allpy: 6ad74e2ba3d2 test/usecase1.py

allpy

Fixed bug: fasta reader broke on files with Windows EOLs broke

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Fri, 17 Dec 2010 20:54:35 +0300
parents	38888b46c342
children	dd94230c6f08

line source

1 from allpy import protein

3 # Create sequences from string representation of sequence body

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

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

7 # Create alignment from sequences

8 alignment = protein.Alignment()

9 alignment.append_sequence(sequence_1)

10 alignment.append_sequence(sequence_2)

11 alignment.realign("muscle")

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

14 for row in alignment.rows():

15 gaps = 0

16 monomers = 0

17 for column in alignment.columns:

18 if column in row:

19 monomers += 1

20 else:

21 gaps += 1

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

24 # Print number of gaps in each column

25 gaps = []

26 for column in alignment.columns:

27 column_gaps = 0

28 for sequence in alignment.sequences:

29 if sequence not in column:

30 column_gaps += 1

31 gaps.append(column_gaps)

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

34 # Write alignment to file

35 alignment.to_fasta(open("new_file.fasta", "w"))