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()