write and read disk data

.gitignore

@@ -4,4 +4,5 @@
 /Manifest.toml
 /notebook
 /SPID
-/test/manualtest.jl
+/test/manualtest_id.jl
+/test/manualtest_qt.jl

Project.toml

@@ -12,6 +12,7 @@ Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
 DataPipes = "02685ad9-2d12-40c3-9f73-c6aeda6a7ff5"
 Dictionaries = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4"
 GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
+JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
 PlotlyJS = "f0f68f2c-4968-5e81-91da-67840de0976a"
@@ -29,10 +30,11 @@ UnitfulMoles = "999f2bd7-36bf-5ba7-9bc1-c9473aa75374"
 [compat]
 AnovaGLM = "0.2"
 CSV = "0.10"
-Clustering = "0.15"
 ChemistryQuantitativeAnalysis = "0.3"
+Clustering = "0.15"
 DataPipes = "0.3"
 Dictionaries = "0.3"
+JLD2 = "0.4"
 MLStyle = "0.4"
 PlotlyJS = "0.18"
 Plots = "1"

src/SphingolipidsID.jl

@@ -2,7 +2,7 @@ module SphingolipidsID
 
 using CSV, PrettyTables,
  MLStyle, DataPipes, SplitApplyCombine, TypedTables, Dictionaries,
- Statistics, StatsBase, Clustering, Plots, GLM, ThreadsX, LinearAlgebra, ChemistryQuantitativeAnalysis
+ Statistics, StatsBase, Clustering, Plots, GLM, ThreadsX, LinearAlgebra, ChemistryQuantitativeAnalysis, JLD2
 using AnovaBase: getterms, anova, @formula
 using UnitfulMoles: parse_compound, ustrip, @u_str
 export SPDB, LIBRARY_POS, FRAGMENT_POS, ADDUCTCODE, CLASSDB,
@@ -386,18 +386,18 @@ propertynames(sd::SerialDilution) = Tuple(unique((:raw, :batch, :config, propert
 #SerialDilution(raw::T, table::Table, level::Vector, config::Dictionary) where {T <: Data} = SerialDilution{T}(raw, table, level, config)
 
 """
- Quantification
+ Quantification{A}
 
 Type containg information of analyte settings, calibration data, qc data, serial dilution data, and sample data.
 
 * `batch`: `Batch` containg analyte settings, calibration data, and sample data.
 * `config`: `Dictionary` containing config information. `config[:qcdata]` stores a `QCData`, `config[:serialdilution]` stores a `SerialDilution`, and `config[:quantdata]` stores a `QuantData` (sample data).
 """
-struct Quantification
- batch::Batch
+struct Quantification{A}
+ batch::Batch{A}
  config::Dictionary
- Quantification() = new()
- Quantification(batch::Batch, config::Dictionary) = new(batch, config)
+ Quantification() = new{Any}()
+ Quantification(batch::Batch{A}, config::Dictionary) where A = new{A}(batch, config)
 end # Wrap MethodTable
 
 function getproperty(quant::Quantification, p::Symbol)

src/interface.jl

@@ -341,6 +341,8 @@ copy_wo_project(aquery::Query) = Query(aquery.project, copy_wo_project.(aquery.r
 reuse_copy(aquery::Query) = Query(aquery.project, reuse_copy(aquery.result), deepcopy(aquery.query), true)
 reuse_copy(v::Vector) = copy(v)
 reuse_copy(v::T) where {T <: SubArray} = T(parent(v), v.indices, v.offset1, v.stride1)
+copy(analyte::AnalyteSP) = AnalyteSP(analyte.compound, analyte.rt, analyte.state, analyte.cpdsc, analyte.score)
+copy(cpd::CompoundSP) = CompoundSP(cpd.class, cpd.chain, cpd.fragment, cpd.signal, cpd.state, cpd.result, cpd.project)
 
 # equivalent: ion1 and ion2 are the same
 equivalent_in(ion, collection) = any(equivalent(ion, x) for x in collection)

src/quantification.jl

@@ -36,13 +36,10 @@ function quantification_mrm(analyte::AbstractVector{<: AbstractAnalyteID}, quant
  Quantification(Batch(MethodTable{Table}(vcat(isdtable, analytetable), signal, Int[], conctable, nothing)), dictionary(pairs((; signal, anion, rt_tol, mz_tol, quantifier, qualifier, default_mz2, isd_fn, coelution_fn))))
 end
 
-function transition_matching!(data::MRM, project = nothing; rt_tol = 0.1, mz_tol = 0.35, rt_correction = nothing)
+function transition_matching!(data::MRM, method = nothing; rt_tol = 0.1, mz_tol = 0.35, rt_correction = nothing)
  featuretable = data.table
  sort!(featuretable, [:id, :injection_order])
- set!(data.config, :method, nothing)
- isnothing(project) && (featuretable.match_id .= featuretable.id; return sort!(featuretable, [:match_id, :id, :injection_order, :match_score]))
- method = project.quantification.batch.method
- data.config[:method] = method
+ isnothing(method) && (featuretable.match_id .= featuretable.id; return sort!(featuretable, [:match_id, :id, :injection_order, :match_score]))
  i = 0
  for ft in groupview(getproperty(:id), featuretable)
  mz1 = mean(ft.mz1)
@@ -137,6 +134,7 @@ qcdata_mrm(project::Project, featuretable::Table; kwargs...) = qcdata_mrm!(proje
 qcdata_mrm(featuretable::Table, project = nothing; kwargs...) = qcdata_mrm!(deepcopy(featuretable), project; kwargs...)
 qcdata_mrm!(project::Project, featuretable::Table; kwargs...) = qcdata_mrm!(featuretable, project; kwargs...)
 function qcdata_mrm!(featuretable::Table, project = nothing;
+ method = isnothing(project) ? nothing : isdefined(project.quantification, :batch) ? project.quantification.batch.method : nothing,
  rt_correction = nothing, 
  rt_tol = isnothing(project) ? 0.1 : last(project.data).config[:rt_tol], 
  raw_rt_tol = isnothing(rt_correction) ? 0.3 : rt_correction.config[:rt_tol],
@@ -155,13 +153,13 @@ function qcdata_mrm!(featuretable::Table, project = nothing;
  other_fn = default_other_fn
  n = length(unique(featuretable.datafile))
  mrm = MRM!(Table(featuretable; match_id = zeros(Int, length(featuretable)), match_score = -getproperty(featuretable, signal)); combine = false, rt_tol = raw_rt_tol, mz_tol, n = 1, signal = nothing, est_fn, err_fn, err_tol, other_fn)
- transition_matching!(mrm, project; rt_correction, rt_tol, mz_tol)
- at = analysistable(mrm.table; method = mrm.config[:method], data = signal)
+ transition_matching!(mrm, method; rt_correction, rt_tol, mz_tol)
+ at = analysistable(mrm.table; method, data = signal)
  if !isnothing(project)
  signal = :estimated_concentration
  set_quantification!(at, project.quantification.batch; estimated_concentration = signal)
  end
- config = dictionary(pairs((; rt_correction, rt_tol, mz_tol, n, signal, est_fn, err_fn, err_tol, other_fn)))
+ config = dictionary(pairs((; method, rt_correction, rt_tol, mz_tol, n, signal, est_fn, err_fn, err_tol, other_fn)))
  QCData(mrm, at, config)
 end
 
@@ -192,6 +190,7 @@ serialdilution_mrm(project::Project, featuretable::Table, concentration::Vector;
 serialdilution_mrm(featuretable::Table, concentration::Vector, project = nothing; kwargs...) = serialdilution_mrm!(deepcopy(featuretable), concentration, project; kwargs...)
 serialdilution_mrm!(project::Project, featuretable::Table, concentration::Vector; kwargs...) = serialdilution_mrm!(featuretable, concentration, project; kwargs...)
 function serialdilution_mrm!(featuretable::Table, concentration::Vector, project = nothing; 
+ method = isnothing(project) ? nothing : isdefined(project.quantification, :batch) ? project.quantification.batch.method : nothing,
  pointlevel = nothing, 
  name = r"cal.*_(\d*)-r\d*.*",
  rt_correction = nothing,
@@ -213,9 +212,9 @@ function serialdilution_mrm!(featuretable::Table, concentration::Vector, project
  end
  other_fn = default_other_fn
  mrm = MRM!(Table(featuretable; match_id = zeros(Int, length(featuretable)), match_score = -getproperty(featuretable, signal)); combine = false, rt_tol = raw_rt_tol, mz_tol, n = 1, signal = nothing, est_fn, err_fn, err_tol, other_fn)
- transition_matching!(mrm, project; rt_correction, rt_tol, mz_tol)
- config = dictionary(pairs((; concentration, rt_correction, r2_threshold, nlevel, rt_tol, mz_tol, signal, est_fn, err_fn, err_tol, other_fn)))
- at = analysistable(mrm.table; method = mrm.config[:method], data = signal)
+ transition_matching!(mrm, method; rt_correction, rt_tol, mz_tol)
+ config = dictionary(pairs((; method, concentration, rt_correction, r2_threshold, nlevel, rt_tol, mz_tol, signal, est_fn, err_fn, err_tol, other_fn)))
+ at = analysistable(mrm.table; method, data = signal)
  signaltable = getproperty(at, signal)
  pointlevel = isnothing(pointlevel) ? map(x -> parse(Int, first(match(name, string(x)))), signaltable.sample) : pointlevel
  if signaltable isa ColumnDataTable
@@ -305,6 +304,7 @@ quantdata_mrm(project::Project, featuretable::Table; kwargs...) = quantdata_mrm!
 quantdata_mrm(featuretable::Table, project = nothing; kwargs...) = quantdata_mrm!(deepcopy(featuretable), project; kwargs...)
 quantdata_mrm!(project::Project, featuretable::Table; kwargs...) = quantdata_mrm!(featuretable, project; kwargs...)
 function quantdata_mrm!(featuretable::Table, project = nothing;
+ method = isnothing(project) ? nothing : isdefined(project.quantification, :batch) ? project.quantification.batch.method : nothing,
  rt_correction = nothing, 
  rt_tol = isnothing(project) ? 0.1 : last(project.data).config[:rt_tol], 
  raw_rt_tol = isnothing(rt_correction) ? 0.3 : rt_correction.config[:rt_tol],
@@ -323,12 +323,12 @@ function quantdata_mrm!(featuretable::Table, project = nothing;
  other_fn = default_other_fn
  n = length(unique(featuretable.datafile))
  mrm = MRM!(Table(featuretable; match_id = zeros(Int, length(featuretable)), match_score = -getproperty(featuretable, signal)); combine = false, rt_tol = raw_rt_tol, mz_tol, n = 1, signal = false, est_fn, err_fn, err_tol, other_fn)
- transition_matching!(mrm, project; rt_correction, rt_tol, mz_tol)
- at = analysistable(mrm.table; method = mrm.config[:method], data = signal)
+ transition_matching!(mrm, method; rt_correction, rt_tol, mz_tol)
+ at = analysistable(mrm.table; method, data = signal)
  if !isnothing(project)
  signal = :estimated_concentration
  update_quantification!(project.quantification.batch, at; estimated_concentration = signal)
  end
- config = dictionary(pairs((; rt_correction, rt_tol, mz_tol, n, signal, est_fn, err_fn, err_tol, other_fn)))
+ config = dictionary(pairs((; method, rt_correction, rt_tol, mz_tol, n, signal, est_fn, err_fn, err_tol, other_fn)))
  QuantData(mrm, at, config)
 end

src/utils.jl

@@ -73,7 +73,10 @@ false
 ```
 """
 macro ri_str(expr)
- lc, lv, rv, rc = match(r" *([\(\[]) *([+-]*[\d∞]*\.*\d*) *, *([+-]*[\d∞]*\.*\d*) *([\)\]]) *", expr)
+ return real_interval(expr)
+end
+function real_interval(expr)
+ lc, lv, rv, rc = match(r" *([\(\[]) *([+-]*[\d∞Inf]*\.*\d*) *, *([+-]*[\d∞Inf]*\.*\d*) *([\)\]]) *", expr)
  lop = @match lc begin
  "[" => <=
  "(" => <
@@ -84,19 +87,25 @@ macro ri_str(expr)
  end
  lv = @match lv begin
  "+∞" => Inf
+ "+Inf" => Inf
  "∞" => Inf
+ "Inf" => Inf
  "-∞" => -Inf
+ "-Inf" => -Inf
  if occursin(".", lv) end => parse(Float64, lv)
  _ => parse(Int, lv)
  end
  rv = @match rv begin
  "+∞" => Inf
+ "+Inf" => Inf
  "∞" => Inf
+ "Inf" => Inf
  "-∞" => -Inf
+ "-Inf" => -Inf
  if occursin(".", rv) end => parse(Float64, rv)
  _ => parse(Int, rv)
  end
- return real_interval(lv, rv, lop, rop)
+ real_interval(lv, rv, lop, rop)
 end
 function real_interval(lb, ub, lop, rop)
  lop(lb, ub) || return EmptyInterval()