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#!/usr/bin/env python
"""Test the spark based location parser for parsing GenBank locations.
"""
# test the feature table parser
from Bio.GenBank import LocationParser
# a list of strings to test
test_data = (
"467",
"23..400",
"join(544..589,688..1032)",
"1..1000",
"<345..500",
"<1..888",
"(102.110)",
"(23.45)..600",
"(122.133)..(204.221)",
"123^124",
"145^177",
"join(12..78,134..202)",
"complement(join(2691..4571,4918..5163))",
"join(complement(4918..5163),complement(2691..4571))",
"complement(34..(122.126))",
# The doc example allows "J00194:(100..202)" but not the BNF
"J00194:100..202",
"1..1509",
"<1..9",
"join(10..567,789..1320)",
"join(54..567,789..1254)",
"10..567",
"join(complement(<1..799),complement(5080..5120))",
"complement(1697..2512)",
"complement(4170..4829)",
# added a comma from the documentation
"join(complement(567..795),complement(21..349))",
"join(2004..2195,3..20)",
"<1..>336",
"394..>402",
"join(10000,10200..10450)",
# a few examples from from hum1
"join(AB001090.1:1669..1713)",
"join(AB001090.1:1669..1713,AB001091.1:85..196)",
"join(AB001090.1:1669..1713,AB001091.1:85..196,AB001092.1:40..248,AB001093.1:96..212,AB001094.1:71..223,AB001095.1:87..231,AB001096.1:33..211,AB001097.1:35..175,AB001098.1:213..395,AB001099.1:56..309,AB001100.1:54..196,AB001101.1:171..404,AB001102.1:160..378,210..217)",
"join(9106..9239,9843..9993,11889..11960,16575..16650)",
"join(<1..109,620..>674)",
"join(AB003599.1:<61..315,AB003599.1:587..874,47..325,425..>556)",
"join(<85..194,296..458,547..>653)",
# brad's examples
"5.12",
# this next location is in the BioPerl test records, but not in GenBank.
# I'm not sure if we really need to worry about it, but the parser
# won't handle the ugly thing right now.
# "J00194:(100..202),1..245,300..422"
# one-of syntax
"one-of(1888,1901)..2200",
"39..one-of(1956,2843)"
)
# test all of the data using Andrew's parser
for s in test_data:
print "--> Trying", s
print repr(LocationParser.parse(LocationParser.scan(s)))
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