mirror of
https://github.com/MillironX/XAM.jl.git
synced 2024-11-14 22:33:14 +00:00
8f26bbf4a7
Makes better use of the existing flow in [Automa.jl](b6997f7415/src/Stream.jl (L124-L127)).
204 lines
7.4 KiB
Julia
204 lines
7.4 KiB
Julia
@testset "SAM" begin
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samdir = path_of_format("SAM")
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@testset "MetaInfo" begin
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metainfo = SAM.MetaInfo()
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@test !isfilled(metainfo)
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@test occursin("not filled", repr(metainfo))
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metainfo = SAM.MetaInfo("CO", "some comment (parens)")
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@test isfilled(metainfo)
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@test string(metainfo) == "@CO\tsome comment (parens)"
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@test occursin("CO", repr(metainfo))
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@test SAM.tag(metainfo) == "CO"
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@test SAM.value(metainfo) == "some comment (parens)"
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@test_throws ArgumentError keys(metainfo)
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@test_throws ArgumentError values(metainfo)
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metainfo = SAM.MetaInfo("HD", ["VN" => "1.0", "SO" => "coordinate"])
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@test isfilled(metainfo)
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@test string(metainfo) == "@HD\tVN:1.0\tSO:coordinate"
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@test occursin("HD", repr(metainfo))
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@test SAM.tag(metainfo) == "HD"
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@test SAM.value(metainfo) == "VN:1.0\tSO:coordinate"
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@test keys(metainfo) == ["VN", "SO"]
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@test values(metainfo) == ["1.0", "coordinate"]
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@test SAM.keyvalues(metainfo) == ["VN" => "1.0", "SO" => "coordinate"]
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@test haskey(metainfo, "VN")
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@test haskey(metainfo, "SO")
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@test !haskey(metainfo, "GO")
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@test metainfo["VN"] == "1.0"
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@test metainfo["SO"] == "coordinate"
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@test_throws KeyError metainfo["GO"]
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end
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@testset "Header" begin
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header = SAM.Header()
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@test isempty(header)
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push!(header, SAM.MetaInfo("@HD\tVN:1.0\tSO:coordinate"))
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@test !isempty(header)
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@test length(header) == 1
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push!(header, SAM.MetaInfo("@CO\tsome comment"))
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@test length(header) == 2
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@test isa(collect(header), Vector{SAM.MetaInfo})
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end
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@testset "Record" begin
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record = SAM.Record()
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@test !isfilled(record)
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@test !SAM.ismapped(record)
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@test repr(record) == "XAM.SAM.Record: <not filled>"
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@test_throws ArgumentError SAM.flag(record)
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record = SAM.Record("r001\t99\tchr1\t7\t30\t8M2I4M1D3M\t=\t37\t39\tTTAGATAAAGGATACTG\t*")
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@test isfilled(record)
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@test occursin(r"^XAM.SAM.Record:\n", repr(record))
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@test SAM.ismapped(record)
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@test SAM.isprimary(record)
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@test SAM.hastempname(record)
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@test SAM.tempname(record) == "r001"
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@test SAM.hasflag(record)
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@test SAM.flag(record) === UInt16(99)
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@test SAM.hasrefname(record)
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@test SAM.refname(record) == "chr1"
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@test SAM.hasposition(record)
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@test SAM.position(record) === 7
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@test SAM.hasmappingquality(record)
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@test SAM.mappingquality(record) === UInt8(30)
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@test SAM.hascigar(record)
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@test SAM.cigar(record) == "8M2I4M1D3M"
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@test SAM.hasnextrefname(record)
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@test SAM.nextrefname(record) == "="
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@test SAM.hasnextposition(record)
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@test SAM.nextposition(record) === 37
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@test SAM.hastemplength(record)
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@test SAM.templength(record) === 39
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@test SAM.hassequence(record)
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@test SAM.sequence(record) == dna"TTAGATAAAGGATACTG"
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@test !SAM.hasquality(record)
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@test_throws MissingFieldException SAM.quality(record)
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end
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@testset "Reader" begin
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reader = open(SAM.Reader, joinpath(samdir, "ce#1.sam"))
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@test isa(reader, SAM.Reader)
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@test eltype(reader) === SAM.Record
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# header
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h = header(reader)
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@test string.(findall(header(reader), "SQ")) == ["@SQ\tSN:CHROMOSOME_I\tLN:1009800"]
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# first record
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record = SAM.Record()
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read!(reader, record)
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@test SAM.ismapped(record)
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@test SAM.refname(record) == "CHROMOSOME_I"
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@test SAM.position(record) == leftposition(record) == 2
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@test SAM.rightposition(record) == rightposition(record) == 102
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@test SAM.tempname(record) == seqname(record) == "SRR065390.14978392"
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@test SAM.sequence(record) == sequence(record) == dna"CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA"
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@test SAM.sequence(String, record) == "CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA"
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@test SAM.seqlength(record) == 100
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@test SAM.quality(record) == (b"#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC" .- 33)
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@test SAM.quality(String, record) == "#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"
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@test SAM.flag(record) == 16
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@test SAM.cigar(record) == "27M1D73M"
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@test SAM.alignment(record) == Alignment([
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AlignmentAnchor( 0, 1, OP_START),
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AlignmentAnchor( 27, 28, OP_MATCH),
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AlignmentAnchor( 27, 29, OP_DELETE),
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AlignmentAnchor(100, 102, OP_MATCH)])
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@test record["XG"] == 1
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@test record["XM"] == 5
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@test record["XN"] == 0
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@test record["XO"] == 1
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@test record["AS"] == -18
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@test record["XS"] == -18
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@test record["YT"] == "UU"
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@test eof(reader)
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close(reader)
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# rightposition (also implicitly alignlength)
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records = collect(open(SAM.Reader, joinpath(samdir, "ce#5b.sam")))
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@test SAM.rightposition(records[6]) == rightposition(records[6]) == 83
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# iterator
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@test length(collect(open(SAM.Reader, joinpath(samdir, "ce#1.sam")))) == 1
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@test length(collect(open(SAM.Reader, joinpath(samdir, "ce#2.sam")))) == 2
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# IOStream
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@test length(collect(SAM.Reader(open(joinpath(samdir, "ce#1.sam"))))) == 1
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@test length(collect(SAM.Reader(open(joinpath(samdir, "ce#2.sam"))))) == 2
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end
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@testset "Round trip" begin
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function compare_records(xs, ys)
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if length(xs) != length(ys)
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return false
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end
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for (x, y) in zip(xs, ys)
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if x.data[x.filled] != y.data[y.filled]
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return false
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end
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end
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return true
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end
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for specimen in list_valid_specimens("SAM")
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filepath = joinpath(samdir, filename(specimen))
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mktemp() do path, io
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# copy
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reader = open(SAM.Reader, filepath)
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header_original = header(reader)
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writer = SAM.Writer(io, header_original)
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records = SAM.Record[]
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for record in reader
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push!(records, record)
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write(writer, record)
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end
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close(reader)
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close(writer)
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reader = open(SAM.Reader, path)
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@test header(reader) == header_original
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@test compare_records(collect(reader), records)
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close(reader)
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end
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end
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end
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@testset "In-Place-Reading Pattern" begin
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file_sam = joinpath(samdir, "ce#5b.sam")
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records = open(collect, SAM.Reader, file_sam)
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reader = open(SAM.Reader, file_sam)
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record = SAM.Record()
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i = 0
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while !eof(reader)
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empty!(record) # Reset the record.
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read!(reader, record)
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i = i + 1
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@test records[i] == record
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end
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close(reader)
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# Test blank file.
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file_sam = joinpath(samdir, "xx#blank.sam")
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records = open(collect, SAM.Reader, file_sam)
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@test records == []
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end
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end
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