Mercurial > repos > jjjjia > cpo_prediction

comparison cpo_galaxy_tree.py @ 8:93c25036d3b9 draft

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planemo upload
author jjjjia
date Thu, 23 Aug 2018 19:40:12 -0400
parents 4d2777aa99db
children b7e9a3be2b11
comparison
equal deleted inserted replaced
7:4d2777aa99db 8:93c25036d3b9
15 15
16 # <requirements> 16 # <requirements>
17 # <requirement type="package" version="0.23.4">pandas</requirement> 17 # <requirement type="package" version="0.23.4">pandas</requirement>
18 # <requirement type="package" version="3.6">python</requirement> 18 # <requirement type="package" version="3.6">python</requirement>
19 # <requirement type="package" version="3.1.1">ete3</requirement> 19 # <requirement type="package" version="3.1.1">ete3</requirement>
20 # <requirement type="package" version="5.9.3">pyqt</requirement> 20 # <requirement type="package" version="5.6.0">pyqt</requirement>
21 # </requirements> 21 # </requirements>
22 22
23 import subprocess 23 import subprocess
24 import pandas #conda pandas 24 import pandas #conda pandas
25 import optparse 25 import optparse
26 import os 26 import os
27 os.environ['QT_QPA_PLATFORM']='offscreen'
27 import datetime 28 import datetime
28 import sys 29 import sys
29 import time 30 import time
30 import urllib.request 31 import urllib.request
31 import gzip 32 import gzip
165 166
166 distanceDict = {} #store the distance matrix as rowname:list<string> 167 distanceDict = {} #store the distance matrix as rowname:list<string>
167 for i in range(len(distance)): 168 for i in range(len(distance)):
168 temp = distance[i].split("\t") 169 temp = distance[i].split("\t")
169 distanceDict[temp[0]] = temp[1:] 170 distanceDict[temp[0]] = temp[1:]
170 #region step5: tree construction 171
171
172 '''
173 #region create detailed tree
174
175 plasmidCount = 0
176 for n in t.traverse():
177 if (n.is_leaf() and not n.name == "Reference"):
178 mData = metadata[n.name.replace(".fa","")]
179 face = faces.TextFace(mData.MLSTSpecies,fsize=10,tight_text=True)
180 face.border.margin = 5
181 face.margin_left = 10
182 face.margin_right = 10
183 n.add_face(face, 0, "aligned")
184 face = faces.TextFace(mData.SequenceType,fsize=10,tight_text=True)
185 face.border.margin = 5
186 face.margin_right = 10
187 n.add_face(face, 1, "aligned")
188 face = faces.TextFace(mData.CarbapenemResistanceGenes,fsize=10,tight_text=True)
189 face.border.margin = 5
190 face.margin_right = 10
191 n.add_face(face, 2, "aligned")
192 index = 3
193 if (mData.TotalPlasmids > plasmidCount):
194 plasmidCount = mData.TotalPlasmids
195 for i in range(0, mData.TotalPlasmids):
196 face = faces.TextFace(mData.plasmids[i].PlasmidRepType,fsize=10,tight_text=True)
197 face.border.margin = 5
198 face.margin_right = 10
199 n.add_face(face, index, "aligned")
200 index+=1
201 face = faces.TextFace(mData.plasmids[i].PlasmidMobility,fsize=10,tight_text=True)
202 face.border.margin = 5
203 face.margin_right = 10
204 n.add_face(face, index, "aligned")
205 index+=1
206
207 face = faces.TextFace("Species",fsize=10,tight_text=True)
208 face.border.margin = 5
209 face.margin_right = 10
210 face.margin_left = 10
211 (t&"Reference").add_face(face, 0, "aligned")
212 face = faces.TextFace("Sequence Type",fsize=10,tight_text=True)
213 face.border.margin = 5
214 face.margin_right = 10
215 (t&"Reference").add_face(face, 1, "aligned")
216 face = faces.TextFace("Carbapenamases",fsize=10,tight_text=True)
217 face.border.margin = 5
218 face.margin_right = 10
219 (t&"Reference").add_face(face, 2, "aligned")
220 index = 3
221 for i in range(0, plasmidCount):
222 face = faces.TextFace("plasmid " + str(i) + " replicons",fsize=10,tight_text=True)
223 face.border.margin = 5
224 face.margin_right = 10
225 (t&"Reference").add_face(face, index, "aligned")
226 index+=1
227 face = faces.TextFace("plasmid " + str(i) + " mobility",fsize=10,tight_text=True)
228 face.border.margin = 5
229 face.margin_right = 10
230 (t&"Reference").add_face(face, index, "aligned")
231 index+=1
232
233 t.render("./pipelineTest/tree.png", w=5000,units="mm", tree_style=ts)
234
235 #endregion
236 '''
237 #region create box tree 172 #region create box tree
238 #region step5: tree construction 173 #region step5: tree construction
239 treeFile = "".join(read(treePath)) 174 treeFile = "".join(read(treePath))
240 t = e.Tree(treeFile) 175 t = e.Tree(treeFile)
241 t.set_outgroup(t&"Reference") 176 t.set_outgroup(t&"Reference")
322 n.add_face(addFace(mData.CarbapenemResistanceGenes), index, "aligned") 257 n.add_face(addFace(mData.CarbapenemResistanceGenes), index, "aligned")
323 index = index + 1 258 index = index + 1
324 for i in range(len(distanceDict[list(distanceDict.keys())[0]])): #this loop adds distance matrix 259 for i in range(len(distanceDict[list(distanceDict.keys())[0]])): #this loop adds distance matrix
325 n.add_face(addFace(list(distanceDict[n.name])[i]), index + i, "aligned") 260 n.add_face(addFace(list(distanceDict[n.name])[i]), index + i, "aligned")
326 261
327 t.render("./tree.png", w=5000,units="mm", tree_style=ts) #save it as a png. or an phyloxml 262 t.render("./tree.pdf", w=5000,units="mm", tree_style=ts) #save it as a png. or an phyloxml
328 263
329 #endregion 264 #endregion
330 #endregion 265 #endregion
331 266
332 267