allpy: 9369dbad919d sandbox/common.py

allpy

view sandbox/common.py @ 251:9369dbad919d

Incompatible changes to Monomer interfaces. This branch does not work! - (!!) only changed allpy._monomer, not uses - (!!) removed (temporarily) classes for specific monomer types (DNAMonomer, etc) - refurbished allpy.data.AAcodes to allpy.data.codes with much cleaner interface - refurbished allpy._monomer for simplicity and more friendly interface Now it will (someday) be possible to say: a = Monomer.from_name("alanine") b = protein.Monomer.from_code1("a") c = protein.MonomerType.from_code3("ala") d = dna.Monomer.from_code3("DA") but impossible to say: d = protein.Monomer.from_code3("DA")

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Mon, 13 Dec 2010 20:12:11 +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