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improved and clean dataset construction (clustering requires cd-hit)

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commit eb8eade3f13189db76c806e734c8d6ea0d51d843 1 parent 7292535
waldispuhl waldispuhl authored
31 Recomb/main_RECOMB.aux
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  1 +\relax
  2 +\citation{Waldispuhl2008}
  3 +\citation{Lari1990}
  4 +\citation{Turner2010}
  5 +\citation{Stombaugh2009}
  6 +\citation{Stombaugh2009}
  7 +\citation{Turner2010}
  8 +\citation{Stombaugh2009}
  9 +\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{2}}
  10 +\newlabel{sec:introduction}{{1}{2}}
  11 +\@writefile{toc}{\contentsline {section}{\numberline {2}Methods}{2}}
  12 +\newlabel{sec:methods}{{2}{2}}
  13 +\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Definitions}{2}}
  14 +\@writefile{toc}{\contentsline {subsection}{\numberline {2.2}Energy Model}{2}}
  15 +\@writefile{toc}{\contentsline {subsection}{\numberline {2.3}Inside}{3}}
  16 +\newlabel{eq:Z_in}{{1}{3}}
  17 +\newlabel{eq:Z_rec}{{2}{3}}
  18 +\@writefile{toc}{\contentsline {subsection}{\numberline {2.4}Outside}{4}}
  19 +\newlabel{eq:Y_in}{{3}{4}}
  20 +\newlabel{eq:Y_rec}{{4}{4}}
  21 +\@writefile{toc}{\contentsline {section}{\numberline {3}Inside-Outside}{5}}
  22 +\citation{mpmath}
  23 +\@writefile{toc}{\contentsline {section}{\numberline {4}Results}{6}}
  24 +\newlabel{sec:results}{{4}{6}}
  25 +\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}Implementation}{6}}
  26 +\@writefile{toc}{\contentsline {section}{\numberline {5}Discussion}{6}}
  27 +\newlabel{sec:conclusion}{{5}{6}}
  28 +\@writefile{toc}{\contentsline {section}{\numberline {6}Acknowledgments}{6}}
  29 +\newlabel{sec:acknowledgments}{{6}{6}}
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  31 +\bibdata{RNApyro}
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  425 +Output written on main_RECOMB.pdf (6 pages, 192436 bytes).
  426 +PDF statistics:
  427 + 87 PDF objects out of 1000 (max. 8388607)
  428 + 62 compressed objects within 1 object stream
  429 + 0 named destinations out of 1000 (max. 500000)
  430 + 1 words of extra memory for PDF output out of 10000 (max. 10000000)
  431 +
BIN  Recomb/main_RECOMB.pdf
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BIN  Recomb/main_RECOMB.synctex.gz
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2  Recomb/main_RECOMB.tex
@@ -47,7 +47,7 @@
47 47 \newcommand{\Kron}{\delta}
48 48 \newcommand{\ub}{\bullet}
49 49
50   -\title{RNApyro}
  50 +\title{An inside-outside algorithms for mutant RNAs with applications to error detections in structured RNAs}
51 51 \author{}
52 52 \date{}
53 53
3,560 benchmark/RF00001.seed.afa.txt
0 additions, 3,560 deletions not shown
9 benchmark/runbenchmark.sh
... ... @@ -1,9 +0,0 @@
1   -python ../scripts/benchmark.py -i RF00001_0.ref -o RF00001_0_alpha_50.out
2   -python ../scripts/benchmark.py -i RF00001_1.ref -o RF00001_1_alpha_50.out
3   -python ../scripts/benchmark.py -i RF00001_2.ref -o RF00001_2_alpha_50.out
4   -python ../scripts/benchmark.py -i RF00001_3.ref -o RF00001_3_alpha_50.out
5   -python ../scripts/benchmark.py -i RF00001_4.ref -o RF00001_4_alpha_50.out
6   -python ../scripts/benchmark.py -i RF00001_5.ref -o RF00001_5_alpha_50.out
7   -python ../scripts/benchmark.py -i RF00001_6.ref -o RF00001_6_alpha_50.out
8   -python ../scripts/benchmark.py -i RF00001_7.ref -o RF00001_7_alpha_50.out
9   -python ../scripts/benchmark.py -i RF00001_8.ref -o RF00001_8_alpha_50.out
9 benchmark/runtest.py
@@ -6,11 +6,12 @@ def main(nmut,alpha,prefix):
6 6 infile = "RF00001_%d.in" % numex
7 7 if os.path.exists(infile):
8 8 alphanorm = int (alpha * 100)
9   - commandline1="python ../src/RNAPyroEx.py RF00001_%d.in %d %.1f > RF00001_%d_alpha_%d.out" % (numex,nmut,alpha,numex,alphanorm)
  9 + commandline1="python ../src/RNAPyroEx.py RF00001_%d.in %d %.1f > RF00001_%d_nmut_%d_alpha_%d.out" % (numex,nmut,alpha,numex,nmut,alphanorm)
  10 + print commandline1
10 11 os.system(commandline1)
11   - commandline1="python ../scripts/benchmark.py -i RF00001_%d.ref -o RF00001_%d_alpha_%d.out" % (numex,numex,alphanorm)
12   - os.system(commandline1)
13   -
  12 + commandline2="python ../scripts/benchmark.py -i RF00001_%d.ref -o RF00001_%d_nmut_%d_alpha_%d.out" % (numex,numex,nmut,alphanorm)
  13 + print commandline2
  14 + os.system(commandline2)
14 15
15 16
16 17 ###############################################################################
8 benchmark/runtest.sh
... ... @@ -1,8 +0,0 @@
1   -python ../src/RNAPyroEx.py RF00001_1.in 10 0.5 > RF00001_1_alpha_50.out
2   -python ../src/RNAPyroEx.py RF00001_2.in 10 0.5 > RF00001_2_alpha_50.out
3   -python ../src/RNAPyroEx.py RF00001_3.in 10 0.5 > RF00001_3_alpha_50.out
4   -python ../src/RNAPyroEx.py RF00001_4.in 10 0.5 > RF00001_4_alpha_50.out
5   -python ../src/RNAPyroEx.py RF00001_5.in 10 0.5 > RF00001_5_alpha_50.out
6   -python ../src/RNAPyroEx.py RF00001_6.in 10 0.5 > RF00001_6_alpha_50.out
7   -python ../src/RNAPyroEx.py RF00001_7.in 10 0.5 > RF00001_7_alpha_50.out
8   -python ../src/RNAPyroEx.py RF00001_8.in 10 0.5 > RF00001_8_alpha_50.out
100 scripts/RfamParser.py
@@ -182,7 +182,7 @@ def clusterUnGapped(data):
182 182
183 183 #################################################################################
184 184
185   -def main(filename,nmut,idc,listflag,out):
  185 +def main(filename,nmut,idc,listflag,out,select,cluster):
186 186
187 187 seqline_re = re.compile("(\S+)(\s+)(\S+)");
188 188
@@ -242,11 +242,42 @@ def main(filename,nmut,idc,listflag,out):
242 242 sys.exit(1)
243 243
244 244 hcode=idMap['num2code'][idc]
245   - if out=="":
246   - listout = []
247   - listout.append(random.randint(0,len(cleandata[hcode])-1))
  245 + myRawCluster=cleandata[hcode]
  246 +
  247 + if cluster:
  248 + # cluster 80% of seq similarity using cd-hit
  249 + f = open('all.fasta','w')
  250 + for myid,myseq in myRawCluster.iteritems():
  251 + cleanseq,cleanssa = fitstruct2seq(myseq,info['consensus'],False)
  252 + print >>f, '> ' + str(myid)
  253 + print >>f, cleanseq
  254 + f.close()
  255 + commandline = ' ~/local/cd-hit/cd-hit-est -i all.fasta -o filter.fasta -c 0.8 -n 4 > /dev/null'
  256 + os.system(commandline)
  257 + myCleanCluster = {}
  258 + f = open('filter.fasta','r')
  259 + for line in f:
  260 + selected_ids = []
  261 + if line.startswith('>'):
  262 + id = line[1:].strip()
  263 + myCleanCluster[id] = myRawCluster[id]
  264 + f.close()
  265 + print len(myCleanCluster),'sequences selected'
  266 + else:
  267 + myCleanCluster = myRawCluster
  268 +
  269 +
  270 +
  271 + if select==-1:
  272 + listout = range(len(myCleanCluster))
  273 + elif select==0:
  274 + listout = [-1]
248 275 else:
249   - listout = range(len(cleandata[hcode]))
  276 + listout = []
  277 + while (len(listout)<select):
  278 + index = random.randint(0,len(myCleanCluster)-1)
  279 + if not index in listout:
  280 + listout.append(index)
250 281
251 282 for iseqout in listout:
252 283 ssamatch=True
@@ -258,10 +289,14 @@ def main(filename,nmut,idc,listflag,out):
258 289 fout_in = sys.stdout
259 290 fout_ref = sys.stdout
260 291 else:
261   - fout_in = open(out + "_" + str(iseqout) + ".in","w")
262   - fout_ref = open(out + "_" + str(iseqout) + ".ref","w")
263   -
264   - for myid,myseq in cleandata[hcode].iteritems():
  292 + if select!=0:
  293 + fout_in = open(out + "_" + str(iseqout) + ".in","w")
  294 + fout_ref = open(out + "_" + str(iseqout) + ".ref","w")
  295 + else:
  296 + fout_in = open(out + "_all.fasta","w")
  297 + fout_ref = open(out + "_all.ref","w")
  298 +
  299 + for myid,myseq in myCleanCluster.iteritems():
265 300 cleanseq,cleanssa = fitstruct2seq(myseq,info['consensus'],False)
266 301 if cmpt!=iseqout:
267 302 print >>fout_in, '> ' + str(myid)
@@ -272,23 +307,24 @@ def main(filename,nmut,idc,listflag,out):
272 307 cmpt+=1
273 308 if prevssa != '' and prevssa != cleanssa:
274 309 ssamatch=False
275   - print >>fout_in, '> structure'
276   - print >>fout_in, prevssa
277   - if out!="":
  310 + if select!=0:
  311 + print >>fout_in, '> structure'
  312 + print >>fout_in, prevssa
278 313 print >>fout_ref, '> structure'
279 314 print >>fout_ref, prevssa
  315 +
  316 + cleanseq = myCleanCluster[idout].replace('.','')
  317 + mutant = mutate(cleanseq,nmut)
  318 + print >>fout_in, '> ' + str(idout) + ' (' + str(nmut) + '-mutant) read'
  319 + print >>fout_in, mutant
  320 + if out!="":
  321 + print >>fout_ref, '> ' + str(idout) + ' (' + str(nmut) + '-mutant) read'
  322 + print >>fout_ref, mutant
  323 + print >>fout_ref, '> ' + str(idout) + ' target'
  324 + print >>fout_ref, cleanseq
  325 +
280 326 if not ssamatch:
281 327 print 'WARNING: Structure do not match'
282   -
283   - cleanseq = cleandata[hcode][idout].replace('.','')
284   - mutant = mutate(cleanseq,nmut)
285   - print >>fout_in, '> ' + str(idout) + ' (' + str(nmut) + '-mutant) read'
286   - print >>fout_in, mutant
287   - if out!="":
288   - print >>fout_ref, '> ' + str(idout) + ' (' + str(nmut) + '-mutant) read'
289   - print >>fout_ref, mutant
290   - print >>fout_ref, '> ' + str(idout) + ' target'
291   - print >>fout_ref, cleanseq
292 328
293 329 sys.exit(1)
294 330
@@ -297,7 +333,7 @@ def main(filename,nmut,idc,listflag,out):
297 333 if __name__ == '__main__':
298 334
299 335 try:
300   - opts, args = getopt.getopt(sys.argv[1:], "hf:m:n:lo:", ["help", "file=", "mut=", "id=", "list", "out="]);
  336 + opts, args = getopt.getopt(sys.argv[1:], "hf:m:n:lo:s:c", ["help", "file=", "mut=", "id=", "list", "out=","select=","cluster"]);
301 337 except getopt.GetoptError:
302 338 usage(sys.argv[0]);
303 339
@@ -306,6 +342,8 @@ def main(filename,nmut,idc,listflag,out):
306 342 id=0;
307 343 listflag=False;
308 344 out="";
  345 + select=-1;
  346 + cluster=False;
309 347
310 348 argStart=len(sys.argv);
311 349 for o,a in opts:
@@ -314,20 +352,26 @@ def main(filename,nmut,idc,listflag,out):
314 352 if o in ("-f", "--file"):
315 353 filename = a;
316 354 argStart-=2;
317   - if o in ("-m", "--file"):
  355 + if o in ("-m", "--mut"):
318 356 nmut = int(a);
319 357 argStart -=2;
320   - if o in ("-n", "--file"):
  358 + if o in ("-n", "--num"):
321 359 id = int(a);
322 360 argStart-=2;
323 361 if o in ("-l", "--list"):
324 362 listflag = True;
325 363 argStart-=1;
326 364 if o in ("-o", "--out"):
327   - out = a;
328   - argStart-=2;
  365 + out = a;
  366 + argStart-=2;
  367 + if o in ("-s", "--select"):
  368 + select = int(a);
  369 + argStart-=2;
  370 + if o in ("-c", "--cluster"):
  371 + cluster = True;
  372 + argStart-=1;
329 373
330   - main(filename,nmut,id,listflag,out);
  374 + main(filename,nmut,id,listflag,out,select,cluster);
331 375
332 376
333 377

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