biopipen 0.32.0__py3-none-any.whl → 0.32.3__py3-none-any.whl

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Files changed (39) hide show
  1. biopipen/__init__.py +1 -1
  2. biopipen/core/filters.py +45 -6
  3. biopipen/reports/scrna/TopExpressingGenes.svelte +1 -1
  4. biopipen/reports/utils/misc.liq +6 -4
  5. biopipen/scripts/delim/SampleInfo.R +10 -1
  6. biopipen/scripts/scrna/CellsDistribution.R +31 -6
  7. biopipen/scripts/scrna/MarkersFinder.R +67 -16
  8. biopipen/scripts/scrna/MetaMarkers.R +16 -7
  9. biopipen/scripts/scrna/RadarPlots.R +22 -2
  10. biopipen/scripts/scrna/ScFGSEA.R +1 -1
  11. biopipen/scripts/scrna/SeuratClusterStats-clustree.R +7 -1
  12. biopipen/scripts/scrna/SeuratClusterStats-dimplots.R +9 -2
  13. biopipen/scripts/scrna/SeuratClusterStats-features.R +22 -4
  14. biopipen/scripts/scrna/SeuratClusterStats-hists.R +7 -2
  15. biopipen/scripts/scrna/SeuratClusterStats-ngenes.R +6 -1
  16. biopipen/scripts/scrna/SeuratClusterStats-stats.R +13 -2
  17. biopipen/scripts/scrna/SeuratMap2Ref.R +7 -1
  18. biopipen/scripts/scrna/SeuratPreparing-common.R +21 -6
  19. biopipen/scripts/scrna/SeuratPreparing-doublet_detection.R +6 -3
  20. biopipen/scripts/scrna/TopExpressingGenes.R +9 -7
  21. biopipen/scripts/tcr/CDR3AAPhyschem.R +12 -2
  22. biopipen/scripts/tcr/CloneResidency.R +23 -5
  23. biopipen/scripts/tcr/Immunarch-basic.R +8 -1
  24. biopipen/scripts/tcr/Immunarch-clonality.R +5 -0
  25. biopipen/scripts/tcr/Immunarch-diversity.R +25 -4
  26. biopipen/scripts/tcr/Immunarch-geneusage.R +15 -1
  27. biopipen/scripts/tcr/Immunarch-kmer.R +14 -1
  28. biopipen/scripts/tcr/Immunarch-overlap.R +15 -1
  29. biopipen/scripts/tcr/Immunarch-spectratyping.R +10 -1
  30. biopipen/scripts/tcr/Immunarch-tracking.R +6 -0
  31. biopipen/scripts/tcr/Immunarch-vjjunc.R +33 -0
  32. biopipen/scripts/tcr/TCRClusterStats.R +24 -7
  33. biopipen/scripts/tcr/TESSA.R +6 -1
  34. biopipen/utils/gsea.R +21 -7
  35. biopipen/utils/plot.R +53 -17
  36. {biopipen-0.32.0.dist-info → biopipen-0.32.3.dist-info}/METADATA +3 -2
  37. {biopipen-0.32.0.dist-info → biopipen-0.32.3.dist-info}/RECORD +39 -39
  38. {biopipen-0.32.0.dist-info → biopipen-0.32.3.dist-info}/WHEEL +1 -1
  39. {biopipen-0.32.0.dist-info → biopipen-0.32.3.dist-info}/entry_points.txt +0 -0
@@ -69,6 +69,7 @@ cluster_size_distribution = function(name) {
69
69
 
70
70
  outfile = file.path(odir, "cluster_size_distribution.txt")
71
71
  outplot = file.path(odir, "cluster_size_distribution.png")
72
+ outplot_pdf = file.path(odir, "cluster_size_distribution.pdf")
72
73
  write.table(clsizes, outfile, quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE)
73
74
 
74
75
  plotGG(
@@ -82,14 +83,15 @@ cluster_size_distribution = function(name) {
82
83
  "scale_fill_biopipen()"
83
84
  ),
84
85
  devpars = case$devpars,
85
- outfile = outplot
86
+ outfile = c(outplot, outplot_pdf)
86
87
  )
87
88
 
88
89
  add_report(
89
90
  list(
90
91
  src = outplot,
91
92
  name = ifelse(name == "DEFAULT", FALSE, name),
92
- descr = paste0("Cluster size distribution for each ", case$by)
93
+ descr = paste0("Cluster size distribution for each ", case$by),
94
+ download = outplot_pdf
93
95
  ),
94
96
  ui = "table_of_images",
95
97
  h1 = "Cluster Size Distribution"
@@ -162,6 +164,8 @@ shared_clusters = function(name) {
162
164
  row_samples = samples
163
165
  }
164
166
 
167
+ hmplot = file.path(odir, "shared_clusters.png")
168
+ hmplot_pdf = file.path(odir, "shared_clusters.pdf")
165
169
  # Plot heatmap
166
170
  plotHeatmap(
167
171
  plotdata,
@@ -178,12 +182,13 @@ shared_clusters = function(name) {
178
182
  }
179
183
  ),
180
184
  devpars = case$devpars,
181
- outfile = file.path(odir, "shared_clusters.png")
185
+ outfile = c(hmplot, hmplot_pdf)
182
186
  )
183
187
 
184
188
  add_report(
185
189
  list(
186
- src = file.path(odir, "shared_clusters.png"),
190
+ src = hmplot,
191
+ download = hmplot_pdf,
187
192
  name = ifelse(name == "DEFAULT", FALSE, name),
188
193
  descr = paste0("Shared TCR clusters across samples")
189
194
  ),
@@ -219,16 +224,18 @@ shared_clusters_by_grouping = function(name) {
219
224
  }
220
225
 
221
226
  outfile = file.path(odir, "shared_clusters.png")
227
+ outfile_pdf = file.path(odir, "shared_clusters.pdf")
222
228
  plotVenn(
223
229
  data,
224
230
  ggs = 'ggtitle("Shared TCR Clusters")',
225
231
  devpars = case$devpars,
226
- outfile = outfile
232
+ outfile = c(outfile, outfile_pdf)
227
233
  )
228
234
 
229
235
  add_report(
230
236
  list(
231
237
  src = outfile,
238
+ download = outfile_pdf,
232
239
  name = ifelse(name == "DEFAULT", FALSE, name),
233
240
  descr = paste0("Shared TCR clusters across ", grouping)
234
241
  ),
@@ -275,6 +282,7 @@ sample_diversity = function(name) {
275
282
  }
276
283
  outfile = file.path(odir, "diversity.txt")
277
284
  outplot = file.path(odir, "diversity.png")
285
+ outplot_pdf = file.path(odir, "diversity.pdf")
278
286
  div = repDiversity(data, .method = case$method)
279
287
  write.table(
280
288
  if (ncol(div) == 1) {
@@ -320,7 +328,7 @@ sample_diversity = function(name) {
320
328
  args = list(mapping = mapping),
321
329
  ggs = ggs,
322
330
  devpars = case$devpars,
323
- outfile = outplot
331
+ outfile = c(outplot, outplot_pdf)
324
332
  )
325
333
  } else {
326
334
  if (is.null(case$by) || length(case$by) == 0) {
@@ -338,6 +346,14 @@ sample_diversity = function(name) {
338
346
  )
339
347
  print(p)
340
348
  dev.off()
349
+
350
+ pdf(
351
+ outplot_pdf,
352
+ width=case$devpars$width / case$devpars$res,
353
+ height=case$devpars$height / case$devpars$res
354
+ )
355
+ print(p)
356
+ dev.off()
341
357
  }
342
358
 
343
359
  add_report(
@@ -359,7 +375,8 @@ sample_diversity = function(name) {
359
375
  ),
360
376
  list(
361
377
  kind = "image",
362
- src = outplot
378
+ src = outplot,
379
+ download = outplot_pdf
363
380
  )
364
381
  )
365
382
  ),
@@ -198,10 +198,15 @@ png(file.path(result_dir, "Cluster_size_dist.png"), width=8, height=8, units="in
198
198
  print(p)
199
199
  dev.off()
200
200
 
201
+ pdf(file.path(result_dir, "Cluster_size_dist.pdf"), width=8, height=8)
202
+ print(p)
203
+ dev.off()
204
+
201
205
  add_report(
202
206
  list(
203
207
  src = file.path(result_dir, "Cluster_size_dist.png"),
204
- descr = "Histogram of cluster size distribution"
208
+ descr = "Histogram of cluster size distribution",
209
+ download = file.path(result_dir, "Cluster_size_dist.pdf")
205
210
  ),
206
211
  list(
207
212
  src = file.path(result_dir, "clone_size.png"),
biopipen/utils/gsea.R CHANGED
@@ -201,24 +201,38 @@ runFGSEA = function(
201
201
  }
202
202
  topPathways = unlist(topPathways)
203
203
 
204
- tablefig = file.path(outdir, "gsea_table.png")
205
- png(tablefig, res=100, width=1000, height=200 + 40 * length(topPathways))
206
- print(plotGseaTable(
204
+ p <- plotGseaTable(
207
205
  envs$pathways[topPathways],
208
206
  ranks,
209
207
  gsea_res,
210
208
  gseaParam = if (!is.null(envs$gseaParam)) envs$gseaParam else 1
211
- ))
209
+ )
210
+
211
+ tablefig = file.path(outdir, "gsea_table.png")
212
+ png(tablefig, res=100, width=1000, height=200 + 40 * length(topPathways))
213
+ print(p)
214
+ dev.off()
215
+
216
+ tablefig_pdf = file.path(outdir, "gsea_table.pdf")
217
+ pdf(tablefig_pdf, width=10, height=2 + 0.4 * length(topPathways))
218
+ print(p)
212
219
  dev.off()
213
220
 
214
221
  for (pathway in topPathways) {
215
222
  enrfig = file.path(outdir, paste0("fgsea_", slugify(pathway), ".png"))
216
- png(enrfig, res=100, width=1000, height=800)
217
- print(plotEnrichment(
223
+ p <- plotEnrichment(
218
224
  envs$pathways[[pathway]],
219
225
  ranks,
220
226
  gseaParam = if (!is.null(envs$gseaParam)) envs$gseaParam else 1
221
- ) + labs(title = pathway))
227
+ ) + labs(title = pathway)
228
+
229
+ png(enrfig, res=100, width=1000, height=800)
230
+ print(p)
231
+ dev.off()
232
+
233
+ enrfig_pdf = gsub(".png$", ".pdf", enrfig)
234
+ pdf(enrfig_pdf, width=10, height=8)
235
+ print(p)
222
236
  dev.off()
223
237
  }
224
238
  }
biopipen/utils/plot.R CHANGED
@@ -31,10 +31,19 @@ plotVenn = function(
31
31
  if (is.null(outfile)) {
32
32
  return (p)
33
33
  } else {
34
- devpars$filename = outfile
35
- do.call(png, devpars)
36
- print(p)
37
- dev.off()
34
+ for (outf in outfile) {
35
+ if (endsWith(outf, ".pdf")) {
36
+ pdf(outf, width = devpars$width / devpars$res, height=devpars$height / devpars$res)
37
+ print(p)
38
+ dev.off()
39
+ } else {
40
+ fmt = substring(outf, nchar(outf) - 2)
41
+ devpars$filename = outf
42
+ do.call(fmt, devpars)
43
+ print(p)
44
+ dev.off()
45
+ }
46
+ }
38
47
  }
39
48
  }
40
49
 
@@ -69,10 +78,19 @@ plotGG = function(
69
78
  if (is.null(outfile)) {
70
79
  return (p)
71
80
  } else {
72
- devpars$filename = outfile
73
- do.call(png, devpars)
74
- print(p)
75
- dev.off()
81
+ for (outf in outfile) {
82
+ if (endsWith(outf, ".pdf")) {
83
+ pdf(outf, width = devpars$width / devpars$res, height=devpars$height / devpars$res)
84
+ print(p)
85
+ dev.off()
86
+ } else {
87
+ fmt = substring(outf, nchar(outf) - 2)
88
+ devpars$filename = outf
89
+ do.call(fmt, devpars)
90
+ print(p)
91
+ dev.off()
92
+ }
93
+ }
76
94
  }
77
95
  }
78
96
 
@@ -135,10 +153,19 @@ plotUpset = function(
135
153
  if (is.null(outfile)) {
136
154
  return (p)
137
155
  } else {
138
- devpars$filename = outfile
139
- do.call(png, devpars)
140
- print(p)
141
- dev.off()
156
+ for (outf in outfile) {
157
+ if (endsWith(outf, ".pdf")) {
158
+ pdf(outf, width = devpars$width / devpars$res, height=devpars$height / devpars$res)
159
+ print(p)
160
+ dev.off()
161
+ } else {
162
+ fmt = substring(outf, nchar(outf) - 2)
163
+ devpars$filename = outf
164
+ do.call(fmt, devpars)
165
+ print(p)
166
+ dev.off()
167
+ }
168
+ }
142
169
  }
143
170
  }
144
171
 
@@ -162,12 +189,21 @@ plotHeatmap = function(
162
189
 
163
190
  if (is.null(outfile)) {
164
191
  return(hm)
165
- } else if (outfile == "draw") {
192
+ } else if (identical(outfile, "draw")) {
166
193
  do.call(ComplexHeatmap::draw, c(list(hm), draw))
167
194
  } else {
168
- devpars$filename = outfile
169
- do.call(png, devpars)
170
- do.call(ComplexHeatmap::draw, c(list(hm), draw))
171
- dev.off()
195
+ for (outf in outfile) {
196
+ if (endsWith(outf, ".pdf")) {
197
+ pdf(outf, width = devpars$width / devpars$res, height=devpars$height / devpars$res)
198
+ do.call(ComplexHeatmap::draw, c(list(hm), draw))
199
+ dev.off()
200
+ } else {
201
+ fmt = substring(outf, nchar(outf) - 2)
202
+ devpars$filename = outf
203
+ do.call(fmt, devpars)
204
+ do.call(ComplexHeatmap::draw, c(list(hm), draw))
205
+ dev.off()
206
+ }
207
+ }
172
208
  }
173
209
  }
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.1
1
+ Metadata-Version: 2.3
2
2
  Name: biopipen
3
- Version: 0.32.0
3
+ Version: 0.32.3
4
4
  Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
5
5
  License: MIT
6
6
  Author: pwwang
@@ -12,6 +12,7 @@ Classifier: Programming Language :: Python :: 3.9
12
12
  Classifier: Programming Language :: Python :: 3.10
13
13
  Classifier: Programming Language :: Python :: 3.11
14
14
  Classifier: Programming Language :: Python :: 3.12
15
+ Classifier: Programming Language :: Python :: 3.13
15
16
  Provides-Extra: runinfo
16
17
  Requires-Dist: datar[pandas] (>=0.15.6,<0.16.0)
17
18
  Requires-Dist: pipen-board[report] (>=0.16,<0.17)
@@ -1,9 +1,9 @@
1
- biopipen/__init__.py,sha256=s1FApnNsg-mmWP3shY6ep6EAjZrNFXHlyBXWcP2KV6Q,23
1
+ biopipen/__init__.py,sha256=YDO2wJJsMCLxjOFVlozVz0HadGTsnQ28ZjSGpZRqGso,23
2
2
  biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
3
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  biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
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  biopipen/core/config.toml,sha256=7IXvviRicZ2D1h6x3BVgbLJ96nsh-ikvZ0sVlQepqFE,1944
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  biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
6
- biopipen/core/filters.py,sha256=5bZsbpdW7DCxqiteRdb2gelmXvfqWPmPsFxrpHdWsoE,12987
6
+ biopipen/core/filters.py,sha256=dOar_LBx4F6tRraQi9nWw1AGG0Yb-Zxs3OHLFW9Bvys,15605
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  biopipen/core/proc.py,sha256=60lUP3PcUAaKbDETo9N5PEIoeOYrLgcSmuytmrhcx8g,912
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  biopipen/core/testing.py,sha256=lZ_R5ZbYPO2NPuLHdbzg6HbD_f4j8paVVbyeUqwg6FE,3411
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  biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -56,7 +56,7 @@ biopipen/reports/scrna/ScFGSEA.svelte,sha256=Gqt-XjqsB3XgdR3XukvphwyMExZpScwqgEo
56
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  biopipen/reports/scrna/SeuratClusterStats.svelte,sha256=rTsoOCiVm7lEyBYgu2ZVcKNGi4g6PynYoOSx0DHdTHo,429
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  biopipen/reports/scrna/SeuratMap2Ref.svelte,sha256=1g-FEmvR2YMn0OF66qESNBWmGdHQY3u8QuG4M-T7Y4E,659
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  biopipen/reports/scrna/SeuratPreparing.svelte,sha256=CCQ3qodjfoQeMZhSZp7irvSqBt10m7urzcWEOHsZa8M,365
59
- biopipen/reports/scrna/TopExpressingGenes.svelte,sha256=h2Or2cKCzuY2cypq1PKrqiHFVMZmFUgFOXoQumvfGSk,471
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+ biopipen/reports/scrna/TopExpressingGenes.svelte,sha256=tt5_Vjym4coFT8Bvz0s6ZcCioTOIwCj83jdCGqPCmUw,491
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  biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=4M8V6jDv1_ZviTsRdoYNQixoTnKiD06oPHzVabUTq6k,978
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  biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.svelte,sha256=7FohWYR2BEqo77W4FuGsuwEEvG7j_Mc2ohXG8TSgODg,907
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  biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte,sha256=bbPWDEXTi-A377Vo2VaEyh_VoxGmFj-P3WX8g_y_-9k,3416
@@ -74,7 +74,7 @@ biopipen/reports/tcr/TCRClusterStats.svelte,sha256=YGK5_Vp85QmUJZO1ZGtg1IWBsh9o-
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  biopipen/reports/tcr/TESSA.svelte,sha256=S1tG0HIU5569ybV0shuTz1CN0JcqFrFNB7M6JCiGhm0,1948
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  biopipen/reports/tcr/VJUsage.svelte,sha256=c9G2-APGG0l-c6b32aFOimrP_QYD-oELBASN4VabXmk,426
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  biopipen/reports/utils/gsea.liq,sha256=5uxNPyIr0xd7nrZePJlIsRyqCPx1uVWso7ehE1F-C4k,3556
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- biopipen/reports/utils/misc.liq,sha256=HLK3mkWtIMQqBtM2IIRFUdKKTcY8cvBtyHJB9DbWBdw,1653
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+ biopipen/reports/utils/misc.liq,sha256=n46w7HeyU7PQdqckvpylH5RdI4p_tyqMtyZORkb4ghw,1860
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  biopipen/reports/vcf/TruvariBenchSummary.svelte,sha256=yew8HRN-YahBzX504Micah5BTnoL_PQzQfN_87TiuOA,577
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  biopipen/reports/vcf/TruvariConsistency.svelte,sha256=BBvtxi1EPmGH7j5M5zMOcLEhKWZOlKoXp1lrQGAmz_0,647
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  biopipen/scripts/bam/BamMerge.py,sha256=Gd5P8V-CSsTAA8ZrUxetR-I49GjJ3VJNjrqu7-EZwXQ,3642
@@ -111,7 +111,7 @@ biopipen/scripts/cnvkit/CNVkitScatter.py,sha256=7DhTiXPHEHbdXn0VFcDOR-wTP6sks08N
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  biopipen/scripts/cnvkit/CNVkitSegment.py,sha256=q5iGAjY6-yIehPcJpi3hX6EuGre0YgWTPkG_d5LEV48,1629
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  biopipen/scripts/cnvkit/guess_baits.py,sha256=7OCMtSMHIJWWZv9qEYVXnB0N4hU_JaGEesKdkr6tvJc,10586
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  biopipen/scripts/delim/RowsBinder.R,sha256=1QtRiPdUoxR8st1nxBMyVXgpcLfeF-iGsMYHz-66L2s,1465
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- biopipen/scripts/delim/SampleInfo.R,sha256=xnpOGHGOMZeD_Ay7PBN9GkqW34sVkTufMIhbxKTw3wU,6727
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+ biopipen/scripts/delim/SampleInfo.R,sha256=T9WrMV4w18JlqwoNO-tY9JV4dTAIyvBBCB34Wad1oWc,6988
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  biopipen/scripts/gene/GeneNameConversion.R,sha256=Jy2ykhCj9ClSdQUfdYavh2LaBm0nOIXY2kJKmpsqOlI,1818
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  biopipen/scripts/gene/GenePromoters.R,sha256=0ukq3-wpN6uq_cyJlQvKDVvy0Dv8cI5Htd9t2xpkEyk,2021
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  biopipen/scripts/gsea/Enrichr.R,sha256=gqN93oE3OeqW_TXZiE_gNH89_o_XFwnOWcHxhTUMvNs,724
@@ -150,42 +150,42 @@ biopipen/scripts/scrna/CellTypeAnnotation-hitype.R,sha256=zol-IF0jd3DTzw9I1UVUMY
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@@ -1,4 +1,4 @@
1
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  Wheel-Version: 1.0
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