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#!/usr/bin/env python
"""Tests of MageParser
"""
from cogent.util.unit_test import TestCase, main
from cogent.parse.mage import MageParser, MageGroupFromString,\
MageListFromString, MagePointFromString
from cogent.format.mage import MagePoint, MageList, MageGroup, Kinemage
__author__ = "Sandra Smit"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Sandra Smit", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Sandra Smit"
__email__ = "sandra.smit@colorado.edu"
__status__ = "Production"
class MageGroupFromStringTests(TestCase):
"""Tests for the MageGroupFromString function"""
def test_MageGroupFromString(self):
"""MageGroupFromString should fill itself from string correctly"""
f = MageGroupFromString
group = f('@group {GA manifold} off')
self.assertEqual(str(group),'@group {GA manifold} off')
group = f('@group {dna} recessiveon off dominant '+\
'master= {master name} nobutton clone={clone_name}\n')
self.assertEqual(str(group),\
'@group {dna} off nobutton recessiveon dominant '+\
'master={master name} clone={clone_name}')
group = f(\
'@subgroup {max_group} recessiveon instance= {inst \tname} lens')
self.assertEqual(str(group),
'@subgroup {max_group} recessiveon lens instance={inst \tname}')
group = f('@subgroup {Pos 1} on')
self.assertEqual(str(group), '@subgroup {Pos 1}')
def test_MageGroupFromString_wrong(self):
"""MageGroupFromString should fail on wrong input"""
f = MageGroupFromString
# unknown keyword
self.assertRaises(KeyError,f,'@group {GA manifold} of')
# wrong nesting
self.assertRaises(ValueError,f,'@group {GA manifold} master={blabla')
class MageListFromStringTests(TestCase):
"""Tests for the MageListFromString function"""
def test_MageListFromString(self):
"""MageListFromString should fill itself from string correctly"""
f = MageListFromString
l = f('@dotlist {label} color= green radius=0.3 off \t nobutton\n' )
self.assertEqual(str(l),\
'@dotlist {label} off nobutton color=green radius=0.3')
l = f('@vectorlist')
self.assertEqual(str(l),'@vectorlist')
l = f('@balllist off angle= 4 width= 2 face=something '+\
'font=\tother size= 3')
self.assertEqual(str(l),'@balllist off angle=4 width=2 '+\
'face=something font=other size=3')
l = f('@dotlist {} on nobutton color=sky')
self.assertEqual(str(l),'@dotlist nobutton color=sky')
def test_MageListFromString_wrong(self):
"""MageListFromString should fail on wrong input"""
f = MageListFromString
self.assertRaises(ValueError,f,
'@somelist {label} color= green radius=0.3 off \t nobutton\n')
self.assertRaises(KeyError,f,
'@vectorlist {label} colors= green radius=0.3 off \t nobutton\n')
class MagePointFromStringTests(TestCase):
"""Tests of the MagePointFromString factory function."""
def test_MagePointFromString(self):
"""MagePoint should fill itself from string correctly"""
m = MagePointFromString('{construction}width5 0.000 0.707 -1.225\n')
self.assertEqual(str(m), \
'{construction} width5 ' + ' '.join(map(str, [0.0,0.707,-1.225])))
m = MagePointFromString('3, 4, 5')
self.assertEqual(str(m), ' '.join(map(str, map(float, [3, 4, 5]))))
m = MagePointFromString('{b2}P 0.000 0.000 0.000')
self.assertEqual(str(m), '{b2} P ' + \
' '.join(map(str, map(float, [0,0,0]))))
m = MagePointFromString('P -2650192.000 4309510.000 3872241.000')
self.assertEqual(str(m), 'P ' + \
' '.join(map(str, map(float, [-2650192,4309510,3872241]))))
m = MagePointFromString('{"}P -2685992.000 5752262.000 535328.000')
self.assertEqual(str(m), '{"} P ' + \
' '.join(map(str, map(float, [-2685992,5752262,535328]))))
m = MagePointFromString('{ 1, d, 0 } P 1.000, 0.618, 0.000')
self.assertEqual(str(m), '{ 1, d, 0 } P ' + \
' '.join(map(str, map(float, [1.000, 0.618, 0.000]))))
m = MagePointFromString('{"}width1 -1.022 0.969 -0.131')
self.assertEqual(str(m), '{"} width1 ' + \
' '.join(map(str, map(float, [-1.022,0.969,-0.131]))))
m = MagePointFromString(\
'width3 {A label with spaces } A blue r=3.7 5, 6, 7')
self.assertEqual(m.Width, 3)
self.assertEqual(m.Label, 'A label with spaces ')
self.assertFloatEqual(m.Coordinates, [5, 6, 7])
self.assertFloatEqual(m.Radius, 3.7)
self.assertEqual(m.Color, 'blue')
self.assertEqual(m.State, 'A')
self.assertEqual(str(m),'{A label with spaces } A blue width3 r=3.7 ' +\
' '.join(map(str, map(float, [5, 6, 7]))))
class MageParserTests(TestCase):
"""Tests for the MageParser"""
def test_MageParser(self):
"""MageParser should work on valid input"""
obs = str(MageParser(EXAMPLE_1.split('\n'))).split('\n')
exp = EXP_EXAMPLE_1.split('\n')
assert len(obs) == len(exp)
#first check per line; easier for debugging
for x in range(len(obs)):
self.assertEqual(obs[x],exp[x])
#double check to see if the whole string is the same
self.assertEqual(str(MageParser(EXAMPLE_1.split('\n'))),EXP_EXAMPLE_1)
EXAMPLE_1 = """
@text
Kinemage of ribosomal RNA SSU Bacteria
@kinemage1
@caption
SSU Bacteria secondary structure elements
@viewid {oblique}
@zoom 1.05
@zslab 467
@center 0.500 0.289 0.204
@matrix
-0.55836 -0.72046 -0.41133 0.82346 -0.42101 -0.38036 0.10085 -0.55108
0.82833
@2viewid {top}
@2zoom 0.82
@2zslab 470
@2center 0.500 0.289 0.204
@2matrix
-0.38337 0.43731 -0.81351 0.87217 -0.11840 -0.47466 -0.30389 -0.89148
-0.33602
@3viewid {side}
@3zoom 0.82
@3zslab 470
@3center 0.500 0.289 0.204
@3matrix
-0.49808 -0.81559 -0.29450 0.86714 -0.46911 -0.16738 -0.00164 -0.33875
0.94088
@4viewid {End-O-Line}
@4zoom 1.43
@4zslab 469
@4center 0.500 0.289 0.204
@4matrix
0.00348 -0.99984 -0.01766 0.57533 -0.01244 0.81784 -0.81792 -0.01301
0.57519
@perspective
@fontsizelabel 24
@onewidth
@zclipoff
@localrotation 1 0 0 .5 .866 0 .5 .289 .816
@group {Tetrahedron}
@vectorlist {Edges} color=white nobutton
P {0 0 0} 0 0 0
0.5 0 0
{1 0 0} 1 0 0
0.5 0.5 0
{0 1 0} 0 1 0
P 0 0 0
0 0.5 0
{0 1 0} 0 1 0
0 0.5 0.5
{0 0 1} 0 0 1
P 0 0 0
0 0 0.5
{0 0 1} 0 0 1
0.5 0 0.5
{1 0 0} 1 0 0
@labellist {labels} color=white nobutton
{U} 0 0 0
{A} 1.1 0 0
{C} 0 1.05 0
{G} 0 0 1.08
@group {Lines}
@vectorlist {A=U&C=G} color= green off
P 0 0.5 0.5
.1 .4 .4
.25 .25 .25
.4 .1 .1
L 0.500, 0.000, 0.000
@vectorlist {A=G&C=U} color= red off
P 0.5 0 0.5
.25 .25 .25
L 0, 0.500, 0.000
@vectorlist {A=C&G=U} color= red off
P 0.5 0.5 0
.25 .25 .25
L 0.000, 0.000, 0.500
@group {SSU Bacteria} recessiveon
@dotlist {Stem} radius=0.03 color= orange
{a} .3 .1 .4
{b} r=.2 .1 .1 .1
@balllist {Junction} radius=.04
{c} red .4 .4 0
{}\t r=.1 green .3 .2 .1
@group {empty group}
@group {Nested}
@subgroup {First}
@spherelist color=\tpurple
{e} .1 .1 .1
@subgroup {Second} master=\t {master name}
@labellist {labels}
{U} 0 0 0
{A} 1.1 0 0
{C} 0 1.05 0
{G} 0 0 1.08
"""
EXP_EXAMPLE_1 =\
"""@kinemage 1
@viewid {oblique}
@zoom 1.05
@zslab 467
@center 0.500 0.289 0.204
@matrix
-0.55836 -0.72046 -0.41133 0.82346 -0.42101 -0.38036 0.10085 -0.55108
0.82833
@2viewid {top}
@2zoom 0.82
@2zslab 470
@2center 0.500 0.289 0.204
@2matrix
-0.38337 0.43731 -0.81351 0.87217 -0.11840 -0.47466 -0.30389 -0.89148
-0.33602
@3viewid {side}
@3zoom 0.82
@3zslab 470
@3center 0.500 0.289 0.204
@3matrix
-0.49808 -0.81559 -0.29450 0.86714 -0.46911 -0.16738 -0.00164 -0.33875
0.94088
@4viewid {End-O-Line}
@4zoom 1.43
@4zslab 469
@4center 0.500 0.289 0.204
@4matrix
0.00348 -0.99984 -0.01766 0.57533 -0.01244 0.81784 -0.81792 -0.01301
0.57519
@perspective
@fontsizelabel 24
@onewidth
@zclipoff
@localrotation 1 0 0 .5 .866 0 .5 .289 .816
@text
Kinemage of ribosomal RNA SSU Bacteria
@caption
SSU Bacteria secondary structure elements
@group {Tetrahedron}
@vectorlist {Edges} nobutton color=white
{0 0 0} P 0.0 0.0 0.0
0.5 0.0 0.0
{1 0 0} 1.0 0.0 0.0
0.5 0.5 0.0
{0 1 0} 0.0 1.0 0.0
P 0.0 0.0 0.0
0.0 0.5 0.0
{0 1 0} 0.0 1.0 0.0
0.0 0.5 0.5
{0 0 1} 0.0 0.0 1.0
P 0.0 0.0 0.0
0.0 0.0 0.5
{0 0 1} 0.0 0.0 1.0
0.5 0.0 0.5
{1 0 0} 1.0 0.0 0.0
@labellist {labels} nobutton color=white
{U} 0.0 0.0 0.0
{A} 1.1 0.0 0.0
{C} 0.0 1.05 0.0
{G} 0.0 0.0 1.08
@group {Lines}
@vectorlist {A=U&C=G} off color=green
P 0.0 0.5 0.5
0.1 0.4 0.4
0.25 0.25 0.25
0.4 0.1 0.1
L 0.5 0.0 0.0
@vectorlist {A=G&C=U} off color=red
P 0.5 0.0 0.5
0.25 0.25 0.25
L 0.0 0.5 0.0
@vectorlist {A=C&G=U} off color=red
P 0.5 0.5 0.0
0.25 0.25 0.25
L 0.0 0.0 0.5
@group {SSU Bacteria} recessiveon
@dotlist {Stem} color=orange radius=0.03
{a} 0.3 0.1 0.4
{b} r=0.2 0.1 0.1 0.1
@balllist {Junction} radius=.04
{c} red 0.4 0.4 0.0
{} green r=0.1 0.3 0.2 0.1
@group {empty group}
@group {Nested}
@subgroup {First}
@spherelist color=purple
{e} 0.1 0.1 0.1
@subgroup {Second} master={master name}
@labellist {labels}
{U} 0.0 0.0 0.0
{A} 1.1 0.0 0.0
{C} 0.0 1.05 0.0
{G} 0.0 0.0 1.08"""
if __name__ == "__main__":
main()
|
