allpy: 578bc81d5e62 sandbox/common.py

allpy

Added explanation for algorithm to add gapped line to base Alignment

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Thu, 16 Dec 2010 19:08:16 +0300
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1 def autoload(filename):

2 seqs = load(filename)

3 maxlen, seqs = measure(seqs)

4 stats, seqs = stat(maxlen, seqs)

5 seqs = color(maxlen, stats, seqs)

6 return seqs

8 def load(filename):

9 seqs = []

10 for block in open(filename).read().split('\n>'):

11 lines = block.split('\n')

12 name = lines[0].lstrip('>').strip()

13 body = "".join(lines[1:])

14 seqs.append((name, body))

15 return seqs

17 def measure(seqs):

18 maxlen = max([len(body) for name, body in seqs])

19 for i, (name, body) in enumerate(seqs):

20 body += "-" * (maxlen - len(body))

21 seqs[i] = name, body

22 return maxlen, seqs

24 def stat(maxlen, seqs):

25 stats = []

26 for x in xrange(maxlen):

27 stat = {}

28 for name, body in seqs:

29 char = body[x]

30 stat[char] = stat.get(char, 0) + 1

31 stats.append(stat)

32 return stats, seqs

34 def color(maxlen, stats, seqs):

35 full = len(seqs)

36 for i, (name, body) in enumerate(seqs):

37 ids = []

38 colors = []

39 for x in xrange(maxlen):

40 id = stats[x][body[x]] * 10 // full

41 norm = id * 256 // 10

42 color = '#%02x%02x%02x' % (norm, norm, norm)

43 ids.append(id)

44 colors.append(color)

45 seqs[i] = name, body, ids, colors

46 return seqs