def parseContents(contents, section):
if section==1:
readNames = []
contained = {}
for line in contents:
if line[0]!=' ':
readNames.append(line.strip())
else:
tokens = line.strip().split()
readNames.append(tokens[0])
contained[tokens[0]] = tokens[-1]
return readNames, contained
elif section==2:
aln = Alignment()
iSeqStart = -1
L = 0
for line in contents:
if line==Tokens.ruler:
# Ruler line
iSeqStart = line.find('.')-4 # = 22 ???
if iSeqStart!=22: print "!!! iSeqStart:", iSeqStart
elif line[0]==' ':
# Separator line
pass
else:
line = line.rstrip()
name = line[0:iSeqStart].strip()
seq = line[iSeqStart:]
if name!='consensus':
if not name in aln.seqDict:
seq = seq.replace(' ', '.')
seq = '.'*L + seq
aln.append(name, seq)
else:
aln.append(name, seq)
L = len(aln['consensus'])
# Pad short sequences with '.'
for name in aln:
aln[name] = aln[name] + '.'*(L-len(aln[name]))
return aln
else:
raise Exception("cap3.parseContents")