def get_tup(s, prefix=None):
key, val = s.strip().split(':')
key = key.replace('-','_')
if prefix:
return '%s_%s' % (prefix, key), cast(val.strip())
else:
return key, cast(val.strip())
def parseNeedle(instr):
"""Extracts various data from output of needle with
-aformat3 markx10
return a dict of dicts keyed by string seqid.
adds keys q_al_enc, t_al_enc to each dict D
such that the following is true:
aligned = D['q_al_str']
degapped = aligned.replace('-','')
aligned == sequtil.decode_aln(degapped, eval(D['q_al_enc']))
"""
# do we have the correct format?
assert instr.find('Align_format: markx10') != -1
# remove footer
instr, _, _ = instr.rsplit('#',2)
# remove header
datablocks = instr.split('>>>')
datablocks.pop(0)
outputData = {}
for i, block in enumerate(datablocks):
# lop off the commented data and run parameters
block = block.split('#=====')[0]
block = block.split('>>#')[1]
# log.debug('\n%(i)i ------>\n%(block)s\n<------- %(i)i' % locals())
# consumes the first line
align_no, block = block.split('\n',1)
assert int(align_no) == i+1
header, query, target = block.split('>')
# get the sequence names
q_name, query = query.split('..',1)
t_name, target = target.split('..',1)
this_key = tuple(sorted([q_name.strip(), t_name.strip()]))
## process the header info
d = dict([get_tup(e) for e in header.split(';') if e.strip()])
## process the query and target
q_data = dict([get_tup(e, 'q') for e in query.split(';') if e.strip()])
t_data = dict([get_tup(e, 't') for e in target.split(';') if e.strip()])
d['align_num'] = i
## add data
d['q_name'] = q_name
d.update(q_data)
d['t_name'] = t_name
d.update(t_data)
d['q_al_display_start'], q_al_str = d['q_al_display_start'].split('\n',1)
d['t_al_display_start'], t_al_str = d['t_al_display_start'].split('\n',1)
d['q_al_str'] = q_al_str.replace('\n','').upper()
d['t_al_str'] = t_al_str.replace('\n','').upper()
d['q_al_enc'] = `sequtil.encode_aln(d['q_al_str'], gapchar='-', self_check=True)`
d['t_al_enc'] = `sequtil.encode_aln(d['t_al_str'], gapchar='-', self_check=True)`
assert not outputData.has_key(this_key)
d = dict((k,cast(v)) for k,v in d.items())
add_calculated_values(d)
outputData[this_key] = d
# log.debug('output data:')
# log.debug(pprint.pformat(outputData))
return outputData