allpy: test/freqs.py annotate

allpy

msf io: fix bugs * convert msf to temp fasta before each read and write * convert temp fasta to msf after each write

rev	line source
dendik@391	1 """Read alignment on stdin. Print CSV table of letter frequences on stdout.
dendik@391	2 """
dendik@391	3 from allpy import protein
dendik@391	4 from allpy.data import codes
dendik@391	5 import sys
dendik@391	6
dendik@391	7 sys.stderr.write(__doc__)
dendik@391	8
dendik@391	9 def freq(monomer):
dendik@391	10 amount = freqs.get(monomer)
dendik@391	11 if amount:
dendik@391	12 return 100.0 * amount / width
dendik@391	13 return ""
dendik@391	14
dendik@391	15 aln = protein.Alignment().append_file(sys.stdin)
dendik@391	16 monomers = [code1 for code1, modified, _, _ in codes.protein if not modified]
dendik@391	17 monomers += ["-"]
dendik@391	18 width = len(aln.sequences)
dendik@391	19 print ", ".join(map(str, monomers))
dendik@391	20 for column in aln.columns_as_lists():
dendik@391	21 freqs = {}
dendik@391	22 for monomer in column:
dendik@391	23 if monomer:
dendik@391	24 monomer = monomer.code1
dendik@391	25 else:
dendik@391	26 monomer = "-"
dendik@391	27 freqs[monomer] = freqs.get(monomer, 0) + 1
dendik@391	28 print ", ".join(map(str, map(freq, monomers)))