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 NT_016354 92123751 bp DNA linear CON 29-AUG-2006
DEFINITION H**o sapiens chromosome 4 genomic contig, reference assembly.
ACCESSION NT_016354 NT_006109 NT_006204 NT_006245 NT_006302 NT_006371
NT_006397 NT_016393 NT_016589 NT_016599 NT_016606 NT_022752
NT_022753 NT_022755 NT_022760 NT_022774 NT_022797 NT_022803
NT_022846 NT_022960 NT_025694 NT_028147 NT_029273 NT_030643
NT_030646 NT_030662 NT_031780 NT_031781 NT_031791 NT_034703
NT_034705 NT_037628 NT_037629 NT_079512
VERSION NT_016354.18 GI:88977422
KEYWORDS .
SOURCE H**o sapiens (human)
ORGANISM H**o sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; H**o.
?
REFERENCE 2 (bases 1 to 92123751)
AUTHORS International Human Genome Sequencing Consortium.
TITLE Finishing the euchromatic sequence of the human genome""".split(
"\n")
self.assertEqual(
list(indent_splitter(lines)),
[
[lines[0]],
[lines[1]],
lines[2:8],
[lines[8]],
[lines[9]],
lines[10:15],
[lines[15]],
lines[16:],
],
)
l3_b = Location(12)
l3 = Location([l3_a, l3_b])
ll = LocationList([l, l2, l3])
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()
