allpy: e70a40d7a993 test/usecase1.py

allpy

test_base: test Alignment creation & output

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Tue, 08 Feb 2011 21:03:10 +0300
parents	0435d9cc18d3
children	07b5351b0b56

line source

1 from allpy import protein

2 from allpy import processors

4 # Create sequences from string representation of sequence body

5 sequence_1 = protein.Sequence.from_string("mkstf", name="E2E4")

6 sequence_2 = protein.Sequence.from_string("mstkfff", description="Longer sequence")

8 # Create alignment from sequences

9 alignment = protein.Alignment()

10 alignment.append_sequence(sequence_1)

11 alignment.append_sequence(sequence_2)

12 alignment.process(processors.Muscle())

14 # For each sequence, print number of gaps and non-gaps in alignment

15 for row in alignment.rows():

16 gaps = 0

17 monomers = 0

18 for column in alignment.columns:

19 if column in row:

20 monomers += 1

21 else:

22 gaps += 1

23 print "%s: %s gaps, %s non-gaps" % (row.sequence.name, gaps, monomers)

25 # Print number of gaps in each column

26 gaps = []

27 for column in alignment.columns:

28 column_gaps = 0

29 for sequence in alignment.sequences:

30 if sequence not in column:

31 column_gaps += 1

32 gaps.append(column_gaps)

33 print " ".join(map(str, gaps))

35 # Write alignment to file

36 alignment.to_file(open("new_file.fasta", "w"))