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--[[
Copyright (c) 2011 Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
Copyright (c) 2011 Center for Bioinformatics, University of Hamburg
Permission to use, copy, modify, and distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]
-- testing the Lua bindings for the Encseq class
dnaseqfile = arg[1].."/lua_dnaseq.fas"
aaseqfile = arg[1].."/lua_aaseq.fas"
dseq1 = "agtccagctgtcagctagcgggcccgatgatatttt"
dseq2 = "gtgctgtac"
aaseq1 = "MVHFTAEEKAAVTSLWSKMNVEEAGGEALG"
aaseq2 = "KMNAVE"
idxsuffixes = {'esq','des','ssp','sds','al1'}
function run_test_num_seqs(es)
assert(es:num_of_sequences() == 2)
end
function run_test_num_files(es)
assert(es:num_of_files() == 1)
end
function run_test_descriptions(es)
rval, err = pcall(GenomeTools_encseq.description, es, 2)
assert(not rval)
assert(string.find(err, "cannot exceed number of sequences"))
end
function run_test_total_length(es)
assert(es:total_length() == 46)
end
function run_test_total_length_protein(es)
assert(es:total_length() == 37)
end
function run_test_get_encoded_char(es, seq1, seq2)
local a = es:alphabet()
for i=1,seq1:len() do
assert(a:decode(es:get_encoded_char(i-1, 0)) == seq1:sub(i,i))
assert(es:get_decoded_char(i-1, 0) == seq1:sub(i,i))
end
for i=seq2:len(),1,-1 do
assert(a:decode(es:get_encoded_char(seq2:len()-i, 1)) == seq2:sub(i,i))
assert(es:get_decoded_char(seq2:len()-i, 1) == seq2:sub(i,i))
end
rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 100, 0)
assert(not rval)
assert(string.find(err, "cannot exceed"))
rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 10, 6)
assert(not rval)
assert(string.find(err, "invalid readmode"))
end
function run_test_seq_startpos(es)
assert(es:seqstartpos(0) == 0)
assert(es:seqstartpos(1) == 37)
rval, err = pcall(GenomeTools_encseq.seqstartpos, es, 2)
assert(not rval)
assert(string.find(err, "cannot exceed number of sequences"))
end
function run_test_seq_startpos_protein(es)
assert(es:seqstartpos(0) == 0)
assert(es:seqstartpos(1) == 31)
rval, err = pcall(GenomeTools_encseq.seqstartpos, es, 2)
assert(not rval)
assert(string.find(err, "cannot exceed number of sequences"))
end
function run_test_seq_length(es)
assert(es:seqlength(0) == 36)
assert(es:seqlength(1) == 9)
rval, err = pcall(GenomeTools_encseq.seqlength, es, 2)
assert(not rval)
assert(string.find(err, "cannot exceed number of sequences"))
end
function run_test_seq_length_protein(es)
assert(es:seqlength(0) == 30)
assert(es:seqlength(1) == 6)
rval, err = pcall(GenomeTools_encseq.seqlength, es, 2)
assert(not rval)
assert(string.find(err, "cannot exceed number of sequences"))
end
function run_test_file_length(es)
assert(es:effective_filelength(0) == 46)
rval, err = pcall(GenomeTools_encseq.seqlength, es, 2)
assert(not rval)
assert(string.find(err, "cannot exceed"))
rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 10, 6)
assert(not rval)
assert(string.find(err, "invalid readmode"))
end
function run_test_file_length_protein(es)
assert(es:effective_filelength(0) == 37)
rval, err = pcall(GenomeTools_encseq.seqlength, es, 2)
assert(not rval)
assert(string.find(err, "cannot exceed"))
end
function run_test_seq_substr_encoded(es, seq1, seq2)
start = 3
stop = 13
res = es:extract_encoded(start, stop)
a = es:alphabet()
for i=start,stop do
assert(a:decode(res[i-start+1]) == seq1:sub(i+1,i+1))
end
start = es:seqstartpos(1)
stop = start + 4
res = es:extract_encoded(start, stop)
for i=start,stop do
assert(a:decode(res[i-start+1]) == seq2:sub(i-start+1,i-start+1))
end
rval, err = pcall(GenomeTools_encseq.extract_encoded, es, 3, 1)
assert(not rval)
assert(string.find(err, "range endposition"))
rval, err = pcall(GenomeTools_encseq.extract_encoded, es, 300, 500)
assert(not rval)
assert(string.find(err, "cannot exceed"))
end
function run_test_seq_substr_decoded(es, seq1, seq2)
start = 3
stop = 13
res = es:extract_decoded(start, stop)
a = es:alphabet()
assert(res == seq1:sub(start+1,stop+1))
start = es:seqstartpos(1)
stop = start + 4
res = es:extract_decoded(start, stop)
assert(res == seq2:sub(1,5))
rval, err = pcall(GenomeTools_encseq.extract_decoded, es, 3, 1)
assert(not rval)
assert(string.find(err, "range endposition"))
rval, err = pcall(GenomeTools_encseq.extract_decoded, es, 300, 500)
assert(not rval)
assert(string.find(err, "cannot exceed"))
end
function run_test_seq_substr_sequential(es, seq1, seq2)
start = 3
stop = 13
er = es:create_reader_with_readmode(0, start)
a = es:alphabet()
for i=start,stop do
assert(a:decode(er:next_encoded_char()) == seq1:sub(i+1,i+1))
end
start = es:seqstartpos(1)
stop = start + 4
er = es:create_reader_with_readmode(0, start)
for i=start,stop do
encchar = a:decode(er:next_encoded_char())
seqchar = seq2:sub(i-start+1, i-start+1)
assert(encchar == seqchar)
end
rval, err = pcall(GenomeTools_encseq.create_reader_with_readmode, es, 0, 300)
assert(not rval)
assert(string.find(err, "cannot exceed"))
rval, err = pcall(GenomeTools_encseq.create_reader_with_readmode, es, 7, 3)
assert(not rval)
assert(string.find(err, "invalid readmode"))
end
ee = gt.encseq_encoder_new()
ee:encode({dnaseqfile}, "dnaseqfile")
ee:encode({aaseqfile}, "aaseqfile")
el = gt.encseq_loader_new()
es = el:load("dnaseqfile")
run_test_descriptions(es)
run_test_num_seqs(es)
run_test_total_length(es)
run_test_num_files(es)
run_test_get_encoded_char(es, dseq1, dseq2)
run_test_seq_length(es)
run_test_seq_startpos(es)
run_test_file_length(es)
run_test_seq_substr_encoded(es, dseq1, dseq2)
run_test_seq_substr_decoded(es, dseq1, dseq2)
run_test_seq_substr_sequential(es, dseq1, dseq2)
a = gt.alphabet_new_dna()
eb = gt.encseq_builder_new(a)
eb:enable_multiseq_support()
eb:add_string(dseq1, "seq1")
eb:add_string(dseq2, "seq2")
es = eb:build()
run_test_descriptions(es)
run_test_num_seqs(es)
run_test_total_length(es)
run_test_num_files(es)
run_test_get_encoded_char(es, dseq1, dseq2)
run_test_seq_length(es)
run_test_seq_startpos(es)
run_test_file_length(es)
run_test_seq_substr_encoded(es, dseq1, dseq2)
run_test_seq_substr_decoded(es, dseq1, dseq2)
run_test_seq_substr_sequential(es, dseq1, dseq2)
es = el:load("aaseqfile")
run_test_descriptions(es)
run_test_num_seqs(es)
run_test_total_length_protein(es)
run_test_num_files(es)
run_test_get_encoded_char(es, aaseq1, aaseq2)
run_test_seq_length_protein(es)
run_test_seq_startpos_protein(es)
run_test_file_length_protein(es)
run_test_seq_substr_encoded(es, aaseq1, aaseq2)
run_test_seq_substr_decoded(es, aaseq1, aaseq2)
run_test_seq_substr_sequential(es, aaseq1, aaseq2)
a = gt.alphabet_new_protein()
eb = gt.encseq_builder_new(a)
eb:enable_multiseq_support()
eb:add_string(aaseq1, "seq1")
eb:add_string(aaseq2, "seq2")
es = eb:build()
run_test_descriptions(es)
run_test_num_seqs(es)
run_test_total_length_protein(es)
run_test_num_files(es)
run_test_get_encoded_char(es, aaseq1, aaseq2)
run_test_seq_length_protein(es)
run_test_seq_startpos_protein(es)
run_test_file_length_protein(es)
run_test_seq_substr_encoded(es, aaseq1, aaseq2)
run_test_seq_substr_decoded(es, aaseq1, aaseq2)
run_test_seq_substr_sequential(es, aaseq1, aaseq2)
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