def clustalw(inputfile="", seqs={}, remove_inputfile=True, params={}):
"""
"""
if inputfile and seqs:
raise "wrong usage!"
elif inputfile and not seqs:
# input is (hopefully) a filename
pass
elif not inputfile and seqs:
# input is (hopefully) sequences
# do a quick check if (sequence) strings are given
ARE_ALL_STRINGS = True
for header, seq in seqs.iteritems():
if not seq:
ARE_ALL_STRINGS = False
break
if not ARE_ALL_STRINGS:
raise Exception, "no sequence string(s) specified: %s" % seqs
# make a kind of semi-unique filename
uniqueid = get_random_string_tag()
inputfile = uniqueid + "_" + "_".join(
[_nonstringheader2stringheader(hdr) for hdr in seqs.keys()[0:5]])
inputfile += ".mfa"
writeMultiFasta(seqs, inputfile)
else:
# no input at all
raise "no input specified"
# okay, do the clustalw
fname_in = inputfile
# get hard-assigned parameters
paramstring = " ".join(["-%s=%s" % (k, v) for k, v in params.iteritems()])
ci, co = osPopen2("%s %s %s" %
(EXECUTABLE_CLUSTALW, fname_in, paramstring))
ci.close()
clwout = co.read()
co.close()
# abstract output filenames from input filename
if fname_in.find(".") == -1:
fname_out = fname_in + ".aln"
fname_tree = fname_in + ".dnd"
else:
_base = fname_in[0:fname_in.rfind(".")]
fname_out = _base + ".aln"
fname_tree = _base + ".dnd"
# parse alignment output file
_seqs, _alignment = _parse_clustalw(fname_out)
# and delete tmp. created files
osRemove(fname_out)
osRemove(fname_tree)
if remove_inputfile: osRemove(fname_in)
# check if the keys (headers) in _seqs correspont to those in seqs
# differences can occur when non-string headers are used
# and return
return (_seqs, _alignment)
def clustalw(inputfile="",seqs={},remove_inputfile=True,params={}):
"""
"""
if inputfile and seqs:
raise "wrong usage!"
elif inputfile and not seqs:
# input is (hopefully) a filename
pass
elif not inputfile and seqs:
# input is (hopefully) sequences
# do a quick check if (sequence) strings are given
ARE_ALL_STRINGS = True
for header, seq in seqs.iteritems():
if not seq:
ARE_ALL_STRINGS = False
break
if not ARE_ALL_STRINGS:
raise Exception, "no sequence string(s) specified: %s" % seqs
# make a kind of semi-unique filename
uniqueid = get_random_string_tag()
inputfile = uniqueid+"_"+"_".join([ _nonstringheader2stringheader(hdr) for hdr in seqs.keys()[0:5] ])
inputfile+=".mfa"
writeMultiFasta(seqs,inputfile)
else:
# no input at all
raise "no input specified"
# okay, do the clustalw
fname_in = inputfile
# get hard-assigned parameters
paramstring = " ".join([ "-%s=%s" % (k,v) for k,v in params.iteritems() ])
ci,co = osPopen2("%s %s %s" % (EXECUTABLE_CLUSTALW,fname_in, paramstring))
ci.close()
clwout = co.read()
co.close()
# abstract output filenames from input filename
if fname_in.find(".") == -1:
fname_out = fname_in+".aln"
fname_tree = fname_in+".dnd"
else:
_base = fname_in[0:fname_in.rfind(".")]
fname_out = _base+".aln"
fname_tree = _base+".dnd"
# parse alignment output file
_seqs,_alignment = _parse_clustalw(fname_out)
# and delete tmp. created files
osRemove(fname_out)
osRemove(fname_tree)
if remove_inputfile: osRemove(fname_in)
# check if the keys (headers) in _seqs correspont to those in seqs
# differences can occur when non-string headers are used
# and return
return (_seqs,_alignment)
def scan_branchpoint(self):
""" """
intronseq = self.dnasequence()
command = """%s -e %s""" % (EXECUTABE_SCAN_BRANCHPOINT, EXECUTABLE_SFM)
ci,co = osPopen2(command)
ci.write(">intron\n%s\n" % intronseq)
ci.close()
gfflines = parsegfftxt( co.read(), offset=self.start )
co.close()
orderable = [ ( int(line[3]), line ) for line in gfflines ]
orderable.sort()
orderable.reverse()
return [ gffline for pos,gffline in orderable ]
