def test_indent_splitter(self):
"""indent_splitter should split lines at correct locations"""
#if lines have same indent, should not group together
lines = [
'abc xxx',
'def yyy'
]
self.assertEqual(list(indent_splitter(lines)),\
[[lines[0]], [lines[1]]])
#if second line is indented, should group with first
lines = [
'abc xxx',
' def yyy'
]
self.assertEqual(list(indent_splitter(lines)),\
[[lines[0], lines[1]]])
#if both lines indented but second is more, should group with first
lines = [
' abc xxx',
' def yyy'
]
self.assertEqual(list(indent_splitter(lines)),\
[[lines[0], lines[1]]])
#if both lines indented equally, should not group
lines = [
' abc xxx',
' def yyy'
]
self.assertEqual(list(indent_splitter(lines)), \
[[lines[0]], [lines[1]]])
#for more complex situation, should produce correct grouping
lines = [
' xyz', #0 -
' xxx', #1 -
' yyy', #2
' uuu', #3
' iii', #4
' qaz', #5 -
' wsx', #6 -
' az', #7
' sx', #8
' gb',#9
' bg', #10
' aaa', #11 -
]
self.assertEqual(list(indent_splitter(lines)), \
[[lines[0]], lines[1:5], [lines[5]], lines[6:11], [lines[11]]])
#real example from genbank file
lines = \
"""LOCUS LAAJ4821 16866 bp DNA MAM 23-AUG-2000
DEFINITION Loxodonta africana complete mitochondrial genomic sequence.
ACCESSION AJ224821
VERSION AJ224821.1 GI:3021460
KEYWORDS complete genome.
SOURCE African elephant.
ORGANISM Mitochondrion Loxodonta africana
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Proboscidea; Elephantidae; Loxodonta.
REFERENCE 1 (bases 1 to 16866)
AUTHORS Hauf,J., Waddell,P.J., Chalwatzis,N., Joger,U. and Zimmermann,F.K.
TITLE The complete mitochondrial genome sequence of the African elephant
(Loxodonta africana), phylogenetic relationships of Proboscidea to
other mammals and D-loop heteroplasmy""".split('\n')
self.assertEqual(list(indent_splitter(lines)), \
[[lines[0]],[lines[1]],[lines[2]],[lines[3]],[lines[4]],lines[5:9],\
lines[9:]])
s = ll.extract('ACGTGCAGTCAGTAGCAT')
# 123456789012345678
self.assertEqual(s, 'G'+'TGC'+'CAG')
#check a case where it wraps around
l5_a = Location(16)
l5_b = Location(4)
l5 = Location([l5_a,l5_b])
ll = LocationList([l5])
s = ll.extract('ACGTGCAGTCAGTAGCAT')
self.assertEqual(s, 'CATACGT')
if __name__ == '__main__':
from sys import argv
if len(argv) > 2 and argv[1] == 'x':
filename = argv[2]
lines = open(filename)
for i in indent_splitter(lines):
print '******'
print i[0]
for j in indent_splitter(i[1:]):
print '?????'
for line in j:
print line
else:
main()
