From c4f3c4b0df70264cfba627263f9f7fb74c51666d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= Date: Sun, 2 Feb 2020 22:50:25 +1100 Subject: [PATCH] Migrate to BioGenerics Basic find and replace. --- Project.toml | 4 ++-- src/bam/bam.jl | 4 ++-- src/bam/reader.jl | 4 ++-- src/bam/record.jl | 20 ++++++++++---------- src/bam/writer.jl | 4 ++-- src/sam/reader.jl | 30 +++++++++++++++--------------- src/sam/record.jl | 18 +++++++++--------- src/sam/sam.jl | 8 ++++---- src/sam/writer.jl | 4 ++-- test/runtests.jl | 19 +++++-------------- 10 files changed, 53 insertions(+), 62 deletions(-) diff --git a/Project.toml b/Project.toml index 10f7cb4..850b570 100644 --- a/Project.toml +++ b/Project.toml @@ -7,7 +7,7 @@ version = "0.1.1" Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b" BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6" BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e" -BioCore = "37cfa864-2cd6-5c12-ad9e-b6597d696c81" +BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea" BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59" BufferedStreams = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d" GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446" @@ -18,7 +18,7 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" Automa = "0.7, 0.8" BGZFStreams = "0.3" BioAlignments = "2" -BioCore = "2" +BioGenerics = "0.1" BioSequences = "2" BufferedStreams = "1" GenomicFeatures = "2" diff --git a/src/bam/bam.jl b/src/bam/bam.jl index e055231..6fd1174 100644 --- a/src/bam/bam.jl +++ b/src/bam/bam.jl @@ -3,7 +3,7 @@ module BAM -using BioCore +using BioGenerics using GenomicFeatures using XAM.SAM @@ -11,7 +11,7 @@ import BGZFStreams import BioAlignments import Indexes import BioSequences -import BioCore: isfilled, header +import BioGenerics: isfilled, header import GenomicFeatures: eachoverlap diff --git a/src/bam/reader.jl b/src/bam/reader.jl index 0fabb8f..953f5ca 100644 --- a/src/bam/reader.jl +++ b/src/bam/reader.jl @@ -10,7 +10,7 @@ Create a data reader of the BAM file format. * `input`: data source * `index=nothing`: filepath to a random access index (currently *bai* is supported) """ -mutable struct Reader{T} <: BioCore.IO.AbstractReader +mutable struct Reader{T} <: BioGenerics.IO.AbstractReader stream::BGZFStreams.BGZFStream{T} header::SAM.Header start_offset::BGZFStreams.VirtualOffset @@ -23,7 +23,7 @@ function Base.eltype(::Type{Reader{T}}) where T return Record end -function BioCore.IO.stream(reader::Reader) +function BioGenerics.IO.stream(reader::Reader) return reader.stream end diff --git a/src/bam/record.jl b/src/bam/record.jl index ad9c6f1..13c5608 100644 --- a/src/bam/record.jl +++ b/src/bam/record.jl @@ -566,42 +566,42 @@ function Base.values(record::Record) end -# BioCore Methods +# BioGenerics Methods # ----------- -function BioCore.isfilled(record::Record) +function BioGenerics.isfilled(record::Record) return record.block_size != 0 end -function BioCore.seqname(record::Record) +function BioGenerics.seqname(record::Record) return tempname(record) end -function BioCore.hasseqname(record::Record) +function BioGenerics.hasseqname(record::Record) return hastempname(record) end -function BioCore.sequence(record::Record) +function BioGenerics.sequence(record::Record) return sequence(record) end -function BioCore.hassequence(record::Record) +function BioGenerics.hassequence(record::Record) return hassequence(record) end -function BioCore.leftposition(record::Record) +function BioGenerics.leftposition(record::Record) return position(record) end -function BioCore.hasleftposition(record::Record) +function BioGenerics.hasleftposition(record::Record) return hasposition(record) end -function BioCore.rightposition(record::Record) +function BioGenerics.rightposition(record::Record) return rightposition(record) end -function BioCore.hasrightposition(record::Record) +function BioGenerics.hasrightposition(record::Record) return hasrightposition(record) end diff --git a/src/bam/writer.jl b/src/bam/writer.jl index f017424..2460b3f 100644 --- a/src/bam/writer.jl +++ b/src/bam/writer.jl @@ -10,7 +10,7 @@ Create a data writer of the BAM file format. * `output`: data sink * `header`: SAM header object """ -mutable struct Writer <: BioCore.IO.AbstractWriter +mutable struct Writer <: BioGenerics.IO.AbstractWriter stream::BGZFStreams.BGZFStream end @@ -25,7 +25,7 @@ function Writer(stream::BGZFStreams.BGZFStream, header::SAM.Header) return Writer(stream) end -function BioCore.IO.stream(writer::Writer) +function BioGenerics.IO.stream(writer::Writer) return writer.stream end diff --git a/src/sam/reader.jl b/src/sam/reader.jl index d26a840..5e4f0ea 100644 --- a/src/sam/reader.jl +++ b/src/sam/reader.jl @@ -1,12 +1,12 @@ # SAM Reader # ========= -mutable struct Reader <: BioCore.IO.AbstractReader - state::BioCore.Ragel.State +mutable struct Reader <: BioGenerics.IO.AbstractReader + state::BioGenerics.Ragel.State header::Header function Reader(input::BufferedStreams.BufferedInputStream) - reader = new(BioCore.Ragel.State(sam_header_machine.start_state, input), Header()) + reader = new(BioGenerics.Ragel.State(sam_header_machine.start_state, input), Header()) readheader!(reader) reader.state.cs = sam_body_machine.start_state return reader @@ -25,7 +25,7 @@ function Reader(input::IO) return Reader(BufferedStreams.BufferedInputStream(input)) end -function BioCore.IO.stream(reader::Reader) +function BioGenerics.IO.stream(reader::Reader) return reader.state.stream end @@ -184,36 +184,36 @@ const sam_metainfo_actions = Dict( :metainfo_dict_key => :(push!(record.dictkey, (mark2:p-1) .- offset)), :metainfo_dict_val => :(push!(record.dictval, (mark2:p-1) .- offset)), :metainfo => quote - BioCore.ReaderHelper.resize_and_copy!(record.data, data, offset+1:p-1) + BioGenerics.ReaderHelper.resize_and_copy!(record.data, data, offset+1:p-1) record.filled = (offset+1:p-1) .- offset end, :anchor => :(), :mark1 => :(mark1 = p), :mark2 => :(mark2 = p)) eval( - BioCore.ReaderHelper.generate_index_function( + BioGenerics.ReaderHelper.generate_index_function( MetaInfo, sam_metainfo_machine, :(mark1 = mark2 = offset = 0), sam_metainfo_actions)) eval( - BioCore.ReaderHelper.generate_readheader_function( + BioGenerics.ReaderHelper.generate_readheader_function( Reader, MetaInfo, sam_header_machine, :(mark1 = mark2 = offset = 0), merge(sam_metainfo_actions, Dict( :metainfo => quote - BioCore.ReaderHelper.resize_and_copy!(record.data, data, BioCore.ReaderHelper.upanchor!(stream):p-1) + BioGenerics.ReaderHelper.resize_and_copy!(record.data, data, BioGenerics.ReaderHelper.upanchor!(stream):p-1) record.filled = (offset+1:p-1) .- offset @assert isfilled(record) push!(reader.header.metainfo, record) - BioCore.ReaderHelper.ensure_margin!(stream) + BioGenerics.ReaderHelper.ensure_margin!(stream) record = MetaInfo() end, :header => :(finish_header = true; @escape), :countline => :(linenum += 1), - :anchor => :(BioCore.ReaderHelper.anchor!(stream, p); offset = p - 1))), + :anchor => :(BioGenerics.ReaderHelper.anchor!(stream, p); offset = p - 1))), quote if !eof(stream) stream.position -= 1 # cancel look-ahead @@ -234,28 +234,28 @@ const sam_record_actions = Dict( :record_qual => :(record.qual = (mark:p-1) .- offset), :record_field => :(push!(record.fields, (mark:p-1) .- offset)), :record => quote - BioCore.ReaderHelper.resize_and_copy!(record.data, data, 1:p-1) + BioGenerics.ReaderHelper.resize_and_copy!(record.data, data, 1:p-1) record.filled = (offset+1:p-1) .- offset end, :anchor => :(), :mark => :(mark = p)) eval( - BioCore.ReaderHelper.generate_index_function( + BioGenerics.ReaderHelper.generate_index_function( Record, sam_record_machine, :(mark = offset = 0), sam_record_actions)) eval( - BioCore.ReaderHelper.generate_read_function( + BioGenerics.ReaderHelper.generate_read_function( Reader, sam_body_machine, :(mark = offset = 0), merge(sam_record_actions, Dict( :record => quote - BioCore.ReaderHelper.resize_and_copy!(record.data, data, BioCore.ReaderHelper.upanchor!(stream):p-1) + BioGenerics.ReaderHelper.resize_and_copy!(record.data, data, BioGenerics.ReaderHelper.upanchor!(stream):p-1) record.filled = (offset+1:p-1) .- offset found_record = true @escape end, :countline => :(linenum += 1), - :anchor => :(BioCore.ReaderHelper.anchor!(stream, p); offset = p - 1))))) + :anchor => :(BioGenerics.ReaderHelper.anchor!(stream, p); offset = p - 1))))) diff --git a/src/sam/record.jl b/src/sam/record.jl index 8989747..a61e0df 100644 --- a/src/sam/record.jl +++ b/src/sam/record.jl @@ -514,39 +514,39 @@ end # Bio Methods # ----------- -function BioCore.isfilled(record::Record) +function BioGenerics.isfilled(record::Record) return !isempty(record.filled) end -function BioCore.seqname(record::Record) +function BioGenerics.seqname(record::Record) return tempname(record) end -function BioCore.hasseqname(record::Record) +function BioGenerics.hasseqname(record::Record) return hastempname(record) end -function BioCore.sequence(record::Record) +function BioGenerics.sequence(record::Record) return sequence(record) end -function BioCore.hassequence(record::Record) +function BioGenerics.hassequence(record::Record) return hassequence(record) end -function BioCore.rightposition(record::Record) +function BioGenerics.rightposition(record::Record) return rightposition(record) end -function BioCore.hasrightposition(record::Record) +function BioGenerics.hasrightposition(record::Record) return hasrightposition(record) end -function BioCore.leftposition(record::Record) +function BioGenerics.leftposition(record::Record) return position(record) end -function BioCore.hasleftposition(record::Record) +function BioGenerics.hasleftposition(record::Record) return hasposition(record) end diff --git a/src/sam/sam.jl b/src/sam/sam.jl index b917f37..d0f006b 100644 --- a/src/sam/sam.jl +++ b/src/sam/sam.jl @@ -3,14 +3,14 @@ module SAM -using BioCore +using BioGenerics import Automa import Automa.RegExp: @re_str import BioAlignments -import BioCore.Exceptions: missingerror -import BioCore.RecordHelper: unsafe_parse_decimal -import BioCore: isfilled, header +import BioGenerics.Exceptions: missingerror +import BioGenerics.RecordHelper: unsafe_parse_decimal +import BioGenerics: isfilled, header import BioSequences import BufferedStreams using Printf: @sprintf diff --git a/src/sam/writer.jl b/src/sam/writer.jl index e7a5ddd..801ed68 100644 --- a/src/sam/writer.jl +++ b/src/sam/writer.jl @@ -10,7 +10,7 @@ Create a data writer of the SAM file format. * `output`: data sink * `header=Header()`: SAM header object """ -mutable struct Writer <: BioCore.IO.AbstractWriter +mutable struct Writer <: BioGenerics.IO.AbstractWriter stream::IO function Writer(output::IO, header::Header=Header()) @@ -20,7 +20,7 @@ mutable struct Writer <: BioCore.IO.AbstractWriter end end -function BioCore.IO.stream(writer::Writer) +function BioGenerics.IO.stream(writer::Writer) return writer.stream end diff --git a/test/runtests.jl b/test/runtests.jl index d76d99f..10ca2d0 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,25 +1,16 @@ using Test + +using BioGenerics +using FormatSpecimens using GenomicFeatures using XAM + import BioAlignments: Alignment, AlignmentAnchor, OP_START, OP_MATCH, OP_DELETE -using FormatSpecimens import BGZFStreams: BGZFStream -import BioCore.Exceptions: MissingFieldException +import BioGenerics.Exceptions: MissingFieldException import BioSequences: @dna_str, @aa_str -import BioCore: - header, - isfilled, - seqname, - hasseqname, - sequence, - hassequence, - leftposition, - rightposition, - hasleftposition, - hasrightposition - # Generate a random range within `range`. function randrange(range) x = rand(range)