def parse_outfiles(pathfile):
complexes = {}
for line in open(pathfile):
words = line.strip().split()
if not len(words) == 2:
logging.warning('skipping non-conforming line: %s' % line)
continue
complex, path = words
print path
if not complexes.has_key(complex): complexes[complex] = {}
scandna = re_scandna.search(open(path).read())
if scandna:
chain, pos, type = re_scandna.search(open(path).read()).groups()
else:
chain, pos, type = ['NA', '0', 'NA']
DNApos = '%s.%s.%s' % (chain, pos, type)
print DNApos
if debugoutput: print complex, DNApos
if not complexes[complex].has_key(DNApos):
complexes[complex][DNApos] = {}
for line in open(path):
line = line.strip()
#match = re_substitution_new.match(line)
#if match:
# aa, chainpos, nataa, bound, binding, specbound, specbinding = match.groups()
match = re_subs_2012.match(line)
if match:
aa, chain, pos, nataa, bound, binding, specbound, specbinding = match.groups(
)
aa = get_oneletter(aa)
nataa = get_oneletter(nataa)
if debugoutput:
print aa, chain, pos, nataa
chainpos = '%s.%s' % (chain, pos)
if not complexes[complex][DNApos].has_key(chainpos):
complexes[complex][DNApos][chainpos] = Position(nataa)
complexes[ complex ][ DNApos ][ chainpos ].append( \
Substitution( aa, bound, binding, specbound, specbinding ) )
return complexes
def parse_outfiles(pathfile):
complexes = {}
for line in open(pathfile):
words = line.strip().split()
if not len(words) == 2:
logging.warning('skipping non-conforming line: %s' %line)
continue
complex,path = words
print path
if not complexes.has_key( complex ): complexes[ complex ] = {}
scandna = re_scandna.search( open(path).read() )
if scandna:
chain,pos,type = re_scandna.search( open(path).read() ).groups()
else:
chain,pos,type = ['NA','0','NA']
DNApos = '%s.%s.%s' %(chain,pos,type)
print DNApos
if debugoutput: print complex, DNApos
if not complexes[ complex ].has_key( DNApos ): complexes[ complex ][ DNApos ] = {}
for line in open(path):
line = line.strip()
#match = re_substitution_new.match(line)
#if match:
# aa, chainpos, nataa, bound, binding, specbound, specbinding = match.groups()
match = re_subs_2012.match(line)
if match:
aa, chain, pos, nataa, bound, binding, specbound, specbinding = match.groups()
aa = get_oneletter(aa)
nataa = get_oneletter(nataa)
if debugoutput:
print aa, chain, pos, nataa
chainpos = '%s.%s' %(chain,pos)
if not complexes[ complex ][ DNApos ].has_key(chainpos):
complexes[ complex ][ DNApos ][ chainpos ] = Position(nataa)
complexes[ complex ][ DNApos ][ chainpos ].append( \
Substitution( aa, bound, binding, specbound, specbinding ) )
return complexes
def dna(self):
os = ['> %s\n' % self.filename]
keys = self.residues.keys()
keys.sort()
for chainpos in keys:
res = self.residues[chainpos]
if not res.type in nucleic_acids: continue
letter = get_oneletter(res.type)
os.append(letter)
os.append('\n')
return string.join(os, '')
def dna(self):
os = ['> %s\n' %self.filename]
keys = self.residues.keys()
keys.sort()
for chainpos in keys:
res = self.residues[chainpos]
if not res.type in nucleic_acids: continue
letter = get_oneletter(res.type)
os.append(letter)
os.append('\n')
return string.join( os, '' )
def fasta(self):
os = ['> %s\n' % self.filename]
# note: self.residues is indexed by instances of ChainPos
keys = self.residues.keys()
keys.sort() # ChainPos knows how to sort itself
for chainpos in keys:
res = self.residues[chainpos]
# skip DNA
if res.type in nucleic_acids: continue
letter = get_oneletter(res.type)
os.append(letter)
os.append('\n')
return string.join(os, '')
def fasta( self ):
os = ['> %s\n' %self.filename]
# note: self.residues is indexed by instances of ChainPos
keys = self.residues.keys()
keys.sort() # ChainPos knows how to sort itself
for chainpos in keys:
res = self.residues[chainpos]
# skip DNA
if res.type in nucleic_acids: continue
letter = get_oneletter(res.type)
os.append(letter)
os.append('\n')
return string.join( os, '' )
