10 @@ if __name__ == "__main__":
144 # oFile.write("Serie: {}\tSample: {}\tTag: {}\tContent: {}\n".format(serie, sample, tag, content)) 147 # oFile.write("Serie: {}\tSample: {}\tTag: {}\tContent: {}\n".format(serie, sample, tag, content))
145 saved_files+=1 148 saved_files+=1
146 149
150 + with open(os.path.join(options.outputPath, f.replace(".xml", ".complete-report.csv")), "w") as oFile:
151 + for line in complete_report:
152 + oFile.write(line + "\n")
153 +
147 print("Processed files: {}".format(processed_files)) 154 print("Processed files: {}".format(processed_files))
148 print("Saved files: {}".format(saved_files)) 155 print("Saved files: {}".format(saved_files))
149 156
......