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#72 : Fix SOFT parser skipping entities
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@kMutagene
kMutagene committed Sep 16, 2019
1 parent 3304e61 commit cc3a3f9
Showing 1 changed file with 105 additions and 55 deletions.
160 changes: 105 additions & 55 deletions src/BioFSharp.IO/SOFT.fs
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ module SOFT =
open System.Collections.Generic
open FSharpAux.IO

//TODO : Full parsing, get rid of the "not interesting" cases and just parse everything
//TODO : Full parsing, get rid of the "not interesting" cases and just parse everything. Remodel parser to return these types instead of string maps and such.

type SOFTSeriesSpecifications =
///Provide an identifier for this entity. This identifier is used only as an internal reference within a given file. The identifier will not appear on final GEO records.
Expand Down Expand Up @@ -118,16 +118,15 @@ module SOFT =

let private createPlatformInfos acc name org = {Accession = acc; Name = name; Organism= org}

///Type representation of SOFT `^SAMPLE` Entities
type SampleInfos = {
Accession : string
Title : string
Channels : int
Organism : Map<string,string list>
Source : Map<string,string list>
Characteristics : Map<string,string list>
Molecules : Map<string,string list>
SRAAccession : string
Accession: string
Title : string
Channels: int
Organism: Map<string,string list>
Source:Map<string,string list>
Characteristics: Map<string,string list>
Molecules: Map<string,string list>
SRAAccession: string
}

let private createSampleInfos acc t ch org src char mol sra =
Expand All @@ -142,31 +141,32 @@ module SOFT =
SRAAccession = sra
}

///Type Representation of SOFT `^Series` Entities
type SeriesInfos = {
Accession : string
Title : string
Design : string
Type : string list
Date : string
Publications : string list
Platform : Map<string,PlatformInfos>
Samples : Map<string,SampleInfos>
Accession : string
Title: string
Design: string
Type : string list
SampleIds: string list
Date: string
Publications: string list
Platform : Map<string,PlatformInfos>
SampleAnnotations: Map<string,SampleInfos>
}

let private createSeriesInfo acc t des typ d pub pI sI =
let private createSeriesInfo acc t des typ sIds d pub pI sI =
{
Accession = acc
Title = t
Design = des
Type = typ
SampleIds = sIds
Date = d
Publications = pub
Platform = pI
Samples = sI
SampleAnnotations = sI
}

type private SOFTToken =
type SOFTToken =
|Entity of (string * string)
|Attribute of (string * string)
|DataTable
Expand Down Expand Up @@ -212,7 +212,7 @@ module SOFT =
| a when a.Contains("!Sample_molecule_ch") -> loop nextToken acc t ch org src char ((a,v)::mol) sra
| "!Sample_relation" when (v.Contains("SRA")) -> loop nextToken acc t ch org src char mol (if v.Contains("SRA") then v else sra)
| _ -> loop nextToken acc t ch org src char mol sra

//return finished sample when new entity starts
|Attribute (a,v),Entity (e,ev) -> match a with
| "!Sample_title" -> nextToken,acc,(createSampleInfos acc v ch (Map.ofList (reduceMaps org)) (Map.ofList (reduceMaps src)) (Map.ofList (reduceMaps char)) (Map.ofList (reduceMaps mol)) sra)
Expand All @@ -229,7 +229,7 @@ module SOFT =
token,acc,(createSampleInfos acc t ch (Map.ofList (reduceMaps org)) (Map.ofList (reduceMaps src)) (Map.ofList (reduceMaps char)) (Map.ofList (reduceMaps mol)) sra)
loop token accession "" -1 [] [] [] [] ""

let rec private parsePlatformInfos (token:SOFTToken) (en: IEnumerator<SOFTToken>) (accession: string) =
let private parsePlatformInfos (token:SOFTToken) (en: IEnumerator<SOFTToken>) (accession: string) =
let rec loop (token:SOFTToken) acc name org =
if en.MoveNext() then
let nextToken = en.Current
Expand All @@ -243,7 +243,7 @@ module SOFT =
| Attribute (a,v),Entity (e,ev) -> match a with
| "!Platform_title" -> token,acc,createPlatformInfos acc v org
| "!Platform_organism" -> token,acc,createPlatformInfos acc name org
| _ -> token,acc,createPlatformInfos acc name org
| _ -> nextToken,acc,createPlatformInfos acc name org
//not interesting
| _ -> loop nextToken acc name org
else
Expand All @@ -252,38 +252,88 @@ module SOFT =

let private parseSOFT (soft: seq<SOFTToken>) =
let en = soft.GetEnumerator()
let rec loop (token: SOFTToken) (seriesAccession: string) (seriesTitle: string) (seriesDesign: string) (seriesType:string list) (date: string) (publications: string list) (samples: (string*SampleInfos) list) (platform: (string*PlatformInfos) list) =
if en.MoveNext() then
let nextToken = en.Current
match nextToken with
|Entity (e,v) ->
match e with
//gather Series Info
| "^SERIES" -> loop nextToken (v) seriesTitle seriesDesign seriesType date publications samples platform
//call sample parser
| "^SAMPLE" -> let token', smplAcc, smpl = parseSample token en v
loop (token') seriesAccession seriesTitle seriesDesign seriesType date publications ((smplAcc,smpl)::samples) platform
//call platform parser
| "^PLATFORM" -> let token', pltfrmlAcc, pltfrm = parsePlatformInfos token en v
loop nextToken seriesAccession seriesTitle seriesDesign seriesType date publications samples ((pltfrmlAcc,pltfrm)::platform)
//ignore unexpected/uninteresting entities
| _ -> loop nextToken seriesAccession seriesTitle seriesDesign seriesType date publications samples platform
//Attributes are only found here when on series level or uninteresting
|Attribute (a,v) -> match a with
| "!Series_title" -> loop nextToken seriesAccession (v) seriesDesign seriesType date publications samples platform
| "!Series_submission_date" -> loop nextToken seriesAccession seriesTitle seriesDesign seriesType (v) publications samples platform
| "!Series_pubmed_id" | "!Series_web_link" -> loop nextToken seriesAccession seriesTitle seriesDesign seriesType date ((sprintf "%s = %s" a v)::publications) samples platform
| "!Series_overall_design" -> loop nextToken seriesAccession seriesTitle v seriesType date publications samples platform
| "!Series_type" -> loop nextToken seriesAccession seriesTitle seriesDesign (v::seriesType) date publications samples platform
//attributes of uninteresting entities
| _ -> loop nextToken seriesAccession seriesTitle seriesDesign seriesType date publications samples platform
//not interesting
|_ -> loop nextToken seriesAccession seriesTitle seriesDesign seriesType date publications samples platform

else
createSeriesInfo seriesAccession seriesTitle seriesDesign seriesType date publications (Map.ofList platform) ( Map.ofList samples)
let rec loop (token: SOFTToken) (seriesAccession: string) (seriesTitle: string) (seriesDesign: string) (seriesType:string list) (seriesSamples:string list) (date: string) (publications: string list) (samples: (string*SampleInfos) list) (platform: (string*PlatformInfos) list) =

match token with
|Entity (e,v) ->
match e with
//gather Series Info
| "^SERIES" ->
if en.MoveNext() then
let nextToken = en.Current
loop nextToken (v) seriesTitle seriesDesign seriesType seriesSamples date publications samples platform
else
createSeriesInfo seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications (Map.ofList platform) ( Map.ofList samples)
//call sample parser
| "^SAMPLE" -> //printfn "SAMPLE??? %s" v
let token', smplAcc, smpl = parseSample token en v
loop (token') seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications ((smplAcc,smpl)::samples) platform
//call platform parser
| "^PLATFORM" -> let token', pltfrmlAcc, pltfrm = parsePlatformInfos token en v
loop (token') seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications samples ((pltfrmlAcc,pltfrm)::platform)
//ignore unexpected/uninteresting entities
| _ ->
if en.MoveNext() then
let nextToken = en.Current
loop nextToken seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications samples platform
else
createSeriesInfo seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications (Map.ofList platform) ( Map.ofList samples)
//Attributes are only found here when on series level or uninteresting
|Attribute (a,v) -> match a with
| "!Series_title" ->
if en.MoveNext() then
let nextToken = en.Current
loop nextToken seriesAccession (v) seriesDesign seriesType seriesSamples date publications samples platform
else
createSeriesInfo seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications (Map.ofList platform) ( Map.ofList samples)
| "!Series_submission_date" ->
if en.MoveNext() then
let nextToken = en.Current
loop nextToken seriesAccession seriesTitle seriesDesign seriesType seriesSamples (v) publications samples platform
else
createSeriesInfo seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications (Map.ofList platform) ( Map.ofList samples)
| "!Series_pubmed_id" | "!Series_web_link" ->
if en.MoveNext() then
let nextToken = en.Current
loop nextToken seriesAccession seriesTitle seriesDesign seriesType seriesSamples date ((sprintf "%s = %s" a v)::publications) samples platform
else
createSeriesInfo seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications (Map.ofList platform) ( Map.ofList samples)
| "!Series_overall_design" ->
if en.MoveNext() then
let nextToken = en.Current
loop nextToken seriesAccession seriesTitle v seriesType seriesSamples date publications samples platform
else
createSeriesInfo seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications (Map.ofList platform) ( Map.ofList samples)
| "!Series_type" ->
if en.MoveNext() then
let nextToken = en.Current
loop nextToken seriesAccession seriesTitle seriesDesign (v::seriesType) seriesSamples date publications samples platform
else
createSeriesInfo seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications (Map.ofList platform) ( Map.ofList samples)
| "!Series_sample_id" ->
if en.MoveNext() then
let nextToken = en.Current
loop nextToken seriesAccession seriesTitle seriesDesign seriesType (v::seriesSamples) date publications samples platform
else
createSeriesInfo seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications (Map.ofList platform) ( Map.ofList samples)
//attributes of uninteresting entities
| _ ->
if en.MoveNext() then
let nextToken = en.Current
loop nextToken seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications samples platform
else
createSeriesInfo seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications (Map.ofList platform) ( Map.ofList samples)
//not interesting
|_ ->
if en.MoveNext() then
let nextToken = en.Current
loop nextToken seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications samples platform
else
createSeriesInfo seriesAccession seriesTitle seriesDesign seriesType seriesSamples date publications (Map.ofList platform) ( Map.ofList samples)

if en.MoveNext() then
loop en.Current "" "" "" [] "" [] [] []
loop en.Current "" "" "" [] [] "" [] [] []
else failwith "empty input"

///Read SOFT SeriesInfo from a SOFT series file
Expand Down

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