def main(args):
for f in args:
mbrFile,mbrPath = mystemp(suffix='.mbr')
fStub,fExt = os.path.splitext(f)
oFile = safeOFW('.'.join((fStub,'Hg18rm',fExt[1:])),'w')
print os.curdir
try:
subprocess.call(['megablast', '-m8', '-i',f,
'-d', hg18db,'-o', mbrPath])
humanQrys =B.m8TitleSet(mbrPath,qrySet=True)
for rec in fasta.generalIterator(f):
if len(humanQrys)==0:
break
if rec.title in humanQrys:
continue
else:
print >> oFile, rec
oFile.close()
except BaseException:
os.unlink(oFile.name)
print '%s -failed' %f
raise
finally:
os.unlink(mbrPath)
return 0
def main(args,maxMismatch=0,seedLen=36):
for f in args:
bowtieFile,bowtiePath = mystemp(suffix='.bowtie')
fStub,fExt = os.path.splitext(f)
oFile = safeOFW('.'.join((fStub,'Hg18rm',fExt[1:])),'w')
print os.curdir
try:
subprocess.call(['bowtie', '-f','-l',str(seedLen),'-n',str(maxMismatch),
hg18db, f, bowtiePath])
humanQrys =B.readTitleSet(bowtiePath)
if len(humanQrys)==0:
raise RuntimeError, "No Alignments found"
for rec in fasta.generalIterator(f):
if rec.title in humanQrys:
continue
else:
print >> oFile, rec
oFile.close()
except BaseException:
os.unlink(oFile.name)
print '%s -failed' %f
raise
finally:
os.unlink(bowtiePath)
return 0
def main(args):
fFile= args[-1]
titles=set(args[:-1])
for rec in fasta.generalIterator(fFile):
if rec.title in titles:
print rec
return 0
def somethingUsefull(args, oFile):
for f in args:
for rec in fasta.generalIterator(f):
if fasta.isAllDRNA(rec.sequence):
print >> oFile, rec
else:
n = 0
for uaSeq in fasta.expandAmbiguousSequence(rec.sequence):
uaTitle = rec.title + "|ua%s" % n
n += 1
print >> oFile, rec.__class__(title=uaTitle, sequence=uaSeq)
def main(args):
for rec in fasta.generalIterator(args[0]):
rec.title+='|%.1f' % rec.Tm()
print rec
return 0