def test_build(self):
'Test building an NLMSA and querying results'
from pygr import seqdb, cnestedlist
genomedict = {}
for orgstr in msaSpeciesList:
genomedict[orgstr] = pygr.Data.getResource('TEST.Seq.Genome.' +
orgstr)
uniondict = seqdb.PrefixUnionDict(genomedict)
if smallSampleKey:
maflist = (os.path.join(mafDir, smallSampleKey + '.maf'), )
else:
maflist = glob.glob(os.path.join(mafDir, '*.maf'))
maflist.sort()
msaname = os.path.join(self.path, 'dm2_multiz15way')
# 500MB VERSION
msa1 = cnestedlist.NLMSA(msaname,
'w',
uniondict,
maflist,
maxlen=536870912,
maxint=22369620)
msa1.__doc__ = 'TEST NLMSA for dm2 multiz15way'
pygr.Data.addResource('TEST.MSA.UCSC.dm2_multiz15way', msa1)
pygr.Data.save()
msa = pygr.Data.getResource('TEST.MSA.UCSC.dm2_multiz15way')
outfileName = os.path.join(testInputDir,
'splicesite_dm2%s.txt' % smallSamplePostfix)
outputName = os.path.join(
testInputDir,
'splicesite_dm2%s_multiz15way.txt' % smallSamplePostfix)
newOutputName = os.path.join(self.path, 'splicesite_new1.txt')
tmpInputName = self.copyFile(outfileName)
tmpOutputName = self.copyFile(outputName)
outfile = open(newOutputName, 'w')
for lines in open(tmpInputName, 'r').xreadlines():
chrid, intstart, intend, nobs = string.split(lines.strip(), '\t')
intstart, intend, nobs = int(intstart), int(intend), int(nobs)
site1 = msa.seqDict['dm2' + '.' + chrid][intstart:intstart + 2]
site2 = msa.seqDict['dm2' + '.' + chrid][intend - 2:intend]
edges1 = msa[site1].edges()
edges2 = msa[site2].edges()
if len(edges1) == 0: # EMPTY EDGES
wlist = str(site1), 'dm2', chrid, intstart, intstart + 2, \
'', '', '', '', ''
outfile.write('\t'.join(map(str, wlist)) + '\n')
if len(edges2) == 0: # EMPTY EDGES
wlist = str(site2), 'dm2', chrid, intend - 2, intend, '', \
'', '', '', ''
outfile.write('\t'.join(map(str, wlist)) + '\n')
saveList = []
for src, dest, e in edges1:
if len(str(src)) != 2 or len(str(dest)) != 2:
continue
dotindex = (~msa.seqDict)[src].index('.')
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], \
(~msa.seqDict)[src][dotindex + 1:]
dotindex = (~msa.seqDict)[dest].index('.')
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], \
(~msa.seqDict)[dest][dotindex + 1:]
wlist = str(src), srcspecies, src1, src.start, src.stop, \
str(dest), destspecies, dest1, dest.start, dest.stop
saveList.append('\t'.join(map(str, wlist)) + '\n')
for src, dest, e in edges2:
if len(str(src)) != 2 or len(str(dest)) != 2:
continue
dotindex = (~msa.seqDict)[src].index('.')
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], \
(~msa.seqDict)[src][dotindex + 1:]
dotindex = (~msa.seqDict)[dest].index('.')
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], \
(~msa.seqDict)[dest][dotindex + 1:]
wlist = str(src), srcspecies, src1, src.start, src.stop, \
str(dest), destspecies, dest1, dest.start, dest.stop
saveList.append('\t'.join(map(str, wlist)) + '\n')
saveList.sort() # SORTED IN ORDER TO COMPARE WITH PREVIOUS RESULTS
for saveline in saveList:
outfile.write(saveline)
outfile.close()
md5old = hashlib.md5()
md5old.update(open(newOutputName, 'r').read())
md5new = hashlib.md5()
md5new.update(open(tmpOutputName, 'r').read())
assert md5old.digest() == md5new.digest()
# TEXT<->BINARY TEST
msafilelist = glob.glob(msaname + '*')
msa.save_seq_dict()
cnestedlist.dump_textfile(
msaname, os.path.join(self.path, 'dm2_multiz15way.txt'))
for filename in msafilelist:
os.remove(filename)
runPath = os.path.realpath(os.curdir)
os.chdir(self.path)
cnestedlist.textfile_to_binaries('dm2_multiz15way.txt')
os.chdir(runPath)
msa1 = cnestedlist.NLMSA(msaname, 'r')
msa1.__doc__ = 'TEST NLMSA for dm2 multiz15way'
pygr.Data.addResource('TEST.MSA.UCSC.dm2_multiz15way', msa1)
pygr.Data.save()
msa = pygr.Data.getResource('TEST.MSA.UCSC.dm2_multiz15way')
newOutputName = os.path.join(self.path, 'splicesite_new2.txt')
tmpInputName = self.copyFile(outfileName)
tmpOutputName = self.copyFile(outputName)
outfile = open(newOutputName, 'w')
for lines in open(tmpInputName, 'r').xreadlines():
chrid, intstart, intend, nobs = string.split(lines.strip(), '\t')
intstart, intend, nobs = int(intstart), int(intend), int(nobs)
site1 = msa.seqDict['dm2' + '.' + chrid][intstart:intstart + 2]
site2 = msa.seqDict['dm2' + '.' + chrid][intend - 2:intend]
edges1 = msa[site1].edges()
edges2 = msa[site2].edges()
if len(edges1) == 0: # EMPTY EDGES
wlist = str(site1), 'dm2', chrid, intstart, intstart + 2, \
'', '', '', '', ''
outfile.write('\t'.join(map(str, wlist)) + '\n')
if len(edges2) == 0: # EMPTY EDGES
wlist = str(site2), 'dm2', chrid, intend - 2, intend, '', \
'', '', '', ''
outfile.write('\t'.join(map(str, wlist)) + '\n')
saveList = []
for src, dest, e in edges1:
if len(str(src)) != 2 or len(str(dest)) != 2:
continue
dotindex = (~msa.seqDict)[src].index('.')
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], \
(~msa.seqDict)[src][dotindex + 1:]
dotindex = (~msa.seqDict)[dest].index('.')
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], \
(~msa.seqDict)[dest][dotindex + 1:]
wlist = str(src), srcspecies, src1, src.start, src.stop, \
str(dest), destspecies, dest1, dest.start, dest.stop
saveList.append('\t'.join(map(str, wlist)) + '\n')
for src, dest, e in edges2:
if len(str(src)) != 2 or len(str(dest)) != 2:
continue
dotindex = (~msa.seqDict)[src].index('.')
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], \
(~msa.seqDict)[src][dotindex + 1:]
dotindex = (~msa.seqDict)[dest].index('.')
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], \
(~msa.seqDict)[dest][dotindex + 1:]
wlist = str(src), srcspecies, src1, src.start, src.stop, \
str(dest), destspecies, dest1, dest.start, dest.stop
saveList.append('\t'.join(map(str, wlist)) + '\n')
saveList.sort() # SORTED IN ORDER TO COMPARE WITH PREVIOUS RESULTS
for saveline in saveList:
outfile.write(saveline)
outfile.close()
md5old = hashlib.md5()
md5old.update(open(newOutputName, 'r').read())
md5new = hashlib.md5()
md5new.update(open(tmpOutputName, 'r').read())
assert md5old.digest() == md5new.digest()
def test_build(self):
'Test building an NLMSA and querying results'
from pygr import seqdb, cnestedlist
genomedict = {}
for orgstr in msaSpeciesList:
genomedict[orgstr] = pygr.Data.getResource('TEST.Seq.Genome.'
+ orgstr)
uniondict = seqdb.PrefixUnionDict(genomedict)
if smallSampleKey:
axtlist = glob.glob(os.path.join(axtDir, '*' + os.sep
+ smallSampleKey + '.*.net.axt'))
else:
axtlist = glob.glob(os.path.join(axtDir, '*' + os.sep
+ '*.*.net.axt'))
axtlist.sort()
msaname = os.path.join(self.path, 'hg18_pairwise5way')
# 500MB VERSION
msa1 = cnestedlist.NLMSA(msaname, 'w', uniondict, axtFiles=axtlist,
maxlen=536870912, maxint=22369620)
msa1.__doc__ = 'TEST NLMSA for hg18 pairwise5way'
pygr.Data.addResource('TEST.MSA.UCSC.hg18_pairwise5way', msa1)
pygr.Data.save()
msa = pygr.Data.getResource('TEST.MSA.UCSC.hg18_pairwise5way')
outfileName = os.path.join(testInputDir, 'splicesite_hg18%s.txt'
% smallSamplePostfix)
outputName = os.path.join(testInputDir,
'splicesite_hg18%s_pairwise5way.txt'
% smallSamplePostfix)
newOutputName = 'splicesite_new1.txt'
tmpInputName = self.copyFile(outfileName)
tmpOutputName = self.copyFile(outputName)
tmpNewOutputName = os.path.join(self.path, newOutputName)
outfile = open(tmpNewOutputName, 'w')
for lines in open(tmpInputName, 'r').xreadlines():
chrid, intstart, intend, nobs = string.split(lines.strip(), '\t')
intstart, intend, nobs = int(intstart), int(intend), int(nobs)
site1 = msa.seqDict['hg18' + '.' + chrid][intstart:intstart + 2]
site2 = msa.seqDict['hg18' + '.' + chrid][intend - 2:intend]
edges1 = msa[site1].edges()
edges2 = msa[site2].edges()
if len(edges1) == 0: # EMPTY EDGES
wlist = str(site1), 'hg18', chrid, intstart, intstart + 2, \
'', '', '', '', ''
outfile.write('\t'.join(map(str, wlist)) + '\n')
if len(edges2) == 0: # EMPTY EDGES
wlist = str(site2), 'hg18', chrid, intend - 2, intend, '', \
'', '', '', ''
outfile.write('\t'.join(map(str, wlist)) + '\n')
saveList = []
for src, dest, e in edges1:
if len(str(src)) != 2 or len(str(dest)) != 2:
continue
dotindex = (~msa.seqDict)[src].index('.')
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], \
(~msa.seqDict)[src][dotindex + 1:]
dotindex = (~msa.seqDict)[dest].index('.')
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], \
(~msa.seqDict)[dest][dotindex + 1:]
wlist = str(src), srcspecies, src1, src.start, src.stop, \
str(dest), destspecies, dest1, dest.start, dest.stop
saveList.append('\t'.join(map(str, wlist)) + '\n')
for src, dest, e in edges2:
if len(str(src)) != 2 or len(str(dest)) != 2:
continue
dotindex = (~msa.seqDict)[src].index('.')
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], \
(~msa.seqDict)[src][dotindex + 1:]
dotindex = (~msa.seqDict)[dest].index('.')
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], \
(~msa.seqDict)[dest][dotindex + 1:]
wlist = str(src), srcspecies, src1, src.start, src.stop, \
str(dest), destspecies, dest1, dest.start, dest.stop
saveList.append('\t'.join(map(str, wlist)) + '\n')
saveList.sort() # SORTED IN ORDER TO COMPARE WITH PREVIOUS RESULTS
for saveline in saveList:
outfile.write(saveline)
outfile.close()
md5old = hashlib.md5()
md5old.update(open(tmpNewOutputName, 'r').read())
md5new = hashlib.md5()
md5new.update(open(tmpOutputName, 'r').read())
assert md5old.digest() == md5new.digest()
# TEXT<->BINARY TEST
msafilelist = glob.glob(msaname + '*')
msa.save_seq_dict()
cnestedlist.dump_textfile(msaname, os.path.join(self.path,
'hg18_pairwise5way.txt'))
for filename in msafilelist:
os.remove(filename)
runPath = os.path.realpath(os.curdir)
os.chdir(self.path)
cnestedlist.textfile_to_binaries('hg18_pairwise5way.txt')
os.chdir(runPath)
msa1 = cnestedlist.NLMSA(msaname, 'r')
msa1.__doc__ = 'TEST NLMSA for hg18 pairwise5way'
pygr.Data.addResource('TEST.MSA.UCSC.hg18_pairwise5way', msa1)
pygr.Data.save()
msa = pygr.Data.getResource('TEST.MSA.UCSC.hg18_pairwise5way')
newOutputName = 'splicesite_new2.txt'
tmpInputName = self.copyFile(outfileName)
tmpOutputName = self.copyFile(outputName)
tmpNewOutputName = os.path.join(self.path, newOutputName)
outfile = open(tmpNewOutputName, 'w')
for lines in open(tmpInputName, 'r').xreadlines():
chrid, intstart, intend, nobs = string.split(lines.strip(), '\t')
intstart, intend, nobs = int(intstart), int(intend), int(nobs)
site1 = msa.seqDict['hg18' + '.' + chrid][intstart:intstart + 2]
site2 = msa.seqDict['hg18' + '.' + chrid][intend - 2:intend]
edges1 = msa[site1].edges()
edges2 = msa[site2].edges()
if len(edges1) == 0: # EMPTY EDGES
wlist = str(site1), 'hg18', chrid, intstart, intstart + 2, \
'', '', '', '', ''
outfile.write('\t'.join(map(str, wlist)) + '\n')
if len(edges2) == 0: # EMPTY EDGES
wlist = str(site2), 'hg18', chrid, intend - 2, intend, '', \
'', '', '', ''
outfile.write('\t'.join(map(str, wlist)) + '\n')
saveList = []
for src, dest, e in edges1:
if len(str(src)) != 2 or len(str(dest)) != 2:
continue
dotindex = (~msa.seqDict)[src].index('.')
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], \
(~msa.seqDict)[src][dotindex + 1:]
dotindex = (~msa.seqDict)[dest].index('.')
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], \
(~msa.seqDict)[dest][dotindex + 1:]
wlist = str(src), srcspecies, src1, src.start, src.stop, \
str(dest), destspecies, dest1, dest.start, dest.stop
saveList.append('\t'.join(map(str, wlist)) + '\n')
for src, dest, e in edges2:
if len(str(src)) != 2 or len(str(dest)) != 2:
continue
dotindex = (~msa.seqDict)[src].index('.')
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], \
(~msa.seqDict)[src][dotindex + 1:]
dotindex = (~msa.seqDict)[dest].index('.')
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], \
(~msa.seqDict)[dest][dotindex + 1:]
wlist = str(src), srcspecies, src1, src.start, src.stop, \
str(dest), destspecies, dest1, dest.start, dest.stop
saveList.append('\t'.join(map(str, wlist)) + '\n')
saveList.sort() # SORTED IN ORDER TO COMPARE WITH PREVIOUS RESULTS
for saveline in saveList:
outfile.write(saveline)
outfile.close()
md5old = hashlib.md5()
md5old.update(open(tmpNewOutputName, 'r').read())
md5new = hashlib.md5()
md5new.update(open(tmpOutputName, 'r').read())
assert md5old.digest() == md5new.digest()
def build_test(self): # BUILD NLMSA AND QUERY RESULT COMPARISON
from pygr import seqdb, cnestedlist
genomedict = {}
for orgstr in msaSpeciesList:
genomedict[orgstr] = pygr.Data.getResource('TEST.Seq.Genome.' + orgstr)
uniondict = seqdb.PrefixUnionDict(genomedict)
import glob
maflist = glob.glob(os.path.join(mafDir, 'chr4h.maf')) # CHR4H TESTING
maflist.sort()
msaname = os.path.join(self.path, 'dm2_multiz15way')
msa1 = cnestedlist.NLMSA(msaname, 'w', uniondict, maflist, maxlen = 536870912, maxint = 22369620) # 500MB VERSION
msa1.save_seq_dict()
msa1.__doc__ = 'TEST NLMSA for dm2 multiz15way'
pygr.Data.addResource('TEST.MSA.UCSC.dm2_multiz15way', msa1)
pygr.Data.save()
msa = pygr.Data.getResource('TEST.MSA.UCSC.dm2_multiz15way')
outfileName = os.path.join(testInputDir, 'splicesite_dm2_chr4h.txt') # CHR4H TESTING
outputName = os.path.join(testInputDir, 'splicesite_dm2_chr4h_multiz15way.txt') # CHR4H TESTING
newOutputName = os.path.join(self.path, 'splicesite_new1.txt')
tmpInputName = self.copyFile(outfileName)
tmpOutputName = self.copyFile(outputName)
outfile = open(newOutputName, 'w')
for lines in open(tmpInputName, 'r').xreadlines():
chrid, intstart, intend, nobs = string.split(lines.strip(), '\t')
intstart, intend, nobs = int(intstart), int(intend), int(nobs)
site1 = msa.seqDict['dm2' + '.' + chrid][intstart:intstart+2]
site2 = msa.seqDict['dm2' + '.' + chrid][intend-2:intend]
edges1 = msa[site1].edges()
edges2 = msa[site2].edges()
if len(edges1) == 0: # EMPTY EDGES
wlist = str(site1), 'dm2', chrid, intstart, intstart+2, '', '', '', '', ''
outfile.write('\t'.join(map(str, wlist)) + '\n')
if len(edges2) == 0: # EMPTY EDGES
wlist = str(site2), 'dm2', chrid, intend-2, intend, '', '', '', '', ''
outfile.write('\t'.join(map(str, wlist)) + '\n')
saveList = []
for src, dest, e in edges1:
if len(str(src)) != 2 or len(str(dest)) != 2: continue
dotindex = (~msa.seqDict)[src].index('.')
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], (~msa.seqDict)[src][dotindex+1:]
dotindex = (~msa.seqDict)[dest].index('.')
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], (~msa.seqDict)[dest][dotindex+1:]
wlist = str(src), srcspecies, src1, src.start, src.stop, str(dest), \
destspecies, dest1, dest.start, dest.stop
saveList.append('\t'.join(map(str, wlist)) + '\n')
for src, dest, e in edges2:
if len(str(src)) != 2 or len(str(dest)) != 2: continue
dotindex = (~msa.seqDict)[src].index('.')
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], (~msa.seqDict)[src][dotindex+1:]
dotindex = (~msa.seqDict)[dest].index('.')
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], (~msa.seqDict)[dest][dotindex+1:]
wlist = str(src), srcspecies, src1, src.start, src.stop, str(dest), \
destspecies, dest1, dest.start, dest.stop
saveList.append('\t'.join(map(str, wlist)) + '\n')
saveList.sort() # SORTED IN ORDER TO COMPARE WITH PREVIOUS RESULTS
for saveline in saveList:
outfile.write(saveline)
outfile.close()
md5old = hashlib.md5()
md5old.update(open(newOutputName, 'r').read())
md5new = hashlib.md5()
md5new.update(open(tmpOutputName, 'r').read())
assert md5old.digest() == md5new.digest() # MD5 COMPARISON INSTEAD OF COMPARING EACH CONTENTS
# TEXT<->BINARY TEST
msafilelist = glob.glob(msaname + '*')
cnestedlist.dump_textfile(msaname, os.path.join(self.path, 'dm2_multiz15way.txt'))
for filename in msafilelist: os.remove(filename)
runPath = os.path.realpath(os.curdir)
os.chdir(self.path)
cnestedlist.textfile_to_binaries('dm2_multiz15way.txt')
os.chdir(runPath)
msa1 = cnestedlist.NLMSA(msaname, 'r')
msa1.__doc__ = 'TEST NLMSA for dm2 multiz15way'
pygr.Data.addResource('TEST.MSA.UCSC.dm2_multiz15way', msa1)
pygr.Data.save()
msa = pygr.Data.getResource('TEST.MSA.UCSC.dm2_multiz15way')
newOutputName = os.path.join(self.path, 'splicesite_new2.txt')
tmpInputName = self.copyFile(outfileName)
tmpOutputName = self.copyFile(outputName)
outfile = open(newOutputName, 'w')
for lines in open(tmpInputName, 'r').xreadlines():
chrid, intstart, intend, nobs = string.split(lines.strip(), '\t')
intstart, intend, nobs = int(intstart), int(intend), int(nobs)
site1 = msa.seqDict['dm2' + '.' + chrid][intstart:intstart+2]
site2 = msa.seqDict['dm2' + '.' + chrid][intend-2:intend]
edges1 = msa[site1].edges()
edges2 = msa[site2].edges()
if len(edges1) == 0: # EMPTY EDGES
wlist = str(site1), 'dm2', chrid, intstart, intstart+2, '', '', '', '', ''
outfile.write('\t'.join(map(str, wlist)) + '\n')
if len(edges2) == 0: # EMPTY EDGES
wlist = str(site2), 'dm2', chrid, intend-2, intend, '', '', '', '', ''
outfile.write('\t'.join(map(str, wlist)) + '\n')
saveList = []
for src, dest, e in edges1:
if len(str(src)) != 2 or len(str(dest)) != 2: continue
dotindex = (~msa.seqDict)[src].index('.')
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], (~msa.seqDict)[src][dotindex+1:]
dotindex = (~msa.seqDict)[dest].index('.')
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], (~msa.seqDict)[dest][dotindex+1:]
wlist = str(src), srcspecies, src1, src.start, src.stop, str(dest), \
destspecies, dest1, dest.start, dest.stop
saveList.append('\t'.join(map(str, wlist)) + '\n')
for src, dest, e in edges2:
if len(str(src)) != 2 or len(str(dest)) != 2: continue
dotindex = (~msa.seqDict)[src].index('.')
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], (~msa.seqDict)[src][dotindex+1:]
dotindex = (~msa.seqDict)[dest].index('.')
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], (~msa.seqDict)[dest][dotindex+1:]
wlist = str(src), srcspecies, src1, src.start, src.stop, str(dest), \
destspecies, dest1, dest.start, dest.stop
saveList.append('\t'.join(map(str, wlist)) + '\n')
saveList.sort() # SORTED IN ORDER TO COMPARE WITH PREVIOUS RESULTS
for saveline in saveList:
outfile.write(saveline)
outfile.close()
md5old = hashlib.md5()
md5old.update(open(newOutputName, 'r').read())
md5new = hashlib.md5()
md5new.update(open(tmpOutputName, 'r').read())
assert md5old.digest() == md5new.digest() # MD5 COMPARISON INSTEAD OF COMPARING EACH CONTENTS
def build_test(self): # BUILD NLMSA AND QUERY RESULT COMPARISON
from pygr import seqdb, cnestedlist
genomedict = {}
for orgstr in msaSpeciesList:
genomedict[orgstr] = pygr.Data.getResource("TEST.Seq.Genome." + orgstr)
uniondict = seqdb.PrefixUnionDict(genomedict)
if smallSampleKey:
maflist = (os.path.join(mafDir, smallSampleKey + ".maf"),)
else:
maflist = glob.glob(os.path.join(mafDir, "*.maf"))
maflist.sort()
msaname = os.path.join(self.path, "hg18_multiz28way")
msa1 = cnestedlist.NLMSA(msaname, "w", uniondict, maflist, maxlen=536870912, maxint=22369620) # 500MB VERSION
msa1.save_seq_dict()
msa1.__doc__ = "TEST NLMSA for hg18 multiz28way"
pygr.Data.addResource("TEST.MSA.UCSC.hg18_multiz28way", msa1)
pygr.Data.save()
msa = pygr.Data.getResource("TEST.MSA.UCSC.hg18_multiz28way")
outfileName = os.path.join(testInputDir, "splicesite_hg18%s.txt" % smallSamplePostfix)
outputName = os.path.join(testInputDir, "splicesite_hg18%s_multiz28way.txt" % smallSamplePostfix)
newOutputName = os.path.join(self.path, "splicesite_new1.txt")
tmpInputName = self.copyFile(outfileName)
tmpOutputName = self.copyFile(outputName)
outfile = open(newOutputName, "w")
for lines in open(tmpInputName, "r").xreadlines():
chrid, intstart, intend, nobs = string.split(lines.strip(), "\t")
intstart, intend, nobs = int(intstart), int(intend), int(nobs)
site1 = msa.seqDict["hg18" + "." + chrid][intstart : intstart + 2]
site2 = msa.seqDict["hg18" + "." + chrid][intend - 2 : intend]
edges1 = msa[site1].edges()
edges2 = msa[site2].edges()
if len(edges1) == 0: # EMPTY EDGES
wlist = str(site1), "hg18", chrid, intstart, intstart + 2, "", "", "", "", ""
outfile.write("\t".join(map(str, wlist)) + "\n")
if len(edges2) == 0: # EMPTY EDGES
wlist = str(site2), "hg18", chrid, intend - 2, intend, "", "", "", "", ""
outfile.write("\t".join(map(str, wlist)) + "\n")
saveList = []
for src, dest, e in edges1:
if len(str(src)) != 2 or len(str(dest)) != 2:
continue
dotindex = (~msa.seqDict)[src].index(".")
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], (~msa.seqDict)[src][dotindex + 1 :]
dotindex = (~msa.seqDict)[dest].index(".")
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], (~msa.seqDict)[dest][dotindex + 1 :]
wlist = (
str(src),
srcspecies,
src1,
src.start,
src.stop,
str(dest),
destspecies,
dest1,
dest.start,
dest.stop,
)
saveList.append("\t".join(map(str, wlist)) + "\n")
for src, dest, e in edges2:
if len(str(src)) != 2 or len(str(dest)) != 2:
continue
dotindex = (~msa.seqDict)[src].index(".")
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], (~msa.seqDict)[src][dotindex + 1 :]
dotindex = (~msa.seqDict)[dest].index(".")
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], (~msa.seqDict)[dest][dotindex + 1 :]
wlist = (
str(src),
srcspecies,
src1,
src.start,
src.stop,
str(dest),
destspecies,
dest1,
dest.start,
dest.stop,
)
saveList.append("\t".join(map(str, wlist)) + "\n")
saveList.sort() # SORTED IN ORDER TO COMPARE WITH PREVIOUS RESULTS
for saveline in saveList:
outfile.write(saveline)
outfile.close()
import md5
md5old = md5.new()
md5old.update(open(newOutputName, "r").read())
md5new = md5.new()
md5new.update(open(tmpOutputName, "r").read())
assert md5old.digest() == md5new.digest() # MD5 COMPARISON INSTEAD OF COMPARING EACH CONTENTS
# TEXT<->BINARY TEST
msafilelist = glob.glob(msaname + "*")
cnestedlist.dump_textfile(msaname, os.path.join(self.path, "hg18_multiz28way.txt"))
for filename in msafilelist:
os.remove(filename)
runPath = os.path.realpath(os.curdir)
os.chdir(self.path)
cnestedlist.textfile_to_binaries("hg18_multiz28way.txt")
os.chdir(runPath)
msa1 = cnestedlist.NLMSA(msaname, "r")
msa1.__doc__ = "TEST NLMSA for hg18 multiz28way"
pygr.Data.addResource("TEST.MSA.UCSC.hg18_multiz28way", msa1)
pygr.Data.save()
msa = pygr.Data.getResource("TEST.MSA.UCSC.hg18_multiz28way")
newOutputName = os.path.join(self.path, "splicesite_new2.txt")
tmpInputName = self.copyFile(outfileName)
tmpOutputName = self.copyFile(outputName)
outfile = open(newOutputName, "w")
for lines in open(tmpInputName, "r").xreadlines():
chrid, intstart, intend, nobs = string.split(lines.strip(), "\t")
intstart, intend, nobs = int(intstart), int(intend), int(nobs)
site1 = msa.seqDict["hg18" + "." + chrid][intstart : intstart + 2]
site2 = msa.seqDict["hg18" + "." + chrid][intend - 2 : intend]
edges1 = msa[site1].edges()
edges2 = msa[site2].edges()
if len(edges1) == 0: # EMPTY EDGES
wlist = str(site1), "hg18", chrid, intstart, intstart + 2, "", "", "", "", ""
outfile.write("\t".join(map(str, wlist)) + "\n")
if len(edges2) == 0: # EMPTY EDGES
wlist = str(site2), "hg18", chrid, intend - 2, intend, "", "", "", "", ""
outfile.write("\t".join(map(str, wlist)) + "\n")
saveList = []
for src, dest, e in edges1:
if len(str(src)) != 2 or len(str(dest)) != 2:
continue
dotindex = (~msa.seqDict)[src].index(".")
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], (~msa.seqDict)[src][dotindex + 1 :]
dotindex = (~msa.seqDict)[dest].index(".")
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], (~msa.seqDict)[dest][dotindex + 1 :]
wlist = (
str(src),
srcspecies,
src1,
src.start,
src.stop,
str(dest),
destspecies,
dest1,
dest.start,
dest.stop,
)
saveList.append("\t".join(map(str, wlist)) + "\n")
for src, dest, e in edges2:
if len(str(src)) != 2 or len(str(dest)) != 2:
continue
dotindex = (~msa.seqDict)[src].index(".")
srcspecies, src1 = (~msa.seqDict)[src][:dotindex], (~msa.seqDict)[src][dotindex + 1 :]
dotindex = (~msa.seqDict)[dest].index(".")
destspecies, dest1 = (~msa.seqDict)[dest][:dotindex], (~msa.seqDict)[dest][dotindex + 1 :]
wlist = (
str(src),
srcspecies,
src1,
src.start,
src.stop,
str(dest),
destspecies,
dest1,
dest.start,
dest.stop,
)
saveList.append("\t".join(map(str, wlist)) + "\n")
saveList.sort() # SORTED IN ORDER TO COMPARE WITH PREVIOUS RESULTS
for saveline in saveList:
outfile.write(saveline)
outfile.close()
import md5
md5old = md5.new()
md5old.update(open(newOutputName, "r").read())
md5new = md5.new()
md5new.update(open(tmpOutputName, "r").read())
assert md5old.digest() == md5new.digest() # MD5 COMPARISON INSTEAD OF COMPARING EACH CONTENTS
