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author johnheap
date Mon, 03 Jun 2019 15:58:48 -0400
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15:597fe882966e 16:c4e87b277576
1 1 """
2 2 * Copyright 2018 University of Liverpool
3 3 * Author: John Heap, Computational Biology Facility, UoL
4 4 * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL
5 5 *
6 6 * Licensed under the Apache License, Version 2.0 (the "License");
7 <!DOCTYPE html> 7 * you may not use this file except in compliance with the License.
8 <html lang="en"> 8 * You may obtain a copy of the License at
9 <head> 9 *
10 <meta charset="utf-8"> 10 * http://www.apache.org/licenses/LICENSE-2.0
11 <link rel="dns-prefetch" href="https://github.githubassets.com"> 11 *
12 <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com"> 12 * Unless required by applicable law or agreed to in writing, software
13 <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com"> 13 * distributed under the License is distributed on an "AS IS" BASIS,
14 <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com"> 14 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15 <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com"> 15 * See the License for the specific language governing permissions and
16 <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com"> 16 * limitations under the License.
17 <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/"> 17 *
18 18 """
19 19
20 20 import subprocess
21 <link crossorigin="anonymous" media="all" integrity="sha512-3+HOqCwtQal5hOJQ+mdxiq5zmGOTjF6RhjDsPLxbKDYgGlLFeCwzoIanb7j5IiCuXKUqyC2q8FdkC4nmx2P2rA==" rel="stylesheet" href="https://github.githubassets.com/assets/frameworks-a2fba223d5af91496cac70d4ec3624df.css" /> 21 import re
22 <link crossorigin="anonymous" media="all" integrity="sha512-MRlTIqIyb8caK5+o8llXVntXovciHyAM4qE3kWU2S7SIjAPDxYp4mE0jQp4kP5UYegy+lG9y1I6VlsdzEjb5Qw==" rel="stylesheet" href="https://github.githubassets.com/assets/site-294181adec18ed639e160b96b45d17ac.css" /> 22 import os
23 <link crossorigin="anonymous" media="all" integrity="sha512-XjvAy/mMWN5aOA+pyb/FgAgcVgJkPkwTCwvFK07Ez/H44lvl55ZLGwtpyL4MaMrwDE8QYO+1VYljKFjqr4/iJA==" rel="stylesheet" href="https://github.githubassets.com/assets/github-5b066aa36cc405c9cbcbadf1bde399ed.css" /> 23 import sys
24 import shutil
25 import pandas as pd
26 import numpy as np
27 import matplotlib as mpl
28 mpl.use('Agg')
29 import matplotlib.pyplot as plt
30 from matplotlib.mlab import PCA
31 import seaborn as sns
32
33 # some globals for convenience
34
35 pList = ['P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7', 'P8', 'P9', 'P10', 'P11', 'P12', 'P13', 'P14', 'P15']
36
37 quietString = "" #" >>"+os.path.dirname(os.path.realpath(__file__))+"/log/Vap_log.txt 2>&1"
38
39 def assembleWithVelvet(name, kmers, inslen, covcut, fastq1name,fastq2name):
40 #argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq"
41 argString = "velveth " + name + "_k"+ kmers+" "+ kmers + " -shortPaired -fastq " + fastq1name+" "+fastq2name+quietString
42 print(argString)
43 returncode = subprocess.call(argString, shell=True)
44 if returncode != 0:
45 return "Error in velveth"
46 argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -cov_cutoff "+covcut+" -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString
47 #argString = "velvetg " + name + "_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString
48 print(argString)
49 returncode = subprocess.call(argString, shell = True)
50 if returncode != 0:
51 return "Error in velvetg"
52 shutil.copyfile(name + "_k"+kmers+"//contigs.fa",name + ".fa") # my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa";
53 return "ok"
54
55 def contigTranslation(name):
56 argString = "transeq " + name + ".fa " + name + "_6frame.fas -frame=6 " #+quietString
57 print(argString)
58 returncode = subprocess.call(argString, shell=True)
59
60
61 def HMMerMotifSearch(name):
62 motifs = ['1', '2a', '2b', '3', '4a', '4b', '4c', '5', '6', '7', '8a', '8b', '9a', '9b',
63 '9c', '10a', '10b', '11a', '11b', '12', '13a', '13b', '13c', '13d', '14', '15a', '15b', '15c']
64 lineCounts = []
65 compoundList = []
66 dir_path = os.path.dirname(os.path.realpath(__file__))
67 phylopath = dir_path + "/data/Motifs/Phylotype"
68 for m in motifs:
69 argString = "hmmsearch " + phylopath + m + ".hmm " + name + "_6frame.fas > Phy" + m + ".out" # +quietString
70 # argString = "hmmsearch "+phylopath + m + ".hmm " + dir_path+"/data/Test_6frame.fas > Phy" + m + ".out"
71 #print(argString)
72 subprocess.call(argString, shell=True)
73
74 hmmResult = open("Phy" + m + ".out", 'r')
75 tempout = open(dir_path + "/data/" + "Phy" + m + ".txt", 'w')
76 #regex = r"NODE_[0-9]{1,7}_length_[0-9]{1,7}_cov_[0-9]{1,10}.[0-9]{1,7}_[0-9]{1,2}"
77 n = 0
78 outList = []
79 for l in range(0,14):
80 hmmResult.readline() #hacky? miss out the first 14 lines. data we want starts on line 15
81
82
83 for line in hmmResult:
84 if re.search(r"inclusion", line):
85 #print("inclusion threshold reached")
86 break
87 if len(line) <= 1:
88 #print("end of data")
89 break
90 m = line[60:-1]
91 #print(m)
92 #tempout.write(m.group() + "\n")
93 outList.append("" + m + "\n")
94 n += 1
95 compoundList.append(outList)
96 lineCounts.append(n)
97 hmmResult.close()
98
99
100 print(lineCounts)
101 motifGroups = [['1'], ['2a', '2b'], ['3'], ['4a', '4b', '4c'], ['5'], ['6'], ['7'], ['8a', '8b'], ['9a', '9b',
102 '9c'],
103 ['10a', '10b'], ['11a', '11b'], ['12'], ['13a', '13b', '13c', '13d'], ['14'], ['15a', '15b', '15c']]
104 concatGroups = [1, 2, 1, 3, 1, 1, 1, 2, 3, 2, 2, 1, 4, 1, 3]
105 countList = []
106 countIndex = 0
107 totalCount = 0
108
109 for c in concatGroups:
110 a = []
111 for n in range(0, c):
112 a = a + compoundList.pop(0)
113 t = set(a)
114 countList.append(len(t))
115 totalCount += len(t)
116 countList.append(totalCount)
117 #print(countList)
118 #print("--------")
119 return countList
120
121
122
123 def relativeFrequencyTable(countList, name, htmlresource):
124 relFreqList = []
125 c = float(countList[15])
126 if c == 0:
127 return [0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0]
128 for i in range(0, 15):
129 relFreqList.append(countList[i] / c)
130
131 data = {'Phylotype': pList, 'Relative Frequency': relFreqList}
132 relFreq_df = pd.DataFrame(data)
133 j_fname = htmlresource+"/" + name + "_relative_frequency.csv"
134 relFreq_df.to_csv(j_fname)
135 return relFreqList # 0-14 = p1-p15 counts [15] = total counts
136
137
138
139
140 def getDeviationFromMean(frequencyList, name, htmlresource):
141 devList = []
142 dir_path = os.path.dirname(os.path.realpath(__file__))
143 j_fname = dir_path + "/data/congodata.csv"
144 #j_fname = r"data/congodata.csv"
145 congo_df = pd.read_csv(j_fname) # we get the means from congo_df
146 for p in range(0, 15):
147 m = congo_df[pList[p]].mean()
148 dev = -(m - frequencyList[p])
149 devList.append(dev)
150
151 data = {'Phylotype': pList, 'Deviation from Mean': devList}
152 dev_df = pd.DataFrame(data)
153 j_fname = htmlresource+"/" + name + "_deviation_from_mean.csv"
154 dev_df.to_csv(j_fname)
155 return devList
156
157
158 def relativeFrequencyHeatMap(name, freqList, pdf, htmlresource):
159 localFreqList = freqList[:]
160 localFreqList.insert(0, name)
161 dir_path = os.path.dirname(os.path.realpath(__file__))
162 j_fname = dir_path+"/data/congodata.csv"
163 #print(dir_path)
164 congo_df = pd.read_csv(j_fname)
165 congo_df.drop('Colour', axis=1, inplace=True)
166 congo_df.loc[congo_df.index.max() + 1] = localFreqList
167 ysize = len(congo_df) * 20 / 97.0 # make vertical size equivlanet 20' is ok for 97.
168
169 congo_df.set_index('Strain', inplace=True)
170
171 cg = sns.clustermap(congo_df, method='ward', cmap = "RdBu_r", col_cluster=False, yticklabels = congo_df.index.values,figsize = (10,ysize))
172 plt.setp(cg.ax_heatmap.yaxis.get_ticklabels(), rotation=0, fontsize=8) # get y labels printed horizontally
173 ax=cg.ax_heatmap
174 title = "Variant Antigen Profiles of $\itTrypanosoma$ $\itcongolense$ estimated as the phylotype proportion across the\nsample cohort. "
175 title += "Dendrogram reflects the relationships amongst the VSG repertoires of each strain. "
176 title += "Strains\nwere isolated from multiple African countries as described in Silva Pereira et al. (2018)."
177 title += "\nData was produced with the 'Variant Antigen Profiler' (Silva Pereira et al., 2019)."
178
179 #title = "Variant Antigen Profiles of Trypanosoma congolense estimated as the phylotype proportion across the sample cohort. Dendrogram reflects the relationships amongst the VSG repertoires of each strain. Strains were isolated from multiple African countries as described in Silva Pereira et al. (2018). Data was produced with the 'Variant Antigen Profiler' (Silva Pereira and Jackson, 2018)."
180 #ax.set_title(title, ha = "center", va = "bottom",wrap = "True")
181 #title = "Where is this!"
182 ax.text(-0.15,-0.05, title,va = "top",wrap = "True", transform = ax.transAxes )
183
184
185
186
187 # cg.dendrogram_col.linkage # linkage matrix for columns
188 # cg.dendrogram_row.linkage # linkage matrix for rows
189 #plt.savefig(r"results/" + name + "_heatmap.png")
190 plt.savefig(htmlresource+"/heatmap.png",bbox_inches='tight')
191 if pdf == 'PDF_Yes':
192 plt.savefig(htmlresource+"/heatmap.pdf", bbox_inches='tight')
193 #shutil.copyfile("heatmap.pdf",heatmapfn) #
194 #plt.show()
195
196 def deviationFromMeanHeatMap(name,devList, pdf, htmlresource):
197 localDevList = devList[:]
198 localDevList.insert(0, name)
199 dir_path = os.path.dirname(os.path.realpath(__file__))
200 j_fname = dir_path+ "/data/congodata_deviationfromthemean.csv"
201 #j_fname = r"data/congodata_deviationfromthemean.csv"
202 congo_df = pd.read_csv(j_fname)
203 congo_df.drop('Colour', axis=1, inplace=True)
204 congo_df.loc[congo_df.index.max() + 1] = localDevList
205 ysize = len(congo_df) * 20 / 97.0 # make vertical size equivlanet 20' is ok for 97.
206 congo_df.set_index('Strain', inplace=True)
207 cg = sns.clustermap(congo_df, method='ward',cmap = "RdBu_r", col_cluster=False, yticklabels = congo_df.index.values,figsize = (10,ysize))
208 plt.setp(cg.ax_heatmap.yaxis.get_majorticklabels(), rotation=0, fontsize=8) # get y labels printed horizontally
209 ax = cg.ax_heatmap
210 title = "Variant Antigen Profiles of $\itTrypanosoma$ $\itcongolense$ expressed as the deviation from the mean phylotypes "
211 title +="\nproportions of the sample cohort. Dendrogram reflects the relationships amongst the VSG repertoires of "
212 title +="each \nstrain. Strains were isolated from multiple African countries as described in Silva Pereira et al. (2018)."
213 title +="\nData was produced with the 'Variant Antigen Profiler' (Silva Pereira et al., 2019)."
214 #ax.set_title(title,ha = "center", va = "bottom",wrap = "True")
215 ax.text(-0.2, -0.05, title, va="top", transform=ax.transAxes, wrap="True")
216 plt.savefig(htmlresource+"/dheatmap.png",bbox_inches='tight')
217 if pdf == 'PDF_Yes':
218 plt.savefig(htmlresource+"/dheatmap.pdf", bbox_inches='tight')
219 #shutil.copyfile("dheatmap.pdf",dhmapfn)
220 #plt.show()
221
222
223 def plotPCA(name, freqList, pdf, htmlresource):
224 localFreqList = freqList[:]
225 localFreqList.insert(0, name)
226 localFreqList.append(name)
227 dir_path = os.path.dirname(os.path.realpath(__file__))
228 j_fname = dir_path + "/data/congodata.csv"
229 #j_fname = r"data/congodata.csv"
230 congo_df = pd.read_csv(j_fname)
231 congo_df.loc[congo_df.index.max() + 1] = localFreqList
232 # print(congo_df.tail(2))
233 myColours = congo_df['Colour']
234 myCountries = congo_df.drop_duplicates('Colour')['Colour'].tolist()
235 # print(myCountries)
236 congo_df.drop('Colour', axis=1, inplace=True)
237 congo_df.set_index('Strain', inplace=True)
238 dataArray = congo_df.as_matrix()
239 pcaResult = PCA(dataArray)
240 # pcaResult.center(0)
241 # can't seem to find a simple way of prooducing a decent legend.
242 # going to seperate items in to different countires.
243 compoundList = []
244 for i in myCountries:
245 compoundList.append([])
246
247 i = 0
248 for item in pcaResult.Y:
249 col = myCountries.index(myColours[i])
250 compoundList[col].append(-item[0])
251 compoundList[col].append(item[1])
252 i = i + 1
253 colormap = plt.cm.tab20 # nipy_spectral, Set1,Paired
254 cols = [colormap(i) for i in np.linspace(0, 1, 20)]
255 fig, ax = plt.subplots(figsize=(9, 6))
256 #plt.figure(num=1,figsize=(12, 6))
257 i = 0
258 for d in myCountries:
259 a = compoundList[i]
260 b = a[::2]
261 c = a[1::2]
262 ax.scatter(b, c, color=cols[i], label=myCountries[i])
263 i = i + 1
264 leg = ax.legend( bbox_to_anchor=(1.02,1.02), loc = "upper left") #move legend out of plot
265 title = "Principal Component Analysis of the Variant Antigen Profiles of $\itTrypanosoma$ $\itcongolense$. " \
266 "The plot reflects the\nrelationships amongst the VSG repertoires of each strain. Strains are color-coded " \
267 "by location of collection according\nto key. Strains were isolated from multiple African countries as described in Silva Pereira et al. (2018)."
268 title +="\nData was produced with the 'Variant Antigen Profiler' (Silva Pereira et al., 2019)."
269 #plt.title(title, ha = "center", va = "bottom",wrap = "True")
270 tx = ax.text(-0.1, -0.07, title, va="top", transform=ax.transAxes, wrap="True")
271 #fig.add_axes([0,0.05,1.05,1.05])
272 #fig.tight_layout(rect=[0, 0.03, 1, 0.95])
273 fig.subplots_adjust(bottom = 0.3)
274
275 fig.savefig(htmlresource+"/vapPCA.png", bbox_extra_artists=(leg,tx), bbox_inches='tight')
276 #fig.savefig(htmlresource+"/vapPCA.png", bbox_extra_artists=(leg,))
277 if pdf == 'PDF_Yes':
278 fig.savefig(htmlresource+"/vapPCA.pdf",bbox_extra_artists=(leg,tx), bbox_inches='tight')
279 #shutil.copyfile("vapPCA.pdf",PCAfn) # my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa";
280 #plt.show()
281
282 def createHTML(name,htmlfn,freqList,devList):
283 #assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource
284 htmlString = r"<html><title>T.congolense VAP</title><body><div style='text-align:center'><h2><i>Trypanosoma congolense</i> Variant Antigen Profile</h2><h3>"
285 htmlString += name
286 htmlString += r"<br/>Genomic Analysis</h3>"
287 htmlString += "<p style = 'margin-left:23%; margin-right:23%'>Table Legend: Variant Antigen Profiles of <i>Trypanosoma congolense</i> estimated as the phylotype proportion and as the deviation from the mean across the sample cohort.<br>" \
288 "Data was produced with the 'Variant Antigen Profiler' (Silva Pereira et al., 2019).</p>"
289 htmlString += r"<style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style>"
290
291 htmlString += r"<table style='width:50%;margin-left:25%;text-align:center'><tr><th>Phylotype</th><th>Relative Frequency</th><th>Deviation from Mean</th></tr>"
292 tabString = ""
293 # flush out table with correct values
294 for i in range(0, 15):
295 f= format(freqList[i],'.4f')
296 d= format(devList[i],'.4f')
297 tabString += "<tr><td>phy" + str(i + 1) + "</td><td>" + f + "</td><td>" + d + "</td></tr>"
298 #tabString += "<tr><td>phy" + str(i + 1) + "</td><td>" + str(freqList[i]) + "</td><td>" + str(devList[i]) + "</td></tr>"
299 htmlString += tabString + "</table><br><br><br><br><br>"
300
301 htmlString += r"<h3>The Variation Heat Map and Dendrogram</h3><p>The absolute phylotype variation in the sample compared to model dataset.</p>"
302 imgString = r"<img src = 'heatmap.png' alt='Variation Heatmap' style='max-width:100%'><br><br>"
303 htmlString += imgString
304
305 htmlString += r"<br><br><br><br><h3>The Deviation Heat Map and Dendrogram</h3><p>The phylotype variation expressed as the deviation from your sample mean compared to the model dataset</p>"
306 imgString = r"<img src = 'dheatmap.png' alt='Deviation Heatmap' style='max-width:100%'><br><br>"
307 htmlString += imgString
308
309 htmlString += r"<br><br><br><br><h3>The Variation PCA plot</h3><p>PCA analysis corresponding to absolute variation. Colour coded according to location</p>"
310 imgString = r"<img src = 'vapPCA.png' alt='PCA Analysis' style='max-width:100%'><br><br>"
311 htmlString += imgString + r"</div></body></html>"
312
313 with open(htmlfn, "w") as htmlfile:
314 htmlfile.write(htmlString)
315
316
317 def assemble(args,dict):
318 #argdict = {'name': 2, 'pdfexport': 3, 'kmers': 4, 'inslen': 5, 'covcut': 6, 'forward': 7, 'reverse': 8, 'html_file': 9,'html_resource': 10}
319 assembleWithVelvet(args[dict['name']],args[dict['kmers']], args[dict['inslen']],args[dict['covcut']], args[dict['forward']],args[dict['reverse']])
320 contigTranslation(args[dict['name']])
321 myCountList = HMMerMotifSearch(args[dict['name']])
322 myFreqList = relativeFrequencyTable(myCountList, args[dict['name']],args[dict['html_resource']]) # saves out inputname_relative_frequncy.csv
323 # myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,
324 # 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,
325 # 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,
326 # 0.0372233400402414, 0.17102615694165]
327
328
329 myDevList = getDeviationFromMean(myFreqList, args[dict['name']], args[dict['html_resource']]) # saves out inputname_deviation_from_mean.csv
330 relativeFrequencyHeatMap(args[dict['name']], myFreqList,args[dict['pdfexport']], args[dict['html_resource']])
331 deviationFromMeanHeatMap(args[dict['name']], myDevList,args[dict['pdfexport']], args[dict['html_resource']])
332 plotPCA(args[dict['name']], myFreqList,args[dict['pdfexport']], args[dict['html_resource']])
333 createHTML(args[dict['name']], args[dict['html_file']], myFreqList, myDevList) # assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource
334
335 def contigs(args,dict):
336 #argdict = {'name': 2, 'pdfexport': 3, 'contigs': 4, 'html_file': 5, 'html_resource': 6}
337
338 shutil.copyfile(args[dict['contigs']], args[dict['name']]+".fa")
339
24 340
25 341
26 342 contigTranslation(args[dict['name']])
27 343 myCountList = HMMerMotifSearch(args[dict['name']])
28 344 myFreqList = relativeFrequencyTable(myCountList, args[dict['name']],
29 <meta name="viewport" content="width=device-width"> 345 args[dict['html_resource']]) # saves out inputname_relative_frequncy.csv
30 346 # myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,
31 <title>VAPPER-Galaxy/Tryp_G.py at master · johnheap/VAPPER-Galaxy · GitHub</title> 347 # 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,
32 <meta name="description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub."> 348 # 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,
33 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> 349 # 0.0372233400402414, 0.17102615694165]
34 <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> 350
35 <meta property="fb:app_id" content="1401488693436528"> 351
36 352 myDevList = getDeviationFromMean(myFreqList, args[dict['name']],
37 <meta name="twitter:image:src" content="https://avatars0.githubusercontent.com/u/24318980?s=400&amp;v=4" /><meta name="twitter:site" content="@github" /><meta name="twitter:card" content="summary" /><meta name="twitter:title" content="johnheap/VAPPER-Galaxy" /><meta name="twitter:description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub." /> 353 args[dict['html_resource']]) # saves out inputname_deviation_from_mean.csv
38 <meta property="og:image" content="https://avatars0.githubusercontent.com/u/24318980?s=400&amp;v=4" /><meta property="og:site_name" content="GitHub" /><meta property="og:type" content="object" /><meta property="og:title" content="johnheap/VAPPER-Galaxy" /><meta property="og:url" content="https://github.com/johnheap/VAPPER-Galaxy" /><meta property="og:description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub." /> 354 relativeFrequencyHeatMap(args[dict['name']], myFreqList, args[dict['pdfexport']], args[dict['html_resource']])
39 355 deviationFromMeanHeatMap(args[dict['name']], myDevList, args[dict['pdfexport']], args[dict['html_resource']])
40 <link rel="assets" href="https://github.githubassets.com/"> 356 plotPCA(args[dict['name']], myFreqList, args[dict['pdfexport']], args[dict['html_resource']])
41 357 createHTML(args[dict['name']], args[dict['html_file']], myFreqList,
42 <meta name="pjax-timeout" content="1000"> 358 myDevList) # assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource
43 359
44 <meta name="request-id" content="A689:5C3D:C6144:14D916:5CF5617A" data-pjax-transient> 360
45 361 def genomicProcess(inputname, exportpdf, forwardFN, reverseFN, htmlfile, htmlresource):
46 362 assembleWithVelvet(inputname,forwardFN,reverseFN)
47 363 contigTranslation(inputname)
48 364 myCountList = HMMerMotifSearch(inputname)
49 <meta name="selected-link" value="repo_source" data-pjax-transient> 365 myFreqList = relativeFrequencyTable(myCountList, inputname, htmlresource) # saves out inputname_relative_frequncy.csv
50 366 #myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,
51 <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU"> 367 # 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,
52 <meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA"> 368 # 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,
53 <meta name="google-site-verification" content="GXs5KoUUkNCoaAZn7wPN-t01Pywp9M3sEjnt_3_ZWPc"> 369 # 0.0372233400402414, 0.17102615694165]
54 370
55 <meta name="octolytics-host" content="collector.githubapp.com" /><meta name="octolytics-app-id" content="github" /><meta name="octolytics-event-url" content="https://collector.githubapp.com/github-external/browser_event" /><meta name="octolytics-dimension-request_id" content="A689:5C3D:C6144:14D916:5CF5617A" /><meta name="octolytics-dimension-region_edge" content="iad" /><meta name="octolytics-dimension-region_render" content="iad" /> 371
56 <meta name="analytics-location" content="/&lt;user-name&gt;/&lt;repo-name&gt;/blob/show" data-pjax-transient="true" /> 372 myDevList = getDeviationFromMean(myFreqList, inputname,htmlresource) # saves out inputname_deviation_from_mean.csv
57 373
58 374 relativeFrequencyHeatMap(inputname, myFreqList, exportpdf, htmlresource)
59 375 deviationFromMeanHeatMap(inputname, myDevList, exportpdf, htmlresource)
60 <meta name="google-analytics" content="UA-3769691-2"> 376 plotPCA(inputname, myFreqList, exportpdf, htmlresource)
61 377 createHTML(inputname, htmlfile, myFreqList,myDevList) # assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource
62 378 return
63 <meta class="js-ga-set" name="dimension1" content="Logged Out"> 379
64 380
65 381
66 382 if __name__ == "__main__":
67 383 #contigTranslation('Tcongo')
68 384 #contigTranslation('Test')
69 <meta name="hostname" content="github.com"> 385 #newHMMerMotifSearch('Test')
70 <meta name="user-login" content=""> 386 #HMMerMotifSearch('Tcongo')
71 387 #sys.exit()
72 <meta name="expected-hostname" content="github.com"> 388
73 <meta name="js-proxy-site-detection-payload" content="MTYzNmJkYWI5MWFjYjU5OWIzMjNlMGQxYjEyNWJiODU0ZmQ2MGY0MmUyYWY1MTI1ZTIwOGEzNDY0Mjc4MDRjMXx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiJBNjg5OjVDM0Q6QzYxNDQ6MTREOTE2OjVDRjU2MTdBIiwidGltZXN0YW1wIjoxNTU5NTg1MTQ3LCJob3N0IjoiZ2l0aHViLmNvbSJ9"> 389
74 390 myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,
75 <meta name="enabled-features" content="UNIVERSE_BANNER,MARKETPLACE_INVOICED_BILLING,MARKETPLACE_SOCIAL_PROOF_CUSTOMERS,MARKETPLACE_TRENDING_SOCIAL_PROOF,MARKETPLACE_RECOMMENDATIONS"> 391 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,
76 392 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,
77 <meta name="html-safe-nonce" content="2948e5e4e89293d0a3b1401d89108155900da211"> 393 0.0372233400402414, 0.17102615694165]
78 394 myDevList = [0.000790026,0.0073109,-0.001151769,-0.004502933,-0.013687421,-0.016159773,0.021689891,
79 <meta http-equiv="x-pjax-version" content="af1499c2254d0582d0a98af1dfd7f11b"> 395 0.007863809,-0.003133585,-0.001111709,-0.01313879,0.0036997,-0.00935284,0.005640693,0.015243802]
80 396
81 397 relativeFrequencyHeatMap('test', myFreqList, "PDF_Yes","results")
82 <link href="https://github.com/johnheap/VAPPER-Galaxy/commits/master.atom" rel="alternate" title="Recent Commits to VAPPER-Galaxy:master" type="application/atom+xml"> 398 deviationFromMeanHeatMap('test', myDevList, "PDF_Yes","results")
83 399 plotPCA('test',myFreqList,"PDF_Yes","results")
84 <meta name="go-import" content="github.com/johnheap/VAPPER-Galaxy git https://github.com/johnheap/VAPPER-Galaxy.git"> 400
85 401 createHTML('test',"results/test.html", myFreqList, myDevList)
86 <meta name="octolytics-dimension-user_id" content="24318980" /><meta name="octolytics-dimension-user_login" content="johnheap" /><meta name="octolytics-dimension-repository_id" content="139730674" /><meta name="octolytics-dimension-repository_nwo" content="johnheap/VAPPER-Galaxy" /><meta name="octolytics-dimension-repository_public" content="true" /><meta name="octolytics-dimension-repository_is_fork" content="false" /><meta name="octolytics-dimension-repository_network_root_id" content="139730674" /><meta name="octolytics-dimension-repository_network_root_nwo" content="johnheap/VAPPER-Galaxy" /><meta name="octolytics-dimension-repository_explore_github_marketplace_ci_cta_shown" content="false" /> 402 #contigTranslation("Test")
87 403 #myCountList = HMMerMotifSearch("Test")
88 404
89 <link rel="canonical" href="https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_G.py" data-pjax-transient> 405
90 406 sys.exit()
91
92 <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats">
93
94 <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors">
95
96 <link rel="mask-icon" href="https://github.githubassets.com/pinned-octocat.svg" color="#000000">
97 <link rel="icon" type="image/x-icon" class="js-site-favicon" href="https://github.githubassets.com/favicon.ico">
98
99 <meta name="theme-color" content="#1e2327">
100
101
102
103
104
105 <link rel="manifest" href="/manifest.json" crossOrigin="use-credentials">
106
107 </head>
108
109 <body class="logged-out env-production page-responsive page-blob">
110
111
112 <div class="position-relative js-header-wrapper ">
113 <a href="#start-of-content" tabindex="1" class="px-2 py-4 bg-blue text-white show-on-focus js-skip-to-content">Skip to content</a>
114 <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div>
115
116
117
118
119
120
121 <header class="Header-old header-logged-out js-details-container Details position-relative f4 py-2" role="banner">
122 <div class="container-lg d-lg-flex flex-items-center p-responsive">
123 <div class="d-flex flex-justify-between flex-items-center">
124 <a class="mr-4" href="https://github.com/" aria-label="Homepage" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark">
125 <svg height="32" class="octicon octicon-mark-github text-white" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg>
126 </a>
127
128 <div class="d-lg-none css-truncate css-truncate-target width-fit p-2">
129
130 <svg class="octicon octicon-repo" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
131 <a class="Header-link" href="/johnheap">johnheap</a>
132 /
133 <a class="Header-link" href="/johnheap/VAPPER-Galaxy">VAPPER-Galaxy</a>
134
135
136 </div>
137
138 <div class="d-flex flex-items-center">
139 <a class="d-inline-block d-lg-none f5 text-white no-underline border border-gray-dark rounded-2 px-2 py-1 mr-3 mr-sm-5" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;A689:5C3D:C6144:14D916:5CF5617A&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_G.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="4db17299ef1e6914fe50cf1f55d7204f9f9e582ea6e290408c8afc23cff44645" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo">
140 Sign&nbsp;up
141 </a>
142 <button class="btn-link d-lg-none mt-1 js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false">
143 <svg height="24" class="octicon octicon-three-bars text-white" viewBox="0 0 12 16" version="1.1" width="18" aria-hidden="true"><path fill-rule="evenodd" d="M11.41 9H.59C0 9 0 8.59 0 8c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zm0-4H.59C0 5 0 4.59 0 4c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zM.59 11H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1H.59C0 13 0 12.59 0 12c0-.59 0-1 .59-1z"/></svg>
144 </button>
145 </div>
146 </div>
147
148 <div class="HeaderMenu HeaderMenu--logged-out position-fixed top-0 right-0 bottom-0 height-fit position-lg-relative d-lg-flex flex-justify-between flex-items-center flex-auto">
149 <div class="d-flex d-lg-none flex-justify-end border-bottom bg-gray-light p-3">
150 <button class="btn-link js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false">
151 <svg height="24" class="octicon octicon-x text-gray" viewBox="0 0 12 16" version="1.1" width="18" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
152 </button>
153 </div>
154
155 <nav class="mt-0 px-3 px-lg-0 mb-5 mb-lg-0" aria-label="Global">
156 <ul class="d-lg-flex list-style-none">
157 <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center ">
158 <details class="HeaderMenu-details details-overlay details-reset width-full">
159 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
160 Why GitHub?
161 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative">
162 <path d="M1,1l6.2,6L13,1"></path>
163 </svg>
164 </summary>
165 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 mt-0 pb-4 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4">
166 <a href="/features" class="py-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Features">Features <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a>
167 <ul class="list-style-none f5 pb-3">
168 <li class="edge-item-fix"><a href="/features/code-review/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Code review">Code review</a></li>
169 <li class="edge-item-fix"><a href="/features/project-management/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Project management">Project management</a></li>
170 <li class="edge-item-fix"><a href="/features/integrations" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Integrations">Integrations</a></li>
171 <li class="edge-item-fix"><a href="/features/actions" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Actions">Actions</a>
172 <li class="edge-item-fix"><a href="/features/package-registry" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Package Registry">Package registry</a>
173 <li class="edge-item-fix"><a href="/features#team-management" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Team management">Team management</a></li>
174 <li class="edge-item-fix"><a href="/features#social-coding" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Social coding">Social coding</a></li>
175 <li class="edge-item-fix"><a href="/features#documentation" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Documentation">Documentation</a></li>
176 <li class="edge-item-fix"><a href="/features#code-hosting" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Code hosting">Code hosting</a></li>
177 </ul>
178
179 <ul class="list-style-none mb-0 border-lg-top pt-lg-3">
180 <li class="edge-item-fix"><a href="/customer-stories" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Customer stories">Customer stories <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
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182 </ul>
183 </div>
184 </details>
185 </li>
186 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3">
187 <a href="/enterprise" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Enterprise">Enterprise</a>
188 </li>
189
190 <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center ">
191 <details class="HeaderMenu-details details-overlay details-reset width-full">
192 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
193 Explore
194 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative">
195 <path d="M1,1l6.2,6L13,1"></path>
196 </svg>
197 </summary>
198
199 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-0 mt-0 pb-4 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4">
200 <ul class="list-style-none mb-3">
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202 </ul>
203
204 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Learn &amp; contribute</h4>
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207 <li class="edge-item-fix"><a href="/collections" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Collections">Collections</a></li>
208 <li class="edge-item-fix"><a href="/trending" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Trending">Trending</a></li>
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210 <li class="edge-item-fix"><a href="https://opensource.guide" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Open source guides">Open source guides</a></li>
211 </ul>
212
213 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Connect with others</h4>
214 <ul class="list-style-none mb-0">
215 <li class="edge-item-fix"><a href="https://github.com/events" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Events">Events</a></li>
216 <li class="edge-item-fix"><a href="https://github.community" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Community forum">Community forum</a></li>
217 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to GitHub Education">GitHub Education</a></li>
218 </ul>
219 </div>
220 </details>
221 </li>
222
223 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3">
224 <a href="/marketplace" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Marketplace">Marketplace</a>
225 </li>
226
227 <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center ">
228 <details class="HeaderMenu-details details-overlay details-reset width-full">
229 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
230 Pricing
231 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative">
232 <path d="M1,1l6.2,6L13,1"></path>
233 </svg>
234 </summary>
235
236 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-4 mt-0 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4">
237 <a href="/pricing" class="pb-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Pricing">Plans <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a>
238
239 <ul class="list-style-none mb-3">
240 <li class="edge-item-fix"><a href="/pricing#feature-comparison" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Compare plans">Compare plans</a></li>
241 <li class="edge-item-fix"><a href="https://enterprise.github.com/contact" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Contact Sales">Contact Sales</a></li>
242 </ul>
243
244 <ul class="list-style-none mb-0 border-lg-top pt-lg-3">
245 <li class="edge-item-fix"><a href="/nonprofit" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Nonprofits">Nonprofit <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
246 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Education">Education <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
247 </ul>
248 </div>
249 </details>
250 </li>
251 </ul>
252 </nav>
253
254 <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left">
255 <div class="d-lg-flex mb-3 mb-lg-0">
256 <div class="header-search flex-self-stretch flex-lg-self-auto mr-0 mr-lg-3 mb-3 mb-lg-0 scoped-search site-scoped-search js-site-search position-relative js-jump-to"
257 role="combobox"
258 aria-owns="jump-to-results"
259 aria-label="Search or jump to"
260 aria-haspopup="listbox"
261 aria-expanded="false"
262 >
263 <div class="position-relative">
264 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-site-search-form" role="search" aria-label="Site" data-scope-type="Repository" data-scope-id="139730674" data-scoped-search-url="/johnheap/VAPPER-Galaxy/search" data-unscoped-search-url="/search" action="/johnheap/VAPPER-Galaxy/search" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="&#x2713;" />
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720 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
721 <td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-s"><span class="pl-pds">&quot;&quot;&quot;</span></span></td>
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723 <tr>
724 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
725 <td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Copyright 2018 University of Liverpool</span></td>
726 </tr>
727 <tr>
728 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
729 <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Author: John Heap, Computational Biology Facility, UoL</span></td>
730 </tr>
731 <tr>
732 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
733 <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL</span></td>
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735 <tr>
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739 <tr>
740 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
741 <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span></td>
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755 <tr>
756 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
757 <td id="LC10" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * http://www.apache.org/licenses/LICENSE-2.0</span></td>
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759 <tr>
760 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
761 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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763 <tr>
764 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
765 <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Unless required by applicable law or agreed to in writing, software</span></td>
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768 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
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784 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
785 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
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789 <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">&quot;&quot;&quot;</span></span></td>
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791 <tr>
792 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
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796 <tr>
797 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
798 <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> subprocess</td>
799 </tr>
800 <tr>
801 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
802 <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> re</td>
803 </tr>
804 <tr>
805 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
806 <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td>
807 </tr>
808 <tr>
809 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
810 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td>
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812 <tr>
813 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
814 <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> shutil</td>
815 </tr>
816 <tr>
817 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
818 <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> pandas <span class="pl-k">as</span> pd</td>
819 </tr>
820 <tr>
821 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
822 <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> numpy <span class="pl-k">as</span> np</td>
823 </tr>
824 <tr>
825 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
826 <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib <span class="pl-k">as</span> mpl</td>
827 </tr>
828 <tr>
829 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
830 <td id="LC28" class="blob-code blob-code-inner js-file-line">mpl.use(<span class="pl-s"><span class="pl-pds">&#39;</span>Agg<span class="pl-pds">&#39;</span></span>)</td>
831 </tr>
832 <tr>
833 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
834 <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib.pyplot <span class="pl-k">as</span> plt</td>
835 </tr>
836 <tr>
837 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
838 <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-k">from</span> matplotlib.mlab <span class="pl-k">import</span> <span class="pl-c1">PCA</span></td>
839 </tr>
840 <tr>
841 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
842 <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> seaborn <span class="pl-k">as</span> sns</td>
843 </tr>
844 <tr>
845 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
846 <td id="LC32" class="blob-code blob-code-inner js-file-line">
847 </td>
848 </tr>
849 <tr>
850 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
851 <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> some globals for convenience</span></td>
852 </tr>
853 <tr>
854 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
855 <td id="LC34" class="blob-code blob-code-inner js-file-line">
856 </td>
857 </tr>
858 <tr>
859 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
860 <td id="LC35" class="blob-code blob-code-inner js-file-line">pList <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">&#39;</span>P1<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P2<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P3<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P4<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P5<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P6<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P7<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P8<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P9<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P10<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P11<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P12<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P13<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P14<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P15<span class="pl-pds">&#39;</span></span>]</td>
861 </tr>
862 <tr>
863 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
864 <td id="LC36" class="blob-code blob-code-inner js-file-line">
865 </td>
866 </tr>
867 <tr>
868 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
869 <td id="LC37" class="blob-code blob-code-inner js-file-line">quietString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span> <span class="pl-c"><span class="pl-c">#</span>&quot; &gt;&gt;&quot;+os.path.dirname(os.path.realpath(__file__))+&quot;/log/Vap_log.txt 2&gt;&amp;1&quot;</span></td>
870 </tr>
871 <tr>
872 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
873 <td id="LC38" class="blob-code blob-code-inner js-file-line">
874 </td>
875 </tr>
876 <tr>
877 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
878 <td id="LC39" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">assembleWithVelvet</span>(<span class="pl-smi">name</span>, <span class="pl-smi">kmers</span>, <span class="pl-smi">inslen</span>, <span class="pl-smi">covcut</span>, <span class="pl-smi">fastq1name</span>,<span class="pl-smi">fastq2name</span>):</td>
879 </tr>
880 <tr>
881 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
882 <td id="LC40" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = &quot;velveth &quot; + name + &quot;_k65 65 -shortPaired -fastq &quot; + name + &quot;_R1.fastq &quot; + name + &quot;_R2.fastq&quot;</span></td>
883 </tr>
884 <tr>
885 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
886 <td id="LC41" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>velveth <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_k<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span> kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span> kmers <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span> -shortPaired -fastq <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> fastq1name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>fastq2name<span class="pl-k">+</span>quietString</td>
887 </tr>
888 <tr>
889 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
890 <td id="LC42" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
891 </tr>
892 <tr>
893 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
894 <td id="LC43" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
895 </tr>
896 <tr>
897 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
898 <td id="LC44" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td>
899 </tr>
900 <tr>
901 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
902 <td id="LC45" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Error in velveth<span class="pl-pds">&quot;</span></span></td>
903 </tr>
904 <tr>
905 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
906 <td id="LC46" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>velvetg <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_k<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -exp_cov auto -ins_length <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inslen<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -cov_cutoff <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>covcut<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -clean yes -ins_length_sd 50 -min_pair_count 20<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>quietString</td>
907 </tr>
908 <tr>
909 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
910 <td id="LC47" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = &quot;velvetg &quot; + name + &quot;_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20&quot;+quietString</span></td>
911 </tr>
912 <tr>
913 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
914 <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
915 </tr>
916 <tr>
917 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
918 <td id="LC49" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span> <span class="pl-k">=</span> <span class="pl-c1">True</span>)</td>
919 </tr>
920 <tr>
921 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
922 <td id="LC50" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td>
923 </tr>
924 <tr>
925 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
926 <td id="LC51" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Error in velvetg<span class="pl-pds">&quot;</span></span></td>
927 </tr>
928 <tr>
929 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
930 <td id="LC52" class="blob-code blob-code-inner js-file-line"> shutil.copyfile(name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_k<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>//contigs.fa<span class="pl-pds">&quot;</span></span>,name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.fa<span class="pl-pds">&quot;</span></span>) <span class="pl-c"><span class="pl-c">#</span> my $namechange = &quot;mv &quot;.$input.&quot;_k65/contigs.fa &quot;.$input.&quot;.fa&quot;;</span></td>
931 </tr>
932 <tr>
933 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
934 <td id="LC53" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">&quot;</span>ok<span class="pl-pds">&quot;</span></span></td>
935 </tr>
936 <tr>
937 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
938 <td id="LC54" class="blob-code blob-code-inner js-file-line">
939 </td>
940 </tr>
941 <tr>
942 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
943 <td id="LC55" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">contigTranslation</span>(<span class="pl-smi">name</span>):</td>
944 </tr>
945 <tr>
946 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
947 <td id="LC56" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>transeq <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.fa <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_6frame.fas -frame=6 <span class="pl-pds">&quot;</span></span> <span class="pl-c"><span class="pl-c">#</span>+quietString</span></td>
948 </tr>
949 <tr>
950 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
951 <td id="LC57" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
952 </tr>
953 <tr>
954 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
955 <td id="LC58" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
956 </tr>
957 <tr>
958 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
959 <td id="LC59" class="blob-code blob-code-inner js-file-line">
960 </td>
961 </tr>
962 <tr>
963 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
964 <td id="LC60" class="blob-code blob-code-inner js-file-line">
965 </td>
966 </tr>
967 <tr>
968 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
969 <td id="LC61" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">HMMerMotifSearch</span>(<span class="pl-smi">name</span>):</td>
970 </tr>
971 <tr>
972 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
973 <td id="LC62" class="blob-code blob-code-inner js-file-line"> motifs <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">&#39;</span>1<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>2a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>2b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>3<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>4a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>4b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>4c<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>5<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>6<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>7<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>8a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>8b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>9a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>9b<span class="pl-pds">&#39;</span></span>,</td>
974 </tr>
975 <tr>
976 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
977 <td id="LC63" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&#39;</span>9c<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>10a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>10b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>11a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>11b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>12<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13c<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13d<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>14<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>15a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>15b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>15c<span class="pl-pds">&#39;</span></span>]</td>
978 </tr>
979 <tr>
980 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
981 <td id="LC64" class="blob-code blob-code-inner js-file-line"> lineCounts <span class="pl-k">=</span> []</td>
982 </tr>
983 <tr>
984 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
985 <td id="LC65" class="blob-code blob-code-inner js-file-line"> compoundList <span class="pl-k">=</span> []</td>
986 </tr>
987 <tr>
988 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
989 <td id="LC66" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
990 </tr>
991 <tr>
992 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
993 <td id="LC67" class="blob-code blob-code-inner js-file-line"> phylopath <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Motifs/Phylotype<span class="pl-pds">&quot;</span></span></td>
994 </tr>
995 <tr>
996 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
997 <td id="LC68" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> m <span class="pl-k">in</span> motifs:</td>
998 </tr>
999 <tr>
1000 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
1001 <td id="LC69" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>hmmsearch <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> phylopath <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.hmm <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_6frame.fas &gt; Phy<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.out<span class="pl-pds">&quot;</span></span> <span class="pl-c"><span class="pl-c">#</span> +quietString</span></td>
1002 </tr>
1003 <tr>
1004 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
1005 <td id="LC70" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> argString = &quot;hmmsearch &quot;+phylopath + m + &quot;.hmm &quot; + dir_path+&quot;/data/Test_6frame.fas &gt; Phy&quot; + m + &quot;.out&quot;</span></td>
1006 </tr>
1007 <tr>
1008 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
1009 <td id="LC71" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(argString)</span></td>
1010 </tr>
1011 <tr>
1012 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
1013 <td id="LC72" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1014 </tr>
1015 <tr>
1016 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
1017 <td id="LC73" class="blob-code blob-code-inner js-file-line">
1018 </td>
1019 </tr>
1020 <tr>
1021 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
1022 <td id="LC74" class="blob-code blob-code-inner js-file-line"> hmmResult <span class="pl-k">=</span> <span class="pl-c1">open</span>(<span class="pl-s"><span class="pl-pds">&quot;</span>Phy<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.out<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>r<span class="pl-pds">&#39;</span></span>)</td>
1023 </tr>
1024 <tr>
1025 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
1026 <td id="LC75" class="blob-code blob-code-inner js-file-line"> tempout <span class="pl-k">=</span> <span class="pl-c1">open</span>(dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Phy<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.txt<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>w<span class="pl-pds">&#39;</span></span>)</td>
1027 </tr>
1028 <tr>
1029 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
1030 <td id="LC76" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>regex = r&quot;NODE_[0-9]{1,7}_length_[0-9]{1,7}_cov_[0-9]{1,10}.[0-9]{1,7}_[0-9]{1,2}&quot;</span></td>
1031 </tr>
1032 <tr>
1033 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
1034 <td id="LC77" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
1035 </tr>
1036 <tr>
1037 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
1038 <td id="LC78" class="blob-code blob-code-inner js-file-line"> outList <span class="pl-k">=</span> []</td>
1039 </tr>
1040 <tr>
1041 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
1042 <td id="LC79" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> l <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>,<span class="pl-c1">14</span>):</td>
1043 </tr>
1044 <tr>
1045 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
1046 <td id="LC80" class="blob-code blob-code-inner js-file-line"> hmmResult.readline() <span class="pl-c"><span class="pl-c">#</span>hacky? miss out the first 14 lines. data we want starts on line 15</span></td>
1047 </tr>
1048 <tr>
1049 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
1050 <td id="LC81" class="blob-code blob-code-inner js-file-line">
1051 </td>
1052 </tr>
1053 <tr>
1054 <td id="L82" class="blob-num js-line-number" data-line-number="82"></td>
1055 <td id="LC82" class="blob-code blob-code-inner js-file-line">
1056 </td>
1057 </tr>
1058 <tr>
1059 <td id="L83" class="blob-num js-line-number" data-line-number="83"></td>
1060 <td id="LC83" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> line <span class="pl-k">in</span> hmmResult:</td>
1061 </tr>
1062 <tr>
1063 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td>
1064 <td id="LC84" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> re.search(<span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>inclusion<span class="pl-pds">&quot;</span></span>, line):</td>
1065 </tr>
1066 <tr>
1067 <td id="L85" class="blob-num js-line-number" data-line-number="85"></td>
1068 <td id="LC85" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(&quot;inclusion threshold reached&quot;)</span></td>
1069 </tr>
1070 <tr>
1071 <td id="L86" class="blob-num js-line-number" data-line-number="86"></td>
1072 <td id="LC86" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">break</span></td>
1073 </tr>
1074 <tr>
1075 <td id="L87" class="blob-num js-line-number" data-line-number="87"></td>
1076 <td id="LC87" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-c1">len</span>(line) <span class="pl-k">&lt;=</span> <span class="pl-c1">1</span>:</td>
1077 </tr>
1078 <tr>
1079 <td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
1080 <td id="LC88" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(&quot;end of data&quot;)</span></td>
1081 </tr>
1082 <tr>
1083 <td id="L89" class="blob-num js-line-number" data-line-number="89"></td>
1084 <td id="LC89" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">break</span></td>
1085 </tr>
1086 <tr>
1087 <td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
1088 <td id="LC90" class="blob-code blob-code-inner js-file-line"> m <span class="pl-k">=</span> line[<span class="pl-c1">60</span>:<span class="pl-k">-</span><span class="pl-c1">1</span>]</td>
1089 </tr>
1090 <tr>
1091 <td id="L91" class="blob-num js-line-number" data-line-number="91"></td>
1092 <td id="LC91" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(m)</span></td>
1093 </tr>
1094 <tr>
1095 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
1096 <td id="LC92" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>tempout.write(m.group() + &quot;\n&quot;)</span></td>
1097 </tr>
1098 <tr>
1099 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
1100 <td id="LC93" class="blob-code blob-code-inner js-file-line"> outList.append(<span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-cce">\n</span><span class="pl-pds">&quot;</span></span>)</td>
1101 </tr>
1102 <tr>
1103 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
1104 <td id="LC94" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">+=</span> <span class="pl-c1">1</span></td>
1105 </tr>
1106 <tr>
1107 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
1108 <td id="LC95" class="blob-code blob-code-inner js-file-line"> compoundList.append(outList)</td>
1109 </tr>
1110 <tr>
1111 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
1112 <td id="LC96" class="blob-code blob-code-inner js-file-line"> lineCounts.append(n)</td>
1113 </tr>
1114 <tr>
1115 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
1116 <td id="LC97" class="blob-code blob-code-inner js-file-line"> hmmResult.close()</td>
1117 </tr>
1118 <tr>
1119 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
1120 <td id="LC98" class="blob-code blob-code-inner js-file-line">
1121 </td>
1122 </tr>
1123 <tr>
1124 <td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
1125 <td id="LC99" class="blob-code blob-code-inner js-file-line">
1126 </td>
1127 </tr>
1128 <tr>
1129 <td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
1130 <td id="LC100" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(lineCounts)</td>
1131 </tr>
1132 <tr>
1133 <td id="L101" class="blob-num js-line-number" data-line-number="101"></td>
1134 <td id="LC101" class="blob-code blob-code-inner js-file-line"> motifGroups <span class="pl-k">=</span> [[<span class="pl-s"><span class="pl-pds">&#39;</span>1<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>2a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>2b<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>3<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>4a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>4b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>4c<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>5<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>6<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>7<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>8a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>8b<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>9a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>9b<span class="pl-pds">&#39;</span></span>,</td>
1135 </tr>
1136 <tr>
1137 <td id="L102" class="blob-num js-line-number" data-line-number="102"></td>
1138 <td id="LC102" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&#39;</span>9c<span class="pl-pds">&#39;</span></span>],</td>
1139 </tr>
1140 <tr>
1141 <td id="L103" class="blob-num js-line-number" data-line-number="103"></td>
1142 <td id="LC103" class="blob-code blob-code-inner js-file-line"> [<span class="pl-s"><span class="pl-pds">&#39;</span>10a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>10b<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>11a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>11b<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>12<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>13a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13c<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13d<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>14<span class="pl-pds">&#39;</span></span>], [<span class="pl-s"><span class="pl-pds">&#39;</span>15a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>15b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>15c<span class="pl-pds">&#39;</span></span>]]</td>
1143 </tr>
1144 <tr>
1145 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
1146 <td id="LC104" class="blob-code blob-code-inner js-file-line"> concatGroups <span class="pl-k">=</span> [<span class="pl-c1">1</span>, <span class="pl-c1">2</span>, <span class="pl-c1">1</span>, <span class="pl-c1">3</span>, <span class="pl-c1">1</span>, <span class="pl-c1">1</span>, <span class="pl-c1">1</span>, <span class="pl-c1">2</span>, <span class="pl-c1">3</span>, <span class="pl-c1">2</span>, <span class="pl-c1">2</span>, <span class="pl-c1">1</span>, <span class="pl-c1">4</span>, <span class="pl-c1">1</span>, <span class="pl-c1">3</span>]</td>
1147 </tr>
1148 <tr>
1149 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
1150 <td id="LC105" class="blob-code blob-code-inner js-file-line"> countList <span class="pl-k">=</span> []</td>
1151 </tr>
1152 <tr>
1153 <td id="L106" class="blob-num js-line-number" data-line-number="106"></td>
1154 <td id="LC106" class="blob-code blob-code-inner js-file-line"> countIndex <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
1155 </tr>
1156 <tr>
1157 <td id="L107" class="blob-num js-line-number" data-line-number="107"></td>
1158 <td id="LC107" class="blob-code blob-code-inner js-file-line"> totalCount <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
1159 </tr>
1160 <tr>
1161 <td id="L108" class="blob-num js-line-number" data-line-number="108"></td>
1162 <td id="LC108" class="blob-code blob-code-inner js-file-line">
1163 </td>
1164 </tr>
1165 <tr>
1166 <td id="L109" class="blob-num js-line-number" data-line-number="109"></td>
1167 <td id="LC109" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> c <span class="pl-k">in</span> concatGroups:</td>
1168 </tr>
1169 <tr>
1170 <td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
1171 <td id="LC110" class="blob-code blob-code-inner js-file-line"> a <span class="pl-k">=</span> []</td>
1172 </tr>
1173 <tr>
1174 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
1175 <td id="LC111" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> n <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, c):</td>
1176 </tr>
1177 <tr>
1178 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
1179 <td id="LC112" class="blob-code blob-code-inner js-file-line"> a <span class="pl-k">=</span> a <span class="pl-k">+</span> compoundList.pop(<span class="pl-c1">0</span>)</td>
1180 </tr>
1181 <tr>
1182 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
1183 <td id="LC113" class="blob-code blob-code-inner js-file-line"> t <span class="pl-k">=</span> <span class="pl-c1">set</span>(a)</td>
1184 </tr>
1185 <tr>
1186 <td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
1187 <td id="LC114" class="blob-code blob-code-inner js-file-line"> countList.append(<span class="pl-c1">len</span>(t))</td>
1188 </tr>
1189 <tr>
1190 <td id="L115" class="blob-num js-line-number" data-line-number="115"></td>
1191 <td id="LC115" class="blob-code blob-code-inner js-file-line"> totalCount <span class="pl-k">+=</span> <span class="pl-c1">len</span>(t)</td>
1192 </tr>
1193 <tr>
1194 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
1195 <td id="LC116" class="blob-code blob-code-inner js-file-line"> countList.append(totalCount)</td>
1196 </tr>
1197 <tr>
1198 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
1199 <td id="LC117" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(countList)</span></td>
1200 </tr>
1201 <tr>
1202 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
1203 <td id="LC118" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(&quot;--------&quot;)</span></td>
1204 </tr>
1205 <tr>
1206 <td id="L119" class="blob-num js-line-number" data-line-number="119"></td>
1207 <td id="LC119" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> countList</td>
1208 </tr>
1209 <tr>
1210 <td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
1211 <td id="LC120" class="blob-code blob-code-inner js-file-line">
1212 </td>
1213 </tr>
1214 <tr>
1215 <td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
1216 <td id="LC121" class="blob-code blob-code-inner js-file-line">
1217 </td>
1218 </tr>
1219 <tr>
1220 <td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
1221 <td id="LC122" class="blob-code blob-code-inner js-file-line">
1222 </td>
1223 </tr>
1224 <tr>
1225 <td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
1226 <td id="LC123" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">relativeFrequencyTable</span>(<span class="pl-smi">countList</span>, <span class="pl-smi">name</span>, <span class="pl-smi">htmlresource</span>):</td>
1227 </tr>
1228 <tr>
1229 <td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
1230 <td id="LC124" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> []</td>
1231 </tr>
1232 <tr>
1233 <td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
1234 <td id="LC125" class="blob-code blob-code-inner js-file-line"> c <span class="pl-k">=</span> <span class="pl-c1">float</span>(countList[<span class="pl-c1">15</span>])</td>
1235 </tr>
1236 <tr>
1237 <td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
1238 <td id="LC126" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> c <span class="pl-k">==</span> <span class="pl-c1">0</span>:</td>
1239 </tr>
1240 <tr>
1241 <td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
1242 <td id="LC127" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> [<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>, <span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>, <span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>,<span class="pl-c1">0</span>]</td>
1243 </tr>
1244 <tr>
1245 <td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
1246 <td id="LC128" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</span>):</td>
1247 </tr>
1248 <tr>
1249 <td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
1250 <td id="LC129" class="blob-code blob-code-inner js-file-line"> relFreqList.append(countList[i] <span class="pl-k">/</span> c)</td>
1251 </tr>
1252 <tr>
1253 <td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
1254 <td id="LC130" class="blob-code blob-code-inner js-file-line">
1255 </td>
1256 </tr>
1257 <tr>
1258 <td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
1259 <td id="LC131" class="blob-code blob-code-inner js-file-line"> data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>: pList, <span class="pl-s"><span class="pl-pds">&#39;</span>Relative Frequency<span class="pl-pds">&#39;</span></span>: relFreqList}</td>
1260 </tr>
1261 <tr>
1262 <td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
1263 <td id="LC132" class="blob-code blob-code-inner js-file-line"> relFreq_df <span class="pl-k">=</span> pd.DataFrame(data)</td>
1264 </tr>
1265 <tr>
1266 <td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
1267 <td id="LC133" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_relative_frequency.csv<span class="pl-pds">&quot;</span></span></td>
1268 </tr>
1269 <tr>
1270 <td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
1271 <td id="LC134" class="blob-code blob-code-inner js-file-line"> relFreq_df.to_csv(j_fname)</td>
1272 </tr>
1273 <tr>
1274 <td id="L135" class="blob-num js-line-number" data-line-number="135"></td>
1275 <td id="LC135" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> relFreqList <span class="pl-c"><span class="pl-c">#</span> 0-14 = p1-p15 counts [15] = total counts</span></td>
1276 </tr>
1277 <tr>
1278 <td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
1279 <td id="LC136" class="blob-code blob-code-inner js-file-line">
1280 </td>
1281 </tr>
1282 <tr>
1283 <td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
1284 <td id="LC137" class="blob-code blob-code-inner js-file-line">
1285 </td>
1286 </tr>
1287 <tr>
1288 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
1289 <td id="LC138" class="blob-code blob-code-inner js-file-line">
1290 </td>
1291 </tr>
1292 <tr>
1293 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
1294 <td id="LC139" class="blob-code blob-code-inner js-file-line">
1295 </td>
1296 </tr>
1297 <tr>
1298 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
1299 <td id="LC140" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getDeviationFromMean</span>(<span class="pl-smi">frequencyList</span>, <span class="pl-smi">name</span>, <span class="pl-smi">htmlresource</span>):</td>
1300 </tr>
1301 <tr>
1302 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
1303 <td id="LC141" class="blob-code blob-code-inner js-file-line"> devList <span class="pl-k">=</span> []</td>
1304 </tr>
1305 <tr>
1306 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
1307 <td id="LC142" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
1308 </tr>
1309 <tr>
1310 <td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
1311 <td id="LC143" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/congodata.csv<span class="pl-pds">&quot;</span></span></td>
1312 </tr>
1313 <tr>
1314 <td id="L144" class="blob-num js-line-number" data-line-number="144"></td>
1315 <td id="LC144" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>j_fname = r&quot;data/congodata.csv&quot;</span></td>
1316 </tr>
1317 <tr>
1318 <td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
1319 <td id="LC145" class="blob-code blob-code-inner js-file-line"> congo_df <span class="pl-k">=</span> pd.read_csv(j_fname) <span class="pl-c"><span class="pl-c">#</span> we get the means from congo_df</span></td>
1320 </tr>
1321 <tr>
1322 <td id="L146" class="blob-num js-line-number" data-line-number="146"></td>
1323 <td id="LC146" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</span>):</td>
1324 </tr>
1325 <tr>
1326 <td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
1327 <td id="LC147" class="blob-code blob-code-inner js-file-line"> m <span class="pl-k">=</span> congo_df[pList[p]].mean()</td>
1328 </tr>
1329 <tr>
1330 <td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
1331 <td id="LC148" class="blob-code blob-code-inner js-file-line"> dev <span class="pl-k">=</span> <span class="pl-k">-</span>(m <span class="pl-k">-</span> frequencyList[p])</td>
1332 </tr>
1333 <tr>
1334 <td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
1335 <td id="LC149" class="blob-code blob-code-inner js-file-line"> devList.append(dev)</td>
1336 </tr>
1337 <tr>
1338 <td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
1339 <td id="LC150" class="blob-code blob-code-inner js-file-line">
1340 </td>
1341 </tr>
1342 <tr>
1343 <td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
1344 <td id="LC151" class="blob-code blob-code-inner js-file-line"> data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>: pList, <span class="pl-s"><span class="pl-pds">&#39;</span>Deviation from Mean<span class="pl-pds">&#39;</span></span>: devList}</td>
1345 </tr>
1346 <tr>
1347 <td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
1348 <td id="LC152" class="blob-code blob-code-inner js-file-line"> dev_df <span class="pl-k">=</span> pd.DataFrame(data)</td>
1349 </tr>
1350 <tr>
1351 <td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
1352 <td id="LC153" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_deviation_from_mean.csv<span class="pl-pds">&quot;</span></span></td>
1353 </tr>
1354 <tr>
1355 <td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
1356 <td id="LC154" class="blob-code blob-code-inner js-file-line"> dev_df.to_csv(j_fname)</td>
1357 </tr>
1358 <tr>
1359 <td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
1360 <td id="LC155" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> devList</td>
1361 </tr>
1362 <tr>
1363 <td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
1364 <td id="LC156" class="blob-code blob-code-inner js-file-line">
1365 </td>
1366 </tr>
1367 <tr>
1368 <td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
1369 <td id="LC157" class="blob-code blob-code-inner js-file-line">
1370 </td>
1371 </tr>
1372 <tr>
1373 <td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
1374 <td id="LC158" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">relativeFrequencyHeatMap</span>(<span class="pl-smi">name</span>, <span class="pl-smi">freqList</span>, <span class="pl-smi">pdf</span>, <span class="pl-smi">htmlresource</span>):</td>
1375 </tr>
1376 <tr>
1377 <td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
1378 <td id="LC159" class="blob-code blob-code-inner js-file-line"> localFreqList <span class="pl-k">=</span> freqList[:]</td>
1379 </tr>
1380 <tr>
1381 <td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
1382 <td id="LC160" class="blob-code blob-code-inner js-file-line"> localFreqList.insert(<span class="pl-c1">0</span>, name)</td>
1383 </tr>
1384 <tr>
1385 <td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
1386 <td id="LC161" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
1387 </tr>
1388 <tr>
1389 <td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
1390 <td id="LC162" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/data/congodata.csv<span class="pl-pds">&quot;</span></span></td>
1391 </tr>
1392 <tr>
1393 <td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
1394 <td id="LC163" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(dir_path)</span></td>
1395 </tr>
1396 <tr>
1397 <td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
1398 <td id="LC164" class="blob-code blob-code-inner js-file-line"> congo_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td>
1399 </tr>
1400 <tr>
1401 <td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
1402 <td id="LC165" class="blob-code blob-code-inner js-file-line"> congo_df.drop(<span class="pl-s"><span class="pl-pds">&#39;</span>Colour<span class="pl-pds">&#39;</span></span>, <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1403 </tr>
1404 <tr>
1405 <td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
1406 <td id="LC166" class="blob-code blob-code-inner js-file-line"> congo_df.loc[congo_df.index.max() <span class="pl-k">+</span> <span class="pl-c1">1</span>] <span class="pl-k">=</span> localFreqList</td>
1407 </tr>
1408 <tr>
1409 <td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
1410 <td id="LC167" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(congo_df) <span class="pl-k">*</span> <span class="pl-c1">20</span> <span class="pl-k">/</span> <span class="pl-c1">97.0</span> <span class="pl-c"><span class="pl-c">#</span> make vertical size equivlanet 20&#39; is ok for 97.</span></td>
1411 </tr>
1412 <tr>
1413 <td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
1414 <td id="LC168" class="blob-code blob-code-inner js-file-line">
1415 </td>
1416 </tr>
1417 <tr>
1418 <td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
1419 <td id="LC169" class="blob-code blob-code-inner js-file-line"> congo_df.set_index(<span class="pl-s"><span class="pl-pds">&#39;</span>Strain<span class="pl-pds">&#39;</span></span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1420 </tr>
1421 <tr>
1422 <td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
1423 <td id="LC170" class="blob-code blob-code-inner js-file-line">
1424 </td>
1425 </tr>
1426 <tr>
1427 <td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
1428 <td id="LC171" class="blob-code blob-code-inner js-file-line"> cg <span class="pl-k">=</span> sns.clustermap(congo_df, <span class="pl-v">method</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>ward<span class="pl-pds">&#39;</span></span>, <span class="pl-v">cmap</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>RdBu_r<span class="pl-pds">&quot;</span></span>, <span class="pl-v">col_cluster</span><span class="pl-k">=</span><span class="pl-c1">False</span>, <span class="pl-v">yticklabels</span> <span class="pl-k">=</span> congo_df.index.values,<span class="pl-v">figsize</span> <span class="pl-k">=</span> (<span class="pl-c1">10</span>,ysize))</td>
1429 </tr>
1430 <tr>
1431 <td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
1432 <td id="LC172" class="blob-code blob-code-inner js-file-line"> plt.setp(cg.ax_heatmap.yaxis.get_ticklabels(), <span class="pl-v">rotation</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">fontsize</span><span class="pl-k">=</span><span class="pl-c1">8</span>) <span class="pl-c"><span class="pl-c">#</span> get y labels printed horizontally</span></td>
1433 </tr>
1434 <tr>
1435 <td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
1436 <td id="LC173" class="blob-code blob-code-inner js-file-line"> ax<span class="pl-k">=</span>cg.ax_heatmap</td>
1437 </tr>
1438 <tr>
1439 <td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
1440 <td id="LC174" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Variant Antigen Profiles of $\itTrypanosoma$ $\itcongolense$ estimated as the phylotype proportion across the<span class="pl-cce">\n</span>sample cohort. <span class="pl-pds">&quot;</span></span></td>
1441 </tr>
1442 <tr>
1443 <td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
1444 <td id="LC175" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Dendrogram reflects the relationships amongst the VSG repertoires of each strain. <span class="pl-pds">&quot;</span></span></td>
1445 </tr>
1446 <tr>
1447 <td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
1448 <td id="LC176" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Strains<span class="pl-cce">\n</span>were isolated from multiple African countries as described in Silva Pereira et al. (2018).<span class="pl-pds">&quot;</span></span></td>
1449 </tr>
1450 <tr>
1451 <td id="L177" class="blob-num js-line-number" data-line-number="177"></td>
1452 <td id="LC177" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-cce">\n</span>Data was produced with the &#39;Variant Antigen Profiler&#39; (Silva Pereira et al., 2019).<span class="pl-pds">&quot;</span></span></td>
1453 </tr>
1454 <tr>
1455 <td id="L178" class="blob-num js-line-number" data-line-number="178"></td>
1456 <td id="LC178" class="blob-code blob-code-inner js-file-line">
1457 </td>
1458 </tr>
1459 <tr>
1460 <td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
1461 <td id="LC179" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>title = &quot;Variant Antigen Profiles of Trypanosoma congolense estimated as the phylotype proportion across the sample cohort. Dendrogram reflects the relationships amongst the VSG repertoires of each strain. Strains were isolated from multiple African countries as described in Silva Pereira et al. (2018). Data was produced with the &#39;Variant Antigen Profiler&#39; (Silva Pereira and Jackson, 2018).&quot;</span></td>
1462 </tr>
1463 <tr>
1464 <td id="L180" class="blob-num js-line-number" data-line-number="180"></td>
1465 <td id="LC180" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>ax.set_title(title, ha = &quot;center&quot;, va = &quot;bottom&quot;,wrap = &quot;True&quot;)</span></td>
1466 </tr>
1467 <tr>
1468 <td id="L181" class="blob-num js-line-number" data-line-number="181"></td>
1469 <td id="LC181" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>title = &quot;Where is this!&quot;</span></td>
1470 </tr>
1471 <tr>
1472 <td id="L182" class="blob-num js-line-number" data-line-number="182"></td>
1473 <td id="LC182" class="blob-code blob-code-inner js-file-line"> ax.text(<span class="pl-k">-</span><span class="pl-c1">0.15</span>,<span class="pl-k">-</span><span class="pl-c1">0.05</span>, title,<span class="pl-v">va</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>top<span class="pl-pds">&quot;</span></span>,<span class="pl-v">wrap</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>True<span class="pl-pds">&quot;</span></span>, <span class="pl-v">transform</span> <span class="pl-k">=</span> ax.transAxes )</td>
1474 </tr>
1475 <tr>
1476 <td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
1477 <td id="LC183" class="blob-code blob-code-inner js-file-line">
1478 </td>
1479 </tr>
1480 <tr>
1481 <td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
1482 <td id="LC184" class="blob-code blob-code-inner js-file-line">
1483 </td>
1484 </tr>
1485 <tr>
1486 <td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
1487 <td id="LC185" class="blob-code blob-code-inner js-file-line">
1488 </td>
1489 </tr>
1490 <tr>
1491 <td id="L186" class="blob-num js-line-number" data-line-number="186"></td>
1492 <td id="LC186" class="blob-code blob-code-inner js-file-line">
1493 </td>
1494 </tr>
1495 <tr>
1496 <td id="L187" class="blob-num js-line-number" data-line-number="187"></td>
1497 <td id="LC187" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> cg.dendrogram_col.linkage # linkage matrix for columns</span></td>
1498 </tr>
1499 <tr>
1500 <td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
1501 <td id="LC188" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> cg.dendrogram_row.linkage # linkage matrix for rows</span></td>
1502 </tr>
1503 <tr>
1504 <td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
1505 <td id="LC189" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.savefig(r&quot;results/&quot; + name + &quot;_heatmap.png&quot;)</span></td>
1506 </tr>
1507 <tr>
1508 <td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
1509 <td id="LC190" class="blob-code blob-code-inner js-file-line"> plt.savefig(htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/heatmap.png<span class="pl-pds">&quot;</span></span>,<span class="pl-v">bbox_inches</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>tight<span class="pl-pds">&#39;</span></span>)</td>
1510 </tr>
1511 <tr>
1512 <td id="L191" class="blob-num js-line-number" data-line-number="191"></td>
1513 <td id="LC191" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> pdf <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>PDF_Yes<span class="pl-pds">&#39;</span></span>:</td>
1514 </tr>
1515 <tr>
1516 <td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
1517 <td id="LC192" class="blob-code blob-code-inner js-file-line"> plt.savefig(htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/heatmap.pdf<span class="pl-pds">&quot;</span></span>, <span class="pl-v">bbox_inches</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>tight<span class="pl-pds">&#39;</span></span>)</td>
1518 </tr>
1519 <tr>
1520 <td id="L193" class="blob-num js-line-number" data-line-number="193"></td>
1521 <td id="LC193" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>shutil.copyfile(&quot;heatmap.pdf&quot;,heatmapfn) #</span></td>
1522 </tr>
1523 <tr>
1524 <td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
1525 <td id="LC194" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td>
1526 </tr>
1527 <tr>
1528 <td id="L195" class="blob-num js-line-number" data-line-number="195"></td>
1529 <td id="LC195" class="blob-code blob-code-inner js-file-line">
1530 </td>
1531 </tr>
1532 <tr>
1533 <td id="L196" class="blob-num js-line-number" data-line-number="196"></td>
1534 <td id="LC196" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">deviationFromMeanHeatMap</span>(<span class="pl-smi">name</span>,<span class="pl-smi">devList</span>, <span class="pl-smi">pdf</span>, <span class="pl-smi">htmlresource</span>):</td>
1535 </tr>
1536 <tr>
1537 <td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
1538 <td id="LC197" class="blob-code blob-code-inner js-file-line"> localDevList <span class="pl-k">=</span> devList[:]</td>
1539 </tr>
1540 <tr>
1541 <td id="L198" class="blob-num js-line-number" data-line-number="198"></td>
1542 <td id="LC198" class="blob-code blob-code-inner js-file-line"> localDevList.insert(<span class="pl-c1">0</span>, name)</td>
1543 </tr>
1544 <tr>
1545 <td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
1546 <td id="LC199" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
1547 </tr>
1548 <tr>
1549 <td id="L200" class="blob-num js-line-number" data-line-number="200"></td>
1550 <td id="LC200" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path<span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/congodata_deviationfromthemean.csv<span class="pl-pds">&quot;</span></span></td>
1551 </tr>
1552 <tr>
1553 <td id="L201" class="blob-num js-line-number" data-line-number="201"></td>
1554 <td id="LC201" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>j_fname = r&quot;data/congodata_deviationfromthemean.csv&quot;</span></td>
1555 </tr>
1556 <tr>
1557 <td id="L202" class="blob-num js-line-number" data-line-number="202"></td>
1558 <td id="LC202" class="blob-code blob-code-inner js-file-line"> congo_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td>
1559 </tr>
1560 <tr>
1561 <td id="L203" class="blob-num js-line-number" data-line-number="203"></td>
1562 <td id="LC203" class="blob-code blob-code-inner js-file-line"> congo_df.drop(<span class="pl-s"><span class="pl-pds">&#39;</span>Colour<span class="pl-pds">&#39;</span></span>, <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1563 </tr>
1564 <tr>
1565 <td id="L204" class="blob-num js-line-number" data-line-number="204"></td>
1566 <td id="LC204" class="blob-code blob-code-inner js-file-line"> congo_df.loc[congo_df.index.max() <span class="pl-k">+</span> <span class="pl-c1">1</span>] <span class="pl-k">=</span> localDevList</td>
1567 </tr>
1568 <tr>
1569 <td id="L205" class="blob-num js-line-number" data-line-number="205"></td>
1570 <td id="LC205" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(congo_df) <span class="pl-k">*</span> <span class="pl-c1">20</span> <span class="pl-k">/</span> <span class="pl-c1">97.0</span> <span class="pl-c"><span class="pl-c">#</span> make vertical size equivlanet 20&#39; is ok for 97.</span></td>
1571 </tr>
1572 <tr>
1573 <td id="L206" class="blob-num js-line-number" data-line-number="206"></td>
1574 <td id="LC206" class="blob-code blob-code-inner js-file-line"> congo_df.set_index(<span class="pl-s"><span class="pl-pds">&#39;</span>Strain<span class="pl-pds">&#39;</span></span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1575 </tr>
1576 <tr>
1577 <td id="L207" class="blob-num js-line-number" data-line-number="207"></td>
1578 <td id="LC207" class="blob-code blob-code-inner js-file-line"> cg <span class="pl-k">=</span> sns.clustermap(congo_df, <span class="pl-v">method</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>ward<span class="pl-pds">&#39;</span></span>,<span class="pl-v">cmap</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>RdBu_r<span class="pl-pds">&quot;</span></span>, <span class="pl-v">col_cluster</span><span class="pl-k">=</span><span class="pl-c1">False</span>, <span class="pl-v">yticklabels</span> <span class="pl-k">=</span> congo_df.index.values,<span class="pl-v">figsize</span> <span class="pl-k">=</span> (<span class="pl-c1">10</span>,ysize))</td>
1579 </tr>
1580 <tr>
1581 <td id="L208" class="blob-num js-line-number" data-line-number="208"></td>
1582 <td id="LC208" class="blob-code blob-code-inner js-file-line"> plt.setp(cg.ax_heatmap.yaxis.get_majorticklabels(), <span class="pl-v">rotation</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">fontsize</span><span class="pl-k">=</span><span class="pl-c1">8</span>) <span class="pl-c"><span class="pl-c">#</span> get y labels printed horizontally</span></td>
1583 </tr>
1584 <tr>
1585 <td id="L209" class="blob-num js-line-number" data-line-number="209"></td>
1586 <td id="LC209" class="blob-code blob-code-inner js-file-line"> ax <span class="pl-k">=</span> cg.ax_heatmap</td>
1587 </tr>
1588 <tr>
1589 <td id="L210" class="blob-num js-line-number" data-line-number="210"></td>
1590 <td id="LC210" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Variant Antigen Profiles of $\itTrypanosoma$ $\itcongolense$ expressed as the deviation from the mean phylotypes <span class="pl-pds">&quot;</span></span></td>
1591 </tr>
1592 <tr>
1593 <td id="L211" class="blob-num js-line-number" data-line-number="211"></td>
1594 <td id="LC211" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span><span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-cce">\n</span>proportions of the sample cohort. Dendrogram reflects the relationships amongst the VSG repertoires of <span class="pl-pds">&quot;</span></span></td>
1595 </tr>
1596 <tr>
1597 <td id="L212" class="blob-num js-line-number" data-line-number="212"></td>
1598 <td id="LC212" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span><span class="pl-s"><span class="pl-pds">&quot;</span>each <span class="pl-cce">\n</span>strain. Strains were isolated from multiple African countries as described in Silva Pereira et al. (2018).<span class="pl-pds">&quot;</span></span></td>
1599 </tr>
1600 <tr>
1601 <td id="L213" class="blob-num js-line-number" data-line-number="213"></td>
1602 <td id="LC213" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span><span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-cce">\n</span>Data was produced with the &#39;Variant Antigen Profiler&#39; (Silva Pereira et al., 2019).<span class="pl-pds">&quot;</span></span></td>
1603 </tr>
1604 <tr>
1605 <td id="L214" class="blob-num js-line-number" data-line-number="214"></td>
1606 <td id="LC214" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>ax.set_title(title,ha = &quot;center&quot;, va = &quot;bottom&quot;,wrap = &quot;True&quot;)</span></td>
1607 </tr>
1608 <tr>
1609 <td id="L215" class="blob-num js-line-number" data-line-number="215"></td>
1610 <td id="LC215" class="blob-code blob-code-inner js-file-line"> ax.text(<span class="pl-k">-</span><span class="pl-c1">0.2</span>, <span class="pl-k">-</span><span class="pl-c1">0.05</span>, title, <span class="pl-v">va</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>top<span class="pl-pds">&quot;</span></span>, <span class="pl-v">transform</span><span class="pl-k">=</span>ax.transAxes, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>True<span class="pl-pds">&quot;</span></span>)</td>
1611 </tr>
1612 <tr>
1613 <td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
1614 <td id="LC216" class="blob-code blob-code-inner js-file-line"> plt.savefig(htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/dheatmap.png<span class="pl-pds">&quot;</span></span>,<span class="pl-v">bbox_inches</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>tight<span class="pl-pds">&#39;</span></span>)</td>
1615 </tr>
1616 <tr>
1617 <td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
1618 <td id="LC217" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> pdf <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>PDF_Yes<span class="pl-pds">&#39;</span></span>:</td>
1619 </tr>
1620 <tr>
1621 <td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
1622 <td id="LC218" class="blob-code blob-code-inner js-file-line"> plt.savefig(htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/dheatmap.pdf<span class="pl-pds">&quot;</span></span>, <span class="pl-v">bbox_inches</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>tight<span class="pl-pds">&#39;</span></span>)</td>
1623 </tr>
1624 <tr>
1625 <td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
1626 <td id="LC219" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>shutil.copyfile(&quot;dheatmap.pdf&quot;,dhmapfn)</span></td>
1627 </tr>
1628 <tr>
1629 <td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
1630 <td id="LC220" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td>
1631 </tr>
1632 <tr>
1633 <td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
1634 <td id="LC221" class="blob-code blob-code-inner js-file-line">
1635 </td>
1636 </tr>
1637 <tr>
1638 <td id="L222" class="blob-num js-line-number" data-line-number="222"></td>
1639 <td id="LC222" class="blob-code blob-code-inner js-file-line">
1640 </td>
1641 </tr>
1642 <tr>
1643 <td id="L223" class="blob-num js-line-number" data-line-number="223"></td>
1644 <td id="LC223" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">plotPCA</span>(<span class="pl-smi">name</span>, <span class="pl-smi">freqList</span>, <span class="pl-smi">pdf</span>, <span class="pl-smi">htmlresource</span>):</td>
1645 </tr>
1646 <tr>
1647 <td id="L224" class="blob-num js-line-number" data-line-number="224"></td>
1648 <td id="LC224" class="blob-code blob-code-inner js-file-line"> localFreqList <span class="pl-k">=</span> freqList[:]</td>
1649 </tr>
1650 <tr>
1651 <td id="L225" class="blob-num js-line-number" data-line-number="225"></td>
1652 <td id="LC225" class="blob-code blob-code-inner js-file-line"> localFreqList.insert(<span class="pl-c1">0</span>, name)</td>
1653 </tr>
1654 <tr>
1655 <td id="L226" class="blob-num js-line-number" data-line-number="226"></td>
1656 <td id="LC226" class="blob-code blob-code-inner js-file-line"> localFreqList.append(name)</td>
1657 </tr>
1658 <tr>
1659 <td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
1660 <td id="LC227" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
1661 </tr>
1662 <tr>
1663 <td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
1664 <td id="LC228" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/congodata.csv<span class="pl-pds">&quot;</span></span></td>
1665 </tr>
1666 <tr>
1667 <td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
1668 <td id="LC229" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>j_fname = r&quot;data/congodata.csv&quot;</span></td>
1669 </tr>
1670 <tr>
1671 <td id="L230" class="blob-num js-line-number" data-line-number="230"></td>
1672 <td id="LC230" class="blob-code blob-code-inner js-file-line"> congo_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td>
1673 </tr>
1674 <tr>
1675 <td id="L231" class="blob-num js-line-number" data-line-number="231"></td>
1676 <td id="LC231" class="blob-code blob-code-inner js-file-line"> congo_df.loc[congo_df.index.max() <span class="pl-k">+</span> <span class="pl-c1">1</span>] <span class="pl-k">=</span> localFreqList</td>
1677 </tr>
1678 <tr>
1679 <td id="L232" class="blob-num js-line-number" data-line-number="232"></td>
1680 <td id="LC232" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(congo_df.tail(2))</span></td>
1681 </tr>
1682 <tr>
1683 <td id="L233" class="blob-num js-line-number" data-line-number="233"></td>
1684 <td id="LC233" class="blob-code blob-code-inner js-file-line"> myColours <span class="pl-k">=</span> congo_df[<span class="pl-s"><span class="pl-pds">&#39;</span>Colour<span class="pl-pds">&#39;</span></span>]</td>
1685 </tr>
1686 <tr>
1687 <td id="L234" class="blob-num js-line-number" data-line-number="234"></td>
1688 <td id="LC234" class="blob-code blob-code-inner js-file-line"> myCountries <span class="pl-k">=</span> congo_df.drop_duplicates(<span class="pl-s"><span class="pl-pds">&#39;</span>Colour<span class="pl-pds">&#39;</span></span>)[<span class="pl-s"><span class="pl-pds">&#39;</span>Colour<span class="pl-pds">&#39;</span></span>].tolist()</td>
1689 </tr>
1690 <tr>
1691 <td id="L235" class="blob-num js-line-number" data-line-number="235"></td>
1692 <td id="LC235" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(myCountries)</span></td>
1693 </tr>
1694 <tr>
1695 <td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
1696 <td id="LC236" class="blob-code blob-code-inner js-file-line"> congo_df.drop(<span class="pl-s"><span class="pl-pds">&#39;</span>Colour<span class="pl-pds">&#39;</span></span>, <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1697 </tr>
1698 <tr>
1699 <td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
1700 <td id="LC237" class="blob-code blob-code-inner js-file-line"> congo_df.set_index(<span class="pl-s"><span class="pl-pds">&#39;</span>Strain<span class="pl-pds">&#39;</span></span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
1701 </tr>
1702 <tr>
1703 <td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
1704 <td id="LC238" class="blob-code blob-code-inner js-file-line"> dataArray <span class="pl-k">=</span> congo_df.as_matrix()</td>
1705 </tr>
1706 <tr>
1707 <td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
1708 <td id="LC239" class="blob-code blob-code-inner js-file-line"> pcaResult <span class="pl-k">=</span> PCA(dataArray)</td>
1709 </tr>
1710 <tr>
1711 <td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
1712 <td id="LC240" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> pcaResult.center(0)</span></td>
1713 </tr>
1714 <tr>
1715 <td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
1716 <td id="LC241" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> can&#39;t seem to find a simple way of prooducing a decent legend.</span></td>
1717 </tr>
1718 <tr>
1719 <td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
1720 <td id="LC242" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> going to seperate items in to different countires.</span></td>
1721 </tr>
1722 <tr>
1723 <td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
1724 <td id="LC243" class="blob-code blob-code-inner js-file-line"> compoundList <span class="pl-k">=</span> []</td>
1725 </tr>
1726 <tr>
1727 <td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
1728 <td id="LC244" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> myCountries:</td>
1729 </tr>
1730 <tr>
1731 <td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
1732 <td id="LC245" class="blob-code blob-code-inner js-file-line"> compoundList.append([])</td>
1733 </tr>
1734 <tr>
1735 <td id="L246" class="blob-num js-line-number" data-line-number="246"></td>
1736 <td id="LC246" class="blob-code blob-code-inner js-file-line">
1737 </td>
1738 </tr>
1739 <tr>
1740 <td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
1741 <td id="LC247" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
1742 </tr>
1743 <tr>
1744 <td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
1745 <td id="LC248" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> item <span class="pl-k">in</span> pcaResult.Y:</td>
1746 </tr>
1747 <tr>
1748 <td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
1749 <td id="LC249" class="blob-code blob-code-inner js-file-line"> col <span class="pl-k">=</span> myCountries.index(myColours[i])</td>
1750 </tr>
1751 <tr>
1752 <td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
1753 <td id="LC250" class="blob-code blob-code-inner js-file-line"> compoundList[col].append(<span class="pl-k">-</span>item[<span class="pl-c1">0</span>])</td>
1754 </tr>
1755 <tr>
1756 <td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
1757 <td id="LC251" class="blob-code blob-code-inner js-file-line"> compoundList[col].append(item[<span class="pl-c1">1</span>])</td>
1758 </tr>
1759 <tr>
1760 <td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
1761 <td id="LC252" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> i <span class="pl-k">+</span> <span class="pl-c1">1</span></td>
1762 </tr>
1763 <tr>
1764 <td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
1765 <td id="LC253" class="blob-code blob-code-inner js-file-line"> colormap <span class="pl-k">=</span> plt.cm.tab20 <span class="pl-c"><span class="pl-c">#</span> nipy_spectral, Set1,Paired</span></td>
1766 </tr>
1767 <tr>
1768 <td id="L254" class="blob-num js-line-number" data-line-number="254"></td>
1769 <td id="LC254" class="blob-code blob-code-inner js-file-line"> cols <span class="pl-k">=</span> [colormap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> np.linspace(<span class="pl-c1">0</span>, <span class="pl-c1">1</span>, <span class="pl-c1">20</span>)]</td>
1770 </tr>
1771 <tr>
1772 <td id="L255" class="blob-num js-line-number" data-line-number="255"></td>
1773 <td id="LC255" class="blob-code blob-code-inner js-file-line"> fig, ax <span class="pl-k">=</span> plt.subplots(<span class="pl-v">figsize</span><span class="pl-k">=</span>(<span class="pl-c1">9</span>, <span class="pl-c1">6</span>))</td>
1774 </tr>
1775 <tr>
1776 <td id="L256" class="blob-num js-line-number" data-line-number="256"></td>
1777 <td id="LC256" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.figure(num=1,figsize=(12, 6))</span></td>
1778 </tr>
1779 <tr>
1780 <td id="L257" class="blob-num js-line-number" data-line-number="257"></td>
1781 <td id="LC257" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
1782 </tr>
1783 <tr>
1784 <td id="L258" class="blob-num js-line-number" data-line-number="258"></td>
1785 <td id="LC258" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> d <span class="pl-k">in</span> myCountries:</td>
1786 </tr>
1787 <tr>
1788 <td id="L259" class="blob-num js-line-number" data-line-number="259"></td>
1789 <td id="LC259" class="blob-code blob-code-inner js-file-line"> a <span class="pl-k">=</span> compoundList[i]</td>
1790 </tr>
1791 <tr>
1792 <td id="L260" class="blob-num js-line-number" data-line-number="260"></td>
1793 <td id="LC260" class="blob-code blob-code-inner js-file-line"> b <span class="pl-k">=</span> a[::<span class="pl-c1">2</span>]</td>
1794 </tr>
1795 <tr>
1796 <td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
1797 <td id="LC261" class="blob-code blob-code-inner js-file-line"> c <span class="pl-k">=</span> a[<span class="pl-c1">1</span>::<span class="pl-c1">2</span>]</td>
1798 </tr>
1799 <tr>
1800 <td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
1801 <td id="LC262" class="blob-code blob-code-inner js-file-line"> ax.scatter(b, c, <span class="pl-v">color</span><span class="pl-k">=</span>cols[i], <span class="pl-v">label</span><span class="pl-k">=</span>myCountries[i])</td>
1802 </tr>
1803 <tr>
1804 <td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
1805 <td id="LC263" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> i <span class="pl-k">+</span> <span class="pl-c1">1</span></td>
1806 </tr>
1807 <tr>
1808 <td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
1809 <td id="LC264" class="blob-code blob-code-inner js-file-line"> leg <span class="pl-k">=</span> ax.legend( <span class="pl-v">bbox_to_anchor</span><span class="pl-k">=</span>(<span class="pl-c1">1.02</span>,<span class="pl-c1">1.02</span>), <span class="pl-v">loc</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>upper left<span class="pl-pds">&quot;</span></span>) <span class="pl-c"><span class="pl-c">#</span>move legend out of plot</span></td>
1810 </tr>
1811 <tr>
1812 <td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
1813 <td id="LC265" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Principal Component Analysis of the Variant Antigen Profiles of $\itTrypanosoma$ $\itcongolense$. <span class="pl-pds">&quot;</span></span> \</td>
1814 </tr>
1815 <tr>
1816 <td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
1817 <td id="LC266" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>The plot reflects the<span class="pl-cce">\n</span>relationships amongst the VSG repertoires of each strain. Strains are color-coded <span class="pl-pds">&quot;</span></span> \</td>
1818 </tr>
1819 <tr>
1820 <td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
1821 <td id="LC267" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>by location of collection according<span class="pl-cce">\n</span>to key. Strains were isolated from multiple African countries as described in Silva Pereira et al. (2018).<span class="pl-pds">&quot;</span></span></td>
1822 </tr>
1823 <tr>
1824 <td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
1825 <td id="LC268" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">+=</span><span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-cce">\n</span>Data was produced with the &#39;Variant Antigen Profiler&#39; (Silva Pereira et al., 2019).<span class="pl-pds">&quot;</span></span></td>
1826 </tr>
1827 <tr>
1828 <td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
1829 <td id="LC269" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.title(title, ha = &quot;center&quot;, va = &quot;bottom&quot;,wrap = &quot;True&quot;)</span></td>
1830 </tr>
1831 <tr>
1832 <td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
1833 <td id="LC270" class="blob-code blob-code-inner js-file-line"> tx <span class="pl-k">=</span> ax.text(<span class="pl-k">-</span><span class="pl-c1">0.1</span>, <span class="pl-k">-</span><span class="pl-c1">0.07</span>, title, <span class="pl-v">va</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>top<span class="pl-pds">&quot;</span></span>, <span class="pl-v">transform</span><span class="pl-k">=</span>ax.transAxes, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>True<span class="pl-pds">&quot;</span></span>)</td>
1834 </tr>
1835 <tr>
1836 <td id="L271" class="blob-num js-line-number" data-line-number="271"></td>
1837 <td id="LC271" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>fig.add_axes([0,0.05,1.05,1.05])</span></td>
1838 </tr>
1839 <tr>
1840 <td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
1841 <td id="LC272" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>fig.tight_layout(rect=[0, 0.03, 1, 0.95])</span></td>
1842 </tr>
1843 <tr>
1844 <td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
1845 <td id="LC273" class="blob-code blob-code-inner js-file-line"> fig.subplots_adjust(<span class="pl-v">bottom</span> <span class="pl-k">=</span> <span class="pl-c1">0.3</span>)</td>
1846 </tr>
1847 <tr>
1848 <td id="L274" class="blob-num js-line-number" data-line-number="274"></td>
1849 <td id="LC274" class="blob-code blob-code-inner js-file-line">
1850 </td>
1851 </tr>
1852 <tr>
1853 <td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
1854 <td id="LC275" class="blob-code blob-code-inner js-file-line"> fig.savefig(htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/vapPCA.png<span class="pl-pds">&quot;</span></span>, <span class="pl-v">bbox_extra_artists</span><span class="pl-k">=</span>(leg,tx), <span class="pl-v">bbox_inches</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>tight<span class="pl-pds">&#39;</span></span>)</td>
1855 </tr>
1856 <tr>
1857 <td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
1858 <td id="LC276" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>fig.savefig(htmlresource+&quot;/vapPCA.png&quot;, bbox_extra_artists=(leg,))</span></td>
1859 </tr>
1860 <tr>
1861 <td id="L277" class="blob-num js-line-number" data-line-number="277"></td>
1862 <td id="LC277" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> pdf <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>PDF_Yes<span class="pl-pds">&#39;</span></span>:</td>
1863 </tr>
1864 <tr>
1865 <td id="L278" class="blob-num js-line-number" data-line-number="278"></td>
1866 <td id="LC278" class="blob-code blob-code-inner js-file-line"> fig.savefig(htmlresource<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/vapPCA.pdf<span class="pl-pds">&quot;</span></span>,<span class="pl-v">bbox_extra_artists</span><span class="pl-k">=</span>(leg,tx), <span class="pl-v">bbox_inches</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>tight<span class="pl-pds">&#39;</span></span>)</td>
1867 </tr>
1868 <tr>
1869 <td id="L279" class="blob-num js-line-number" data-line-number="279"></td>
1870 <td id="LC279" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>shutil.copyfile(&quot;vapPCA.pdf&quot;,PCAfn) # my $namechange = &quot;mv &quot;.$input.&quot;_k65/contigs.fa &quot;.$input.&quot;.fa&quot;;</span></td>
1871 </tr>
1872 <tr>
1873 <td id="L280" class="blob-num js-line-number" data-line-number="280"></td>
1874 <td id="LC280" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td>
1875 </tr>
1876 <tr>
1877 <td id="L281" class="blob-num js-line-number" data-line-number="281"></td>
1878 <td id="LC281" class="blob-code blob-code-inner js-file-line">
1879 </td>
1880 </tr>
1881 <tr>
1882 <td id="L282" class="blob-num js-line-number" data-line-number="282"></td>
1883 <td id="LC282" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createHTML</span>(<span class="pl-smi">name</span>,<span class="pl-smi">htmlfn</span>,<span class="pl-smi">freqList</span>,<span class="pl-smi">devList</span>):</td>
1884 </tr>
1885 <tr>
1886 <td id="L283" class="blob-num js-line-number" data-line-number="283"></td>
1887 <td id="LC283" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td>
1888 </tr>
1889 <tr>
1890 <td id="L284" class="blob-num js-line-number" data-line-number="284"></td>
1891 <td id="LC284" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;html&gt;&lt;title&gt;T<span class="pl-c1">.</span>congolense VAP&lt;/title&gt;&lt;body&gt;&lt;div style=&#39;text-align:center&#39;&gt;&lt;h2&gt;&lt;i&gt;Trypanosoma congolense&lt;/i&gt; Variant Antigen Profile&lt;/h2&gt;&lt;h3&gt;<span class="pl-pds">&quot;</span></span></td>
1892 </tr>
1893 <tr>
1894 <td id="L285" class="blob-num js-line-number" data-line-number="285"></td>
1895 <td id="LC285" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> name</td>
1896 </tr>
1897 <tr>
1898 <td id="L286" class="blob-num js-line-number" data-line-number="286"></td>
1899 <td id="LC286" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;br/&gt;Genomic Analysis&lt;/h3&gt;<span class="pl-pds">&quot;</span></span></td>
1900 </tr>
1901 <tr>
1902 <td id="L287" class="blob-num js-line-number" data-line-number="287"></td>
1903 <td id="LC287" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;p style = &#39;margin-left:23%; margin-right:23%&#39;&gt;Table Legend: Variant Antigen Profiles of &lt;i&gt;Trypanosoma congolense&lt;/i&gt; estimated as the phylotype proportion and as the deviation from the mean across the sample cohort.&lt;br&gt;<span class="pl-pds">&quot;</span></span> \</td>
1904 </tr>
1905 <tr>
1906 <td id="L288" class="blob-num js-line-number" data-line-number="288"></td>
1907 <td id="LC288" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Data was produced with the &#39;Variant Antigen Profiler&#39; (Silva Pereira et al., 2019).&lt;/p&gt;<span class="pl-pds">&quot;</span></span></td>
1908 </tr>
1909 <tr>
1910 <td id="L289" class="blob-num js-line-number" data-line-number="289"></td>
1911 <td id="LC289" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;style&gt; table, th, tr, td {border: 1px solid black; border-collapse: collapse;}&lt;/style&gt;<span class="pl-pds">&quot;</span></span></td>
1912 </tr>
1913 <tr>
1914 <td id="L290" class="blob-num js-line-number" data-line-number="290"></td>
1915 <td id="LC290" class="blob-code blob-code-inner js-file-line">
1916 </td>
1917 </tr>
1918 <tr>
1919 <td id="L291" class="blob-num js-line-number" data-line-number="291"></td>
1920 <td id="LC291" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;table style=&#39;width:50%;margin-left:25%;text-align:center&#39;&gt;&lt;tr&gt;&lt;th&gt;Phylotype&lt;/th&gt;&lt;th&gt;Relative Frequency&lt;/th&gt;&lt;th&gt;Deviation from Mean&lt;/th&gt;&lt;/tr&gt;<span class="pl-pds">&quot;</span></span></td>
1921 </tr>
1922 <tr>
1923 <td id="L292" class="blob-num js-line-number" data-line-number="292"></td>
1924 <td id="LC292" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span></td>
1925 </tr>
1926 <tr>
1927 <td id="L293" class="blob-num js-line-number" data-line-number="293"></td>
1928 <td id="LC293" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> flush out table with correct values</span></td>
1929 </tr>
1930 <tr>
1931 <td id="L294" class="blob-num js-line-number" data-line-number="294"></td>
1932 <td id="LC294" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</span>):</td>
1933 </tr>
1934 <tr>
1935 <td id="L295" class="blob-num js-line-number" data-line-number="295"></td>
1936 <td id="LC295" class="blob-code blob-code-inner js-file-line"> f<span class="pl-k">=</span> <span class="pl-c1">format</span>(freqList[i],<span class="pl-s"><span class="pl-pds">&#39;</span>.4f<span class="pl-pds">&#39;</span></span>)</td>
1937 </tr>
1938 <tr>
1939 <td id="L296" class="blob-num js-line-number" data-line-number="296"></td>
1940 <td id="LC296" class="blob-code blob-code-inner js-file-line"> d<span class="pl-k">=</span> <span class="pl-c1">format</span>(devList[i],<span class="pl-s"><span class="pl-pds">&#39;</span>.4f<span class="pl-pds">&#39;</span></span>)</td>
1941 </tr>
1942 <tr>
1943 <td id="L297" class="blob-num js-line-number" data-line-number="297"></td>
1944 <td id="LC297" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;tr&gt;&lt;td&gt;phy<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(i <span class="pl-k">+</span> <span class="pl-c1">1</span>) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;&lt;td&gt;<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> f <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;&lt;td&gt;<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> d <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;&lt;/tr&gt;<span class="pl-pds">&quot;</span></span></td>
1945 </tr>
1946 <tr>
1947 <td id="L298" class="blob-num js-line-number" data-line-number="298"></td>
1948 <td id="LC298" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>tabString += &quot;&lt;tr&gt;&lt;td&gt;phy&quot; + str(i + 1) + &quot;&lt;/td&gt;&lt;td&gt;&quot; + str(freqList[i]) + &quot;&lt;/td&gt;&lt;td&gt;&quot; + str(devList[i]) + &quot;&lt;/td&gt;&lt;/tr&gt;&quot;</span></td>
1949 </tr>
1950 <tr>
1951 <td id="L299" class="blob-num js-line-number" data-line-number="299"></td>
1952 <td id="LC299" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/table&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</span></span></td>
1953 </tr>
1954 <tr>
1955 <td id="L300" class="blob-num js-line-number" data-line-number="300"></td>
1956 <td id="LC300" class="blob-code blob-code-inner js-file-line">
1957 </td>
1958 </tr>
1959 <tr>
1960 <td id="L301" class="blob-num js-line-number" data-line-number="301"></td>
1961 <td id="LC301" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;h3&gt;The Variation Heat Map and Dendrogram&lt;/h3&gt;&lt;p&gt;The absolute phylotype variation in the sample compared to model dataset<span class="pl-c1">.</span>&lt;/p&gt;<span class="pl-pds">&quot;</span></span></td>
1962 </tr>
1963 <tr>
1964 <td id="L302" class="blob-num js-line-number" data-line-number="302"></td>
1965 <td id="LC302" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;img src = &#39;heatmap<span class="pl-c1">.</span>png&#39; alt=&#39;Variation Heatmap&#39; style=&#39;max-width:100%&#39;&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</span></span></td>
1966 </tr>
1967 <tr>
1968 <td id="L303" class="blob-num js-line-number" data-line-number="303"></td>
1969 <td id="LC303" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td>
1970 </tr>
1971 <tr>
1972 <td id="L304" class="blob-num js-line-number" data-line-number="304"></td>
1973 <td id="LC304" class="blob-code blob-code-inner js-file-line">
1974 </td>
1975 </tr>
1976 <tr>
1977 <td id="L305" class="blob-num js-line-number" data-line-number="305"></td>
1978 <td id="LC305" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;h3&gt;The Deviation Heat Map and Dendrogram&lt;/h3&gt;&lt;p&gt;The phylotype variation expressed as the deviation from your sample mean compared to the model dataset&lt;/p&gt;<span class="pl-pds">&quot;</span></span></td>
1979 </tr>
1980 <tr>
1981 <td id="L306" class="blob-num js-line-number" data-line-number="306"></td>
1982 <td id="LC306" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;img src = &#39;dheatmap<span class="pl-c1">.</span>png&#39; alt=&#39;Deviation Heatmap&#39; style=&#39;max-width:100%&#39;&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</span></span></td>
1983 </tr>
1984 <tr>
1985 <td id="L307" class="blob-num js-line-number" data-line-number="307"></td>
1986 <td id="LC307" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td>
1987 </tr>
1988 <tr>
1989 <td id="L308" class="blob-num js-line-number" data-line-number="308"></td>
1990 <td id="LC308" class="blob-code blob-code-inner js-file-line">
1991 </td>
1992 </tr>
1993 <tr>
1994 <td id="L309" class="blob-num js-line-number" data-line-number="309"></td>
1995 <td id="LC309" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;h3&gt;The Variation PCA plot&lt;/h3&gt;&lt;p&gt;PCA analysis corresponding to absolute variation<span class="pl-c1">.</span> Colour coded according to location&lt;/p&gt;<span class="pl-pds">&quot;</span></span></td>
1996 </tr>
1997 <tr>
1998 <td id="L310" class="blob-num js-line-number" data-line-number="310"></td>
1999 <td id="LC310" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;img src = &#39;vapPCA<span class="pl-c1">.</span>png&#39; alt=&#39;PCA Analysis&#39; style=&#39;max-width:100%&#39;&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</span></span></td>
2000 </tr>
2001 <tr>
2002 <td id="L311" class="blob-num js-line-number" data-line-number="311"></td>
2003 <td id="LC311" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString <span class="pl-k">+</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;/div&gt;&lt;/body&gt;&lt;/html&gt;<span class="pl-pds">&quot;</span></span></td>
2004 </tr>
2005 <tr>
2006 <td id="L312" class="blob-num js-line-number" data-line-number="312"></td>
2007 <td id="LC312" class="blob-code blob-code-inner js-file-line">
2008 </td>
2009 </tr>
2010 <tr>
2011 <td id="L313" class="blob-num js-line-number" data-line-number="313"></td>
2012 <td id="LC313" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(htmlfn, <span class="pl-s"><span class="pl-pds">&quot;</span>w<span class="pl-pds">&quot;</span></span>) <span class="pl-k">as</span> htmlfile:</td>
2013 </tr>
2014 <tr>
2015 <td id="L314" class="blob-num js-line-number" data-line-number="314"></td>
2016 <td id="LC314" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td>
2017 </tr>
2018 <tr>
2019 <td id="L315" class="blob-num js-line-number" data-line-number="315"></td>
2020 <td id="LC315" class="blob-code blob-code-inner js-file-line">
2021 </td>
2022 </tr>
2023 <tr>
2024 <td id="L316" class="blob-num js-line-number" data-line-number="316"></td>
2025 <td id="LC316" class="blob-code blob-code-inner js-file-line">
2026 </td>
2027 </tr>
2028 <tr>
2029 <td id="L317" class="blob-num js-line-number" data-line-number="317"></td>
2030 <td id="LC317" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">assemble</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td>
2031 </tr>
2032 <tr>
2033 <td id="L318" class="blob-num js-line-number" data-line-number="318"></td>
2034 <td id="LC318" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argdict = {&#39;name&#39;: 2, &#39;pdfexport&#39;: 3, &#39;kmers&#39;: 4, &#39;inslen&#39;: 5, &#39;covcut&#39;: 6, &#39;forward&#39;: 7, &#39;reverse&#39;: 8, &#39;html_file&#39;: 9,&#39;html_resource&#39;: 10}</span></td>
2035 </tr>
2036 <tr>
2037 <td id="L319" class="blob-num js-line-number" data-line-number="319"></td>
2038 <td id="LC319" class="blob-code blob-code-inner js-file-line"> assembleWithVelvet(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>kmers<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>inslen<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>covcut<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>forward<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>reverse<span class="pl-pds">&#39;</span></span>]])</td>
2039 </tr>
2040 <tr>
2041 <td id="L320" class="blob-num js-line-number" data-line-number="320"></td>
2042 <td id="LC320" class="blob-code blob-code-inner js-file-line"> contigTranslation(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]])</td>
2043 </tr>
2044 <tr>
2045 <td id="L321" class="blob-num js-line-number" data-line-number="321"></td>
2046 <td id="LC321" class="blob-code blob-code-inner js-file-line"> myCountList <span class="pl-k">=</span> HMMerMotifSearch(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]])</td>
2047 </tr>
2048 <tr>
2049 <td id="L322" class="blob-num js-line-number" data-line-number="322"></td>
2050 <td id="LC322" class="blob-code blob-code-inner js-file-line"> myFreqList <span class="pl-k">=</span> relativeFrequencyTable(myCountList, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]]) <span class="pl-c"><span class="pl-c">#</span> saves out inputname_relative_frequncy.csv</span></td>
2051 </tr>
2052 <tr>
2053 <td id="L323" class="blob-num js-line-number" data-line-number="323"></td>
2054 <td id="LC323" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,</span></td>
2055 </tr>
2056 <tr>
2057 <td id="L324" class="blob-num js-line-number" data-line-number="324"></td>
2058 <td id="LC324" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,</span></td>
2059 </tr>
2060 <tr>
2061 <td id="L325" class="blob-num js-line-number" data-line-number="325"></td>
2062 <td id="LC325" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,</span></td>
2063 </tr>
2064 <tr>
2065 <td id="L326" class="blob-num js-line-number" data-line-number="326"></td>
2066 <td id="LC326" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0372233400402414, 0.17102615694165]</span></td>
2067 </tr>
2068 <tr>
2069 <td id="L327" class="blob-num js-line-number" data-line-number="327"></td>
2070 <td id="LC327" class="blob-code blob-code-inner js-file-line">
2071 </td>
2072 </tr>
2073 <tr>
2074 <td id="L328" class="blob-num js-line-number" data-line-number="328"></td>
2075 <td id="LC328" class="blob-code blob-code-inner js-file-line">
2076 </td>
2077 </tr>
2078 <tr>
2079 <td id="L329" class="blob-num js-line-number" data-line-number="329"></td>
2080 <td id="LC329" class="blob-code blob-code-inner js-file-line"> myDevList <span class="pl-k">=</span> getDeviationFromMean(myFreqList, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]]) <span class="pl-c"><span class="pl-c">#</span> saves out inputname_deviation_from_mean.csv</span></td>
2081 </tr>
2082 <tr>
2083 <td id="L330" class="blob-num js-line-number" data-line-number="330"></td>
2084 <td id="LC330" class="blob-code blob-code-inner js-file-line"> relativeFrequencyHeatMap(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], myFreqList,args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]])</td>
2085 </tr>
2086 <tr>
2087 <td id="L331" class="blob-num js-line-number" data-line-number="331"></td>
2088 <td id="LC331" class="blob-code blob-code-inner js-file-line"> deviationFromMeanHeatMap(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], myDevList,args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]])</td>
2089 </tr>
2090 <tr>
2091 <td id="L332" class="blob-num js-line-number" data-line-number="332"></td>
2092 <td id="LC332" class="blob-code blob-code-inner js-file-line"> plotPCA(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], myFreqList,args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]])</td>
2093 </tr>
2094 <tr>
2095 <td id="L333" class="blob-num js-line-number" data-line-number="333"></td>
2096 <td id="LC333" class="blob-code blob-code-inner js-file-line"> createHTML(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>]], myFreqList, myDevList) <span class="pl-c"><span class="pl-c">#</span> assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td>
2097 </tr>
2098 <tr>
2099 <td id="L334" class="blob-num js-line-number" data-line-number="334"></td>
2100 <td id="LC334" class="blob-code blob-code-inner js-file-line">
2101 </td>
2102 </tr>
2103 <tr>
2104 <td id="L335" class="blob-num js-line-number" data-line-number="335"></td>
2105 <td id="LC335" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">contigs</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td>
2106 </tr>
2107 <tr>
2108 <td id="L336" class="blob-num js-line-number" data-line-number="336"></td>
2109 <td id="LC336" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argdict = {&#39;name&#39;: 2, &#39;pdfexport&#39;: 3, &#39;contigs&#39;: 4, &#39;html_file&#39;: 5, &#39;html_resource&#39;: 6}</span></td>
2110 </tr>
2111 <tr>
2112 <td id="L337" class="blob-num js-line-number" data-line-number="337"></td>
2113 <td id="LC337" class="blob-code blob-code-inner js-file-line">
2114 </td>
2115 </tr>
2116 <tr>
2117 <td id="L338" class="blob-num js-line-number" data-line-number="338"></td>
2118 <td id="LC338" class="blob-code blob-code-inner js-file-line"> shutil.copyfile(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>contigs<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.fa<span class="pl-pds">&quot;</span></span>)</td>
2119 </tr>
2120 <tr>
2121 <td id="L339" class="blob-num js-line-number" data-line-number="339"></td>
2122 <td id="LC339" class="blob-code blob-code-inner js-file-line">
2123 </td>
2124 </tr>
2125 <tr>
2126 <td id="L340" class="blob-num js-line-number" data-line-number="340"></td>
2127 <td id="LC340" class="blob-code blob-code-inner js-file-line"> </td>
2128 </tr>
2129 <tr>
2130 <td id="L341" class="blob-num js-line-number" data-line-number="341"></td>
2131 <td id="LC341" class="blob-code blob-code-inner js-file-line">
2132 </td>
2133 </tr>
2134 <tr>
2135 <td id="L342" class="blob-num js-line-number" data-line-number="342"></td>
2136 <td id="LC342" class="blob-code blob-code-inner js-file-line"> contigTranslation(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]])</td>
2137 </tr>
2138 <tr>
2139 <td id="L343" class="blob-num js-line-number" data-line-number="343"></td>
2140 <td id="LC343" class="blob-code blob-code-inner js-file-line"> myCountList <span class="pl-k">=</span> HMMerMotifSearch(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]])</td>
2141 </tr>
2142 <tr>
2143 <td id="L344" class="blob-num js-line-number" data-line-number="344"></td>
2144 <td id="LC344" class="blob-code blob-code-inner js-file-line"> myFreqList <span class="pl-k">=</span> relativeFrequencyTable(myCountList, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],</td>
2145 </tr>
2146 <tr>
2147 <td id="L345" class="blob-num js-line-number" data-line-number="345"></td>
2148 <td id="LC345" class="blob-code blob-code-inner js-file-line"> args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]]) <span class="pl-c"><span class="pl-c">#</span> saves out inputname_relative_frequncy.csv</span></td>
2149 </tr>
2150 <tr>
2151 <td id="L346" class="blob-num js-line-number" data-line-number="346"></td>
2152 <td id="LC346" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,</span></td>
2153 </tr>
2154 <tr>
2155 <td id="L347" class="blob-num js-line-number" data-line-number="347"></td>
2156 <td id="LC347" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,</span></td>
2157 </tr>
2158 <tr>
2159 <td id="L348" class="blob-num js-line-number" data-line-number="348"></td>
2160 <td id="LC348" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,</span></td>
2161 </tr>
2162 <tr>
2163 <td id="L349" class="blob-num js-line-number" data-line-number="349"></td>
2164 <td id="LC349" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0372233400402414, 0.17102615694165]</span></td>
2165 </tr>
2166 <tr>
2167 <td id="L350" class="blob-num js-line-number" data-line-number="350"></td>
2168 <td id="LC350" class="blob-code blob-code-inner js-file-line">
2169 </td>
2170 </tr>
2171 <tr>
2172 <td id="L351" class="blob-num js-line-number" data-line-number="351"></td>
2173 <td id="LC351" class="blob-code blob-code-inner js-file-line">
2174 </td>
2175 </tr>
2176 <tr>
2177 <td id="L352" class="blob-num js-line-number" data-line-number="352"></td>
2178 <td id="LC352" class="blob-code blob-code-inner js-file-line"> myDevList <span class="pl-k">=</span> getDeviationFromMean(myFreqList, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],</td>
2179 </tr>
2180 <tr>
2181 <td id="L353" class="blob-num js-line-number" data-line-number="353"></td>
2182 <td id="LC353" class="blob-code blob-code-inner js-file-line"> args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]]) <span class="pl-c"><span class="pl-c">#</span> saves out inputname_deviation_from_mean.csv</span></td>
2183 </tr>
2184 <tr>
2185 <td id="L354" class="blob-num js-line-number" data-line-number="354"></td>
2186 <td id="LC354" class="blob-code blob-code-inner js-file-line"> relativeFrequencyHeatMap(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], myFreqList, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]])</td>
2187 </tr>
2188 <tr>
2189 <td id="L355" class="blob-num js-line-number" data-line-number="355"></td>
2190 <td id="LC355" class="blob-code blob-code-inner js-file-line"> deviationFromMeanHeatMap(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], myDevList, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]])</td>
2191 </tr>
2192 <tr>
2193 <td id="L356" class="blob-num js-line-number" data-line-number="356"></td>
2194 <td id="LC356" class="blob-code blob-code-inner js-file-line"> plotPCA(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], myFreqList, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]])</td>
2195 </tr>
2196 <tr>
2197 <td id="L357" class="blob-num js-line-number" data-line-number="357"></td>
2198 <td id="LC357" class="blob-code blob-code-inner js-file-line"> createHTML(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>]], myFreqList,</td>
2199 </tr>
2200 <tr>
2201 <td id="L358" class="blob-num js-line-number" data-line-number="358"></td>
2202 <td id="LC358" class="blob-code blob-code-inner js-file-line"> myDevList) <span class="pl-c"><span class="pl-c">#</span> assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td>
2203 </tr>
2204 <tr>
2205 <td id="L359" class="blob-num js-line-number" data-line-number="359"></td>
2206 <td id="LC359" class="blob-code blob-code-inner js-file-line">
2207 </td>
2208 </tr>
2209 <tr>
2210 <td id="L360" class="blob-num js-line-number" data-line-number="360"></td>
2211 <td id="LC360" class="blob-code blob-code-inner js-file-line">
2212 </td>
2213 </tr>
2214 <tr>
2215 <td id="L361" class="blob-num js-line-number" data-line-number="361"></td>
2216 <td id="LC361" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">genomicProcess</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">exportpdf</span>, <span class="pl-smi">forwardFN</span>, <span class="pl-smi">reverseFN</span>, <span class="pl-smi">htmlfile</span>, <span class="pl-smi">htmlresource</span>):</td>
2217 </tr>
2218 <tr>
2219 <td id="L362" class="blob-num js-line-number" data-line-number="362"></td>
2220 <td id="LC362" class="blob-code blob-code-inner js-file-line"> assembleWithVelvet(inputname,forwardFN,reverseFN)</td>
2221 </tr>
2222 <tr>
2223 <td id="L363" class="blob-num js-line-number" data-line-number="363"></td>
2224 <td id="LC363" class="blob-code blob-code-inner js-file-line"> contigTranslation(inputname)</td>
2225 </tr>
2226 <tr>
2227 <td id="L364" class="blob-num js-line-number" data-line-number="364"></td>
2228 <td id="LC364" class="blob-code blob-code-inner js-file-line"> myCountList <span class="pl-k">=</span> HMMerMotifSearch(inputname)</td>
2229 </tr>
2230 <tr>
2231 <td id="L365" class="blob-num js-line-number" data-line-number="365"></td>
2232 <td id="LC365" class="blob-code blob-code-inner js-file-line"> myFreqList <span class="pl-k">=</span> relativeFrequencyTable(myCountList, inputname, htmlresource) <span class="pl-c"><span class="pl-c">#</span> saves out inputname_relative_frequncy.csv</span></td>
2233 </tr>
2234 <tr>
2235 <td id="L366" class="blob-num js-line-number" data-line-number="366"></td>
2236 <td id="LC366" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>myFreqList = [0.111670020120724, 0.103621730382294, 0.0784708249496982, 0.0110663983903421,</span></td>
2237 </tr>
2238 <tr>
2239 <td id="L367" class="blob-num js-line-number" data-line-number="367"></td>
2240 <td id="LC367" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0543259557344064, 0.0563380281690141, 0.0734406438631791, 0.0160965794768612,</span></td>
2241 </tr>
2242 <tr>
2243 <td id="L368" class="blob-num js-line-number" data-line-number="368"></td>
2244 <td id="LC368" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0110663983903421, 0.028169014084507, 0.126760563380282, 0.0583501006036217, 0.062374245472837,</span></td>
2245 </tr>
2246 <tr>
2247 <td id="L369" class="blob-num js-line-number" data-line-number="369"></td>
2248 <td id="LC369" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> 0.0372233400402414, 0.17102615694165]</span></td>
2249 </tr>
2250 <tr>
2251 <td id="L370" class="blob-num js-line-number" data-line-number="370"></td>
2252 <td id="LC370" class="blob-code blob-code-inner js-file-line">
2253 </td>
2254 </tr>
2255 <tr>
2256 <td id="L371" class="blob-num js-line-number" data-line-number="371"></td>
2257 <td id="LC371" class="blob-code blob-code-inner js-file-line">
2258 </td>
2259 </tr>
2260 <tr>
2261 <td id="L372" class="blob-num js-line-number" data-line-number="372"></td>
2262 <td id="LC372" class="blob-code blob-code-inner js-file-line"> myDevList <span class="pl-k">=</span> getDeviationFromMean(myFreqList, inputname,htmlresource) <span class="pl-c"><span class="pl-c">#</span> saves out inputname_deviation_from_mean.csv</span></td>
2263 </tr>
2264 <tr>
2265 <td id="L373" class="blob-num js-line-number" data-line-number="373"></td>
2266 <td id="LC373" class="blob-code blob-code-inner js-file-line">
2267 </td>
2268 </tr>
2269 <tr>
2270 <td id="L374" class="blob-num js-line-number" data-line-number="374"></td>
2271 <td id="LC374" class="blob-code blob-code-inner js-file-line"> relativeFrequencyHeatMap(inputname, myFreqList, exportpdf, htmlresource)</td>
2272 </tr>
2273 <tr>
2274 <td id="L375" class="blob-num js-line-number" data-line-number="375"></td>
2275 <td id="LC375" class="blob-code blob-code-inner js-file-line"> deviationFromMeanHeatMap(inputname, myDevList, exportpdf, htmlresource)</td>
2276 </tr>
2277 <tr>
2278 <td id="L376" class="blob-num js-line-number" data-line-number="376"></td>
2279 <td id="LC376" class="blob-code blob-code-inner js-file-line"> plotPCA(inputname, myFreqList, exportpdf, htmlresource)</td>
2280 </tr>
2281 <tr>
2282 <td id="L377" class="blob-num js-line-number" data-line-number="377"></td>
2283 <td id="LC377" class="blob-code blob-code-inner js-file-line"> createHTML(inputname, htmlfile, myFreqList,myDevList) <span class="pl-c"><span class="pl-c">#</span> assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td>
2284 </tr>
2285 <tr>
2286 <td id="L378" class="blob-num js-line-number" data-line-number="378"></td>
2287 <td id="LC378" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td>
2288 </tr>
2289 <tr>
2290 <td id="L379" class="blob-num js-line-number" data-line-number="379"></td>
2291 <td id="LC379" class="blob-code blob-code-inner js-file-line">
2292 </td>
2293 </tr>
2294 <tr>
2295 <td id="L380" class="blob-num js-line-number" data-line-number="380"></td>
2296 <td id="LC380" class="blob-code blob-code-inner js-file-line">
2297 </td>
2298 </tr>
2299 <tr>
2300 <td id="L381" class="blob-num js-line-number" data-line-number="381"></td>
2301 <td id="LC381" class="blob-code blob-code-inner js-file-line">
2302 </td>
2303 </tr>
2304 <tr>
2305 <td id="L382" class="blob-num js-line-number" data-line-number="382"></td>
2306 <td id="LC382" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-c1">__name__</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>__main__<span class="pl-pds">&quot;</span></span>:</td>
2307 </tr>
2308 <tr>
2309 <td id="L383" class="blob-num js-line-number" data-line-number="383"></td>
2310 <td id="LC383" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>contigTranslation(&#39;Tcongo&#39;)</span></td>
2311 </tr>
2312 <tr>
2313 <td id="L384" class="blob-num js-line-number" data-line-number="384"></td>
2314 <td id="LC384" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>contigTranslation(&#39;Test&#39;)</span></td>
2315 </tr>
2316 <tr>
2317 <td id="L385" class="blob-num js-line-number" data-line-number="385"></td>
2318 <td id="LC385" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>newHMMerMotifSearch(&#39;Test&#39;)</span></td>
2319 </tr>
2320 <tr>
2321 <td id="L386" class="blob-num js-line-number" data-line-number="386"></td>
2322 <td id="LC386" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>HMMerMotifSearch(&#39;Tcongo&#39;)</span></td>
2323 </tr>
2324 <tr>
2325 <td id="L387" class="blob-num js-line-number" data-line-number="387"></td>
2326 <td id="LC387" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>sys.exit()</span></td>
2327 </tr>
2328 <tr>
2329 <td id="L388" class="blob-num js-line-number" data-line-number="388"></td>
2330 <td id="LC388" class="blob-code blob-code-inner js-file-line">
2331 </td>
2332 </tr>
2333 <tr>
2334 <td id="L389" class="blob-num js-line-number" data-line-number="389"></td>
2335 <td id="LC389" class="blob-code blob-code-inner js-file-line">
2336 </td>
2337 </tr>
2338 <tr>
2339 <td id="L390" class="blob-num js-line-number" data-line-number="390"></td>
2340 <td id="LC390" class="blob-code blob-code-inner js-file-line"> myFreqList <span class="pl-k">=</span> [<span class="pl-c1">0.111670020120724</span>, <span class="pl-c1">0.103621730382294</span>, <span class="pl-c1">0.0784708249496982</span>, <span class="pl-c1">0.0110663983903421</span>,</td>
2341 </tr>
2342 <tr>
2343 <td id="L391" class="blob-num js-line-number" data-line-number="391"></td>
2344 <td id="LC391" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.0543259557344064</span>, <span class="pl-c1">0.0563380281690141</span>, <span class="pl-c1">0.0734406438631791</span>, <span class="pl-c1">0.0160965794768612</span>,</td>
2345 </tr>
2346 <tr>
2347 <td id="L392" class="blob-num js-line-number" data-line-number="392"></td>
2348 <td id="LC392" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.0110663983903421</span>, <span class="pl-c1">0.028169014084507</span>, <span class="pl-c1">0.126760563380282</span>, <span class="pl-c1">0.0583501006036217</span>, <span class="pl-c1">0.062374245472837</span>,</td>
2349 </tr>
2350 <tr>
2351 <td id="L393" class="blob-num js-line-number" data-line-number="393"></td>
2352 <td id="LC393" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.0372233400402414</span>, <span class="pl-c1">0.17102615694165</span>]</td>
2353 </tr>
2354 <tr>
2355 <td id="L394" class="blob-num js-line-number" data-line-number="394"></td>
2356 <td id="LC394" class="blob-code blob-code-inner js-file-line"> myDevList <span class="pl-k">=</span> [<span class="pl-c1">0.000790026</span>,<span class="pl-c1">0.0073109</span>,<span class="pl-k">-</span><span class="pl-c1">0.001151769</span>,<span class="pl-k">-</span><span class="pl-c1">0.004502933</span>,<span class="pl-k">-</span><span class="pl-c1">0.013687421</span>,<span class="pl-k">-</span><span class="pl-c1">0.016159773</span>,<span class="pl-c1">0.021689891</span>,</td>
2357 </tr>
2358 <tr>
2359 <td id="L395" class="blob-num js-line-number" data-line-number="395"></td>
2360 <td id="LC395" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.007863809</span>,<span class="pl-k">-</span><span class="pl-c1">0.003133585</span>,<span class="pl-k">-</span><span class="pl-c1">0.001111709</span>,<span class="pl-k">-</span><span class="pl-c1">0.01313879</span>,<span class="pl-c1">0.0036997</span>,<span class="pl-k">-</span><span class="pl-c1">0.00935284</span>,<span class="pl-c1">0.005640693</span>,<span class="pl-c1">0.015243802</span>]</td>
2361 </tr>
2362 <tr>
2363 <td id="L396" class="blob-num js-line-number" data-line-number="396"></td>
2364 <td id="LC396" class="blob-code blob-code-inner js-file-line">
2365 </td>
2366 </tr>
2367 <tr>
2368 <td id="L397" class="blob-num js-line-number" data-line-number="397"></td>
2369 <td id="LC397" class="blob-code blob-code-inner js-file-line"> relativeFrequencyHeatMap(<span class="pl-s"><span class="pl-pds">&#39;</span>test<span class="pl-pds">&#39;</span></span>, myFreqList, <span class="pl-s"><span class="pl-pds">&quot;</span>PDF_Yes<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>)</td>
2370 </tr>
2371 <tr>
2372 <td id="L398" class="blob-num js-line-number" data-line-number="398"></td>
2373 <td id="LC398" class="blob-code blob-code-inner js-file-line"> deviationFromMeanHeatMap(<span class="pl-s"><span class="pl-pds">&#39;</span>test<span class="pl-pds">&#39;</span></span>, myDevList, <span class="pl-s"><span class="pl-pds">&quot;</span>PDF_Yes<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>)</td>
2374 </tr>
2375 <tr>
2376 <td id="L399" class="blob-num js-line-number" data-line-number="399"></td>
2377 <td id="LC399" class="blob-code blob-code-inner js-file-line"> plotPCA(<span class="pl-s"><span class="pl-pds">&#39;</span>test<span class="pl-pds">&#39;</span></span>,myFreqList,<span class="pl-s"><span class="pl-pds">&quot;</span>PDF_Yes<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>)</td>
2378 </tr>
2379 <tr>
2380 <td id="L400" class="blob-num js-line-number" data-line-number="400"></td>
2381 <td id="LC400" class="blob-code blob-code-inner js-file-line">
2382 </td>
2383 </tr>
2384 <tr>
2385 <td id="L401" class="blob-num js-line-number" data-line-number="401"></td>
2386 <td id="LC401" class="blob-code blob-code-inner js-file-line"> createHTML(<span class="pl-s"><span class="pl-pds">&#39;</span>test<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>results/test.html<span class="pl-pds">&quot;</span></span>, myFreqList, myDevList)</td>
2387 </tr>
2388 <tr>
2389 <td id="L402" class="blob-num js-line-number" data-line-number="402"></td>
2390 <td id="LC402" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>contigTranslation(&quot;Test&quot;)</span></td>
2391 </tr>
2392 <tr>
2393 <td id="L403" class="blob-num js-line-number" data-line-number="403"></td>
2394 <td id="LC403" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>myCountList = HMMerMotifSearch(&quot;Test&quot;)</span></td>
2395 </tr>
2396 <tr>
2397 <td id="L404" class="blob-num js-line-number" data-line-number="404"></td>
2398 <td id="LC404" class="blob-code blob-code-inner js-file-line">
2399 </td>
2400 </tr>
2401 <tr>
2402 <td id="L405" class="blob-num js-line-number" data-line-number="405"></td>
2403 <td id="LC405" class="blob-code blob-code-inner js-file-line">
2404 </td>
2405 </tr>
2406 <tr>
2407 <td id="L406" class="blob-num js-line-number" data-line-number="406"></td>
2408 <td id="LC406" class="blob-code blob-code-inner js-file-line"> sys.exit()</td>
2409 </tr>
2410 </table>
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2511 <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>
2512 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
2513 </button>
2514 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
2515 </details-dialog>
2516 </details>
2517 </template>
2518
2519 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
2520 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
2521 </div>
2522 </div>
2523
2524 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>
2525
2526 </body>
2527 </html>
2528