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mdbarnesUCSDmdbarnesUCSD
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Merge pull request #67 from AlexandrovLab/development
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2 parents 94b847a + d51bd16 commit 29549ef

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+265
-363
lines changed

‎COSMIC_v3_SBS_GRCh37_noSBS84-85.txt‎

Lines changed: 0 additions & 97 deletions
This file was deleted.

‎README.md‎

Lines changed: 14 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -30,20 +30,20 @@ $ pip install .
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```
3131
## Signature Subgroups
3232
```python
33-
exclude_signature_subgroups = ['remove_MMR_deficiency_signatures',
34-
'remove_POL_deficiency_signatures',
35-
'remove_HR_deficiency_signatures' ,
36-
'remove_BER_deficiency_signatures',
37-
'remove_Chemotherapy_signatures',
38-
'remove_Immunosuppressants_signatures'
39-
'remove_Treatment_signatures'
40-
'remove_APOBEC_signatures',
41-
'remove_Tobacco_signatures',
42-
'remove_UV_signatures',
43-
'remove_AA_signatures',
44-
'remove_Colibactin_signatures',
45-
'remove_Artifact_signatures',
46-
'remove_Lymphoid_signatures']
33+
exclude_signature_subgroups = ['MMR_deficiency_signatures',
34+
'POL_deficiency_signatures',
35+
'HR_deficiency_signatures' ,
36+
'BER_deficiency_signatures',
37+
'Chemotherapy_signatures',
38+
'Immunosuppressants_signatures'
39+
'Treatment_signatures'
40+
'APOBEC_signatures',
41+
'Tobacco_signatures',
42+
'UV_signatures',
43+
'AA_signatures',
44+
'Colibactin_signatures',
45+
'Artifact_signatures',
46+
'Lymphoid_signatures']
4747
```
4848

4949

‎SigProfilerAssignment/DecompositionPlots/PlotDecomposition_CNV48.py‎

Lines changed: 39 additions & 39 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
1111
from reportlab.pdfbase.ttfonts import TTFont
1212
from reportlab.pdfbase import pdfmetrics
1313
import SigProfilerAssignment as spa_path
14-
from PyPDF2 import PdfFileWriter, PdfFileReader, PdfFileMerger
14+
from PyPDF2 import PdfWriter, PdfReader
1515
# imports for saving plots to memory
1616
import io
1717
from PIL import Image
@@ -230,59 +230,59 @@ def draw_bracket(num_bases, c_draw):
230230
# num_bases - (Integer) The number of signatures the sample is composed of
231231
def crop_margins(pdf_to_edit, num_bases):
232232
pdf_to_edit.seek(0)
233-
pdf_file = PdfFileReader(pdf_to_edit, "rb")
234-
page = pdf_file.getPage(0)
235-
writer = PdfFileWriter()
233+
pdf_file = PdfReader(pdf_to_edit, "rb")
234+
page = pdf_file.pages[0]
235+
writer = PdfWriter()
236236
output_plot_buff = io.BytesIO()
237237

238238
if (num_bases == 1):
239-
page.mediaBox.lowerRight = (935-WIDTH_GRAPH,155)
240-
page.mediaBox.lowerLeft = (0,155)
241-
page.mediaBox.upperRight = (935-WIDTH_GRAPH,640)
242-
page.mediaBox.upperLeft = (0,640)
243-
writer.addPage(page)
239+
page.mediabox.lower_right = (935-WIDTH_GRAPH,155)
240+
page.mediabox.lower_left = (0,155)
241+
page.mediabox.upper_right = (935-WIDTH_GRAPH,640)
242+
page.mediabox.upper_left = (0,640)
243+
writer.add_page(page)
244244
writer.write(output_plot_buff)
245245
elif (num_bases == 2):
246-
page.mediaBox.lowerRight = (935,155)
247-
page.mediaBox.lowerLeft = (0,155)
248-
page.mediaBox.upperRight = (935,640)
249-
page.mediaBox.upperLeft = (0,640)
250-
writer.addPage(page)
246+
page.mediabox.lower_right = (935,155)
247+
page.mediabox.lower_left = (0,155)
248+
page.mediabox.upper_right = (935,640)
249+
page.mediabox.upper_left = (0,640)
250+
writer.add_page(page)
251251
writer.write(output_plot_buff)
252252
elif (num_bases == 3):
253-
page.mediaBox.lowerRight = (935,155)
254-
page.mediaBox.lowerLeft = (0,155)
255-
page.mediaBox.upperRight = (935,640)
256-
page.mediaBox.upperLeft = (0,640)
257-
writer.addPage(page)
253+
page.mediabox.lower_right = (935,155)
254+
page.mediabox.lower_left = (0,155)
255+
page.mediabox.upper_right = (935,640)
256+
page.mediabox.upper_left = (0,640)
257+
writer.add_page(page)
258258
writer.write(output_plot_buff)
259259
elif (num_bases == 4):
260-
page.mediaBox.lowerRight = (935,155)
261-
page.mediaBox.lowerLeft = (0,155)
262-
page.mediaBox.upperRight = (935,640)
263-
page.mediaBox.upperLeft = (0,640)
264-
writer.addPage(page)
260+
page.mediabox.lower_right = (935,155)
261+
page.mediabox.lower_left = (0,155)
262+
page.mediabox.upper_right = (935,640)
263+
page.mediabox.upper_left = (0,640)
264+
writer.add_page(page)
265265
writer.write(output_plot_buff)
266266
elif (num_bases == 5):
267-
page.mediaBox.lowerRight = (935,75)
268-
page.mediaBox.lowerLeft = (0,75)
269-
page.mediaBox.upperRight = (935,745)
270-
page.mediaBox.upperLeft = (0,745)
271-
writer.addPage(page)
267+
page.mediabox.lower_right = (935,75)
268+
page.mediabox.lower_left = (0,75)
269+
page.mediabox.upper_right = (935,745)
270+
page.mediabox.upper_left = (0,745)
271+
writer.add_page(page)
272272
writer.write(output_plot_buff)
273273
elif (num_bases == 6):
274-
page.mediaBox.lowerRight = (935,75)
275-
page.mediaBox.lowerLeft = (0,75)
276-
page.mediaBox.upperRight = (935,745)
277-
page.mediaBox.upperLeft = (0,745)
278-
writer.addPage(page)
274+
page.mediabox.lower_right = (935,75)
275+
page.mediabox.lower_left = (0,75)
276+
page.mediabox.upper_right = (935,745)
277+
page.mediabox.upper_left = (0,745)
278+
writer.add_page(page)
279279
writer.write(output_plot_buff)
280280
elif (num_bases > 6):
281-
page.mediaBox.lowerRight = (935,35)
282-
page.mediaBox.lowerLeft = (0,35)
283-
page.mediaBox.upperRight = (935,745)
284-
page.mediaBox.upperLeft = (0,745)
285-
writer.addPage(page)
281+
page.mediabox.lower_right = (935,35)
282+
page.mediabox.lower_left = (0,35)
283+
page.mediabox.upper_right = (935,745)
284+
page.mediabox.upper_left = (0,745)
285+
writer.add_page(page)
286286
writer.write(output_plot_buff)
287287
return output_plot_buff
288288

‎SigProfilerAssignment/DecompositionPlots/PlotDecomposition_DBS78.py‎

Lines changed: 34 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
1111
from reportlab.pdfbase.ttfonts import TTFont
1212
from reportlab.pdfbase import pdfmetrics
1313
import SigProfilerAssignment as spa_path
14-
from PyPDF2 import PdfFileWriter, PdfFileReader, PdfFileMerger
14+
from PyPDF2 import PdfWriter, PdfReader
1515
# imports for saving plots to memory
1616
import io
1717
from PIL import Image
@@ -203,52 +203,52 @@ def draw_bracket(num_bases, c_draw):
203203

204204
def crop_margins(pdf_to_edit, num_bases):
205205
pdf_to_edit.seek(0)
206-
pdf_file = PdfFileReader(pdf_to_edit, "rb")
207-
page = pdf_file.getPage(0)
208-
writer = PdfFileWriter()
206+
pdf_file = PdfReader(pdf_to_edit, "rb")
207+
page = pdf_file.pages[0]
208+
writer = PdfWriter()
209209
output_plot_buff = io.BytesIO()
210210

211211
if (num_bases == 1):
212-
page.mediaBox.lowerRight = (792,155)
213-
page.mediaBox.lowerLeft = (0,155)
214-
page.mediaBox.upperRight = (792,402)
215-
page.mediaBox.upperLeft = (0,402)
216-
writer.addPage(page)
212+
page.mediabox.lower_right = (792,155)
213+
page.mediabox.lower_left = (0,155)
214+
page.mediabox.upper_right = (792,402)
215+
page.mediabox.upper_left = (0,402)
216+
writer.add_page(page)
217217
writer.write(output_plot_buff)
218218
elif (num_bases == 2):
219-
page.mediaBox.lowerRight = (792,155)
220-
page.mediaBox.lowerLeft = (0,155)
221-
page.mediaBox.upperRight = (792,422)
222-
page.mediaBox.upperLeft = (0,422)
223-
writer.addPage(page)
219+
page.mediabox.lower_right = (792,155)
220+
page.mediabox.lower_left = (0,155)
221+
page.mediabox.upper_right = (792,422)
222+
page.mediabox.upper_left = (0,422)
223+
writer.add_page(page)
224224
writer.write(output_plot_buff)
225225
elif (num_bases == 3):
226-
page.mediaBox.lowerRight = (792,150)
227-
page.mediaBox.lowerLeft = (0,150)
228-
page.mediaBox.upperRight = (792,462)
229-
page.mediaBox.upperLeft = (0,462)
230-
writer.addPage(page)
226+
page.mediabox.lower_right = (792,150)
227+
page.mediabox.lower_left = (0,150)
228+
page.mediabox.upper_right = (792,462)
229+
page.mediabox.upper_left = (0,462)
230+
writer.add_page(page)
231231
writer.write(output_plot_buff)
232232
elif (num_bases == 4):
233-
page.mediaBox.lowerRight = (792,112)
234-
page.mediaBox.lowerLeft = (0,112)
235-
page.mediaBox.upperRight = (792,498)
236-
page.mediaBox.upperLeft = (0,498)
237-
writer.addPage(page)
233+
page.mediabox.lower_right = (792,112)
234+
page.mediabox.lower_left = (0,112)
235+
page.mediabox.upper_right = (792,498)
236+
page.mediabox.upper_left = (0,498)
237+
writer.add_page(page)
238238
writer.write(output_plot_buff)
239239
elif (num_bases == 5):
240-
page.mediaBox.lowerRight = (792,75)
241-
page.mediaBox.lowerLeft = (0,75)
242-
page.mediaBox.upperRight = (792,537)
243-
page.mediaBox.upperLeft = (0,537)
244-
writer.addPage(page)
240+
page.mediabox.lower_right = (792,75)
241+
page.mediabox.lower_left = (0,75)
242+
page.mediabox.upper_right = (792,537)
243+
page.mediabox.upper_left = (0,537)
244+
writer.add_page(page)
245245
writer.write(output_plot_buff)
246246
elif (num_bases > 5):
247-
page.mediaBox.lowerRight = (792,50)
248-
page.mediaBox.lowerLeft = (0,50)
249-
page.mediaBox.upperRight = (792,537)
250-
page.mediaBox.upperLeft = (0,537)
251-
writer.addPage(page)
247+
page.mediabox.lower_right = (792,50)
248+
page.mediabox.lower_left = (0,50)
249+
page.mediabox.upper_right = (792,537)
250+
page.mediabox.upper_left = (0,537)
251+
writer.add_page(page)
252252
writer.write(output_plot_buff)
253253
return output_plot_buff
254254

‎SigProfilerAssignment/DecompositionPlots/PlotDecomposition_ID83.py‎

Lines changed: 34 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
1111
from reportlab.pdfbase.ttfonts import TTFont
1212
from reportlab.pdfbase import pdfmetrics
1313
import SigProfilerAssignment as spa_path
14-
from PyPDF2 import PdfFileWriter, PdfFileReader, PdfFileMerger
14+
from PyPDF2 import PdfWriter, PdfReader
1515
# imports for saving plots to memory
1616
import io
1717
from PIL import Image
@@ -210,52 +210,52 @@ def draw_bracket(num_bases, c_draw):
210210
# num_bases - (Integer) The number of signatures the sample is composed of
211211
def crop_margins(pdf_to_edit, num_bases):
212212
pdf_to_edit.seek(0)
213-
pdf_file = PdfFileReader(pdf_to_edit, "rb")
214-
page = pdf_file.getPage(0)
215-
writer = PdfFileWriter()
213+
pdf_file = PdfReader(pdf_to_edit, "rb")
214+
page = pdf_file.pages[0]
215+
writer = PdfWriter()
216216
output_plot_buff = io.BytesIO()
217217

218218
if (num_bases == 1):
219-
page.mediaBox.lowerRight = (792,150)
220-
page.mediaBox.lowerLeft = (0,150)
221-
page.mediaBox.upperRight = (792,407)
222-
page.mediaBox.upperLeft = (0,407)
223-
writer.addPage(page)
219+
page.mediabox.lower_right = (792,150)
220+
page.mediabox.lower_left = (0,150)
221+
page.mediabox.upper_right = (792,407)
222+
page.mediabox.upper_left = (0,407)
223+
writer.add_page(page)
224224
writer.write(output_plot_buff)
225225
elif (num_bases == 2):
226-
page.mediaBox.lowerRight = (792,150)
227-
page.mediaBox.lowerLeft = (0,150)
228-
page.mediaBox.upperRight = (792,422)
229-
page.mediaBox.upperLeft = (0,422)
230-
writer.addPage(page)
226+
page.mediabox.lower_right = (792,150)
227+
page.mediabox.lower_left = (0,150)
228+
page.mediabox.upper_right = (792,422)
229+
page.mediabox.upper_left = (0,422)
230+
writer.add_page(page)
231231
writer.write(output_plot_buff)
232232
elif (num_bases == 3):
233-
page.mediaBox.lowerRight = (792,150)
234-
page.mediaBox.lowerLeft = (0,150)
235-
page.mediaBox.upperRight = (792,460)
236-
page.mediaBox.upperLeft = (0,460)
237-
writer.addPage(page)
233+
page.mediabox.lower_right = (792,150)
234+
page.mediabox.lower_left = (0,150)
235+
page.mediabox.upper_right = (792,460)
236+
page.mediabox.upper_left = (0,460)
237+
writer.add_page(page)
238238
writer.write(output_plot_buff)
239239
elif (num_bases == 4):
240-
page.mediaBox.lowerRight = (792,105)
241-
page.mediaBox.lowerLeft = (0,105)
242-
page.mediaBox.upperRight = (792,505)
243-
page.mediaBox.upperLeft = (0,505)
244-
writer.addPage(page)
240+
page.mediabox.lower_right = (792,105)
241+
page.mediabox.lower_left = (0,105)
242+
page.mediabox.upper_right = (792,505)
243+
page.mediabox.upper_left = (0,505)
244+
writer.add_page(page)
245245
writer.write(output_plot_buff)
246246
elif (num_bases == 5):
247-
page.mediaBox.lowerRight = (792,55)
248-
page.mediaBox.lowerLeft = (0,55)
249-
page.mediaBox.upperRight = (792,555)
250-
page.mediaBox.upperLeft = (0,555)
251-
writer.addPage(page)
247+
page.mediabox.lower_right = (792,55)
248+
page.mediabox.lower_left = (0,55)
249+
page.mediabox.upper_right = (792,555)
250+
page.mediabox.upper_left = (0,555)
251+
writer.add_page(page)
252252
writer.write(output_plot_buff)
253253
elif (num_bases > 5):
254-
page.mediaBox.lowerRight = (792,35)
255-
page.mediaBox.lowerLeft = (0,35)
256-
page.mediaBox.upperRight = (792,555)
257-
page.mediaBox.upperLeft = (0,555)
258-
writer.addPage(page)
254+
page.mediabox.lower_right = (792,35)
255+
page.mediabox.lower_left = (0,35)
256+
page.mediabox.upper_right = (792,555)
257+
page.mediabox.upper_left = (0,555)
258+
writer.add_page(page)
259259
writer.write(output_plot_buff)
260260
return output_plot_buff
261261

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