def getpos_pdb(fname,answer):
"""
>>> fname = "../dataset/mono.d4.0.nxg.miss.fasta"
>>> answer = "../dataset/answer_mono.d4.0.nxg.txt"
>>> getpos_pdb(fname,answer).next()
None
"""
# get Residue from PDB (use residue no. )
def insert(idch,lpos):
"""
Seq number of insertion is [seq number]A.
#example:
### Insertion residue exits between 3 ~ 4. ###
... 1 2 3 3A 4 5 6 ...
"""
def _f(pos,points):
# remain the insertion points exits previous residue.
_points = [i for i in points if i <= pos]
return pos - len(_points)
inserts = {"1kj2B":[30]}
if inserts.has_key(idch):
lpos = [_f(i,inserts[idch]) for i in lpos]
return idch,lpos
else:
return idch,lpos
pdbids = [idch for idch,start,seq in seq2feature.fasta2seq(fname)]
# For insertion code #
with open(answer) as fp:
for rec in (line.strip().split()
for line in iter(fp.readline,"")):
idch,lpos = rec[0],rec[1:]
if idch not in pdbids:
# make dataset only representive.
continue
# remove redunduncy.
lpos = list(set([int(i) for i in lpos]))
### For Insertion code. ###
idch,lpos = insert(idch,lpos)
## For Debugg ##
if len(lpos) == 0:
pass
#print idch
# lcut return {nsq:res} if window == 0
yield idch,{k:v.values()[0] for k,v in
protdb.lcut(idch[:4],idch[4],lpos,
window=0,is_rollback=True).items()}
def getpos_fasta(fname,answer):
"""
>>> fname = "../dataset/mono.d4.0.nxg.miss.fasta"
>>> answer = "../dataset/answer_mono.d4.0.nxg.txt"
>>> getpos_fasta(fname,answer).next()
None
"""
# yielding answer position residue
ans_sgr = util.ans(answer)
ans2int = lambda idch,pos: 1 if ans_sgr.isans(idch,pos) else -1
for idch,start,seq in seq2feature.fasta2seq(fname):
idch = idch.strip()
yield idch,{pos + start:res for pos,res in enumerate(seq)
if ans_sgr.isans(idch,start + pos)}
