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#!/usr/bin/env python
from os import getcwd, remove, rmdir, mkdir, path
import tempfile, shutil
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.dialign import Dialign
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
class GeneralSetUp(TestCase):
def setUp(self):
"""Dialign general setUp method for all tests"""
self.seqs1 = ['LDTAPCLFSDGSPQKAAYVLWDQTILQQDITPLPSHETHSAQKGELLALICGLRAAK',
'PDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALDAGTSAQRAELIALTQALKM',
'RPGLCQVFADATPTGWGLVMGHQRMRGTFSAPLPIHTAELLAACFARSRSGANIIGTDNSVV',
'MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIV']
self.labels1 = ['>HTL2','>MMLV', '>HEPB', '>ECOL']
self.lines1 = flatten(zip(self.labels1,self.seqs1))
self.out = \
"""
DIALIGN 2.2.1
*************
Program code written by Burkhard Morgenstern and Said Abdeddaim
e-mail contact: dialign (at) gobics (dot) de
Published research assisted by DIALIGN 2 should cite:
Burkhard Morgenstern (1999).
DIALIGN 2: improvement of the segment-to-segment
approach to multiple sequence alignment.
Bioinformatics 15, 211 - 218.
For more information, please visit the DIALIGN home page at
http://bibiserv.techfak.uni-bielefeld.de/dialign/
************************************************************
program call: dialign2-2 -fa -fn /tmp/di/seq1.fasta /tmp/di/seq1.txt
Aligned sequences: length:
================== =======
1) HTL2 57
2) MMLV 58
3) HEPB 62
4) ECOL 54
Average seq. length: 57.8
Please note that only upper-case letters are considered to be aligned.
Alignment (DIALIGN format):
===========================
HTL2 1 ldtapC-LFS DGS------P QKAAYVL--- ----WDQTIL QQDITPLPSH
MMLV 1 pdadhtw-YT DGSSLLQEGQ RKAGAAVtte teviWa---- KALDAG---T
HEPB 1 rpgl-CQVFA DAT------P TGWGLVM--- ----GHQRMR GTFSAPLPIH
ECOL 1 mlkqv-EIFT DGSCLGNPGP GGYGAIL--- ----RYRGRE KTFSAGytrT
0000000588 8882222229 9999999000 0000666666 6666633334
HTL2 37 ethSAQKGEL LALICGLRAa k--------- ---
MMLV 43 ---SAQRAEL IALTQALKm- ---------- ---
HEPB 37 t------AEL LAA-CFARSr sganiigtdn svv
ECOL 43 ---TNNRMEL MAAIv----- ---------- ---
0003333455 5533333300 0000000000 000
Sequence tree:
==============
Tree constructed using UPGMAbased on DIALIGN fragment weight scores
((HTL2 :0.130254MMLV :0.130254):0.067788(HEPB :0.120520ECOL :0.120520):0.077521);
"""
self.temp_dir = tempfile.mkdtemp()
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seq1.txt'),'w')
f.write('\n'.join(self.lines1))
f.close()
except OSError:
pass
class DialignTests(GeneralSetUp):
"""Tests for the Dialign application controller"""
def test_base_command(self):
"""Dialign BaseCommand should return the correct BaseCommand"""
c = Dialign()
self.assertEqual(c.BaseCommand,
''.join(['cd ','"%s/"; ' % getcwd(),'dialign2-2']))
c.Parameters["-fa"].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd ','"%s/"; ' % getcwd(),'dialign2-2 -fa']))
def test_align(self):
"""test aligning samples"""
c = Dialign(WorkingDir=self.temp_dir,
params={"-fn":path.join(self.temp_dir,"seq1.txt")})
c.Parameters["-fa"].on()
res = c(path.join(self.temp_dir, 'seq1.txt'))
align = "".join(res["Align"].readlines())
def test_cleaning_up(self):
"""not a test, just removes the temp files"""
shutil.rmtree(self.temp_dir)
if __name__ == '__main__':
main()
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