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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,177 @@ | ||
| using System; | ||
| using System.Collections; | ||
| using System.Collections.Generic; | ||
| using System.IO; | ||
| using System.Linq; | ||
| using System.Text.RegularExpressions; | ||
| using Compression.Utilities; | ||
| using VariantAnnotation.GeneAnnotation; | ||
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| namespace SAUtils.InputFileParsers.Omim | ||
| { | ||
| public class OmimReader : IEnumerable<OmimEntry> | ||
| { | ||
| #region members | ||
|
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| private readonly FileInfo _omimFileInfo; | ||
| private int _mimNumberCol; | ||
| private int _hgncCol; | ||
| private int _geneDescriptionCol; | ||
| private int _phenotypeCol; | ||
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| #endregion | ||
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| public OmimReader(FileInfo omimFileInfo) | ||
| { | ||
| _omimFileInfo = omimFileInfo; | ||
| } | ||
| public IEnumerator<OmimEntry> GetEnumerator() | ||
| { | ||
| return GetOmimItems().GetEnumerator(); | ||
| } | ||
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|
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| IEnumerator IEnumerable.GetEnumerator() | ||
| { | ||
| return GetEnumerator(); | ||
| } | ||
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| private IEnumerable<OmimEntry> GetOmimItems() | ||
| { | ||
| using (var reader = GZipUtilities.GetAppropriateStreamReader(_omimFileInfo.FullName)) | ||
| { | ||
| string line; | ||
| while ((line = reader.ReadLine()) != null) | ||
| { | ||
| if (IsHeader(line)) | ||
| { | ||
| ParseHeader(line); | ||
| continue; | ||
| } | ||
| if(!IsContentLine(line)) continue; | ||
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| var contents = line.Split('\t'); | ||
| var mimNumber =Convert.ToInt32(contents[_mimNumberCol]); | ||
| var geneSymbol = contents[_hgncCol]; | ||
| var description = contents[_geneDescriptionCol].Replace(@"\\'",@"'"); | ||
| var phenotypeInfo = contents[_phenotypeCol].Replace(@",,", @","); | ||
| var phenotypes = ParsePhenotypes(phenotypeInfo); | ||
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| if(string.IsNullOrEmpty(geneSymbol)) continue; | ||
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| yield return new OmimEntry(geneSymbol, description, mimNumber, phenotypes); | ||
| } | ||
| } | ||
| } | ||
|
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| private void ParseHeader(string line) | ||
| { | ||
| line = line.Trim('#').Trim(' '); | ||
| var colNames = line.Split('\t').Select(x => x.Trim(' ')).ToList(); | ||
| for (var index = 0; index < colNames.Count; index++) | ||
| { | ||
| switch (colNames[index]) | ||
| { | ||
| case "Mim Number": | ||
| _mimNumberCol = index; | ||
| break; | ||
| case "Gene Name": | ||
| _geneDescriptionCol = index; | ||
| break; | ||
| case "Approved Symbol": | ||
| _hgncCol = index; | ||
| break; | ||
| case "Phenotypes": | ||
| _phenotypeCol = index; | ||
| break; | ||
| } | ||
| } | ||
| } | ||
|
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| private static List<OmimEntry.Phenotype> ParsePhenotypes(string line) | ||
| { | ||
| var phenotypes = new List<OmimEntry.Phenotype>(); | ||
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| if (string.IsNullOrEmpty(line)) return phenotypes; | ||
|
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| var infos = line.Split(';'); | ||
| phenotypes.AddRange(infos.Select(ExtractPhenotype)); | ||
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| return phenotypes; | ||
| } | ||
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| private static OmimEntry.Phenotype ExtractPhenotype(string info) | ||
| { | ||
| info = info.Trim(' ').Replace(@"\\'","'"); | ||
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| if (string.IsNullOrWhiteSpace(info) || string.IsNullOrEmpty(info)) return null; | ||
|
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| var phenotypeRegex = new Regex(@"^(.+?)(?:,\s(\d{6}))?\s\((\d)\)(?:,\s)?(.*)?$"); | ||
| var match = phenotypeRegex.Match(info); | ||
| var phenotypeGroup = match.Groups[1].ToString(); | ||
| string phenotype; | ||
| OmimEntry.Comments comments; | ||
| ParsePhenotypeMapping(phenotypeGroup, out phenotype, out comments); | ||
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| var mimNumber = string.IsNullOrEmpty(match.Groups[2].Value) ? 0 : Convert.ToInt32(match.Groups[2].Value); | ||
| var mapping = (OmimEntry.Mapping) Convert.ToInt16(match.Groups[3].Value); | ||
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| var inheritance = string.IsNullOrEmpty(match.Groups[4].Value) ? null : match.Groups[4].ToString(); | ||
| var inheritances = ExtractInheritances(inheritance); | ||
| return new OmimEntry.Phenotype(mimNumber,phenotype,mapping,comments,inheritances); | ||
| } | ||
|
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| private static HashSet<string> ExtractInheritances(string inheritance) | ||
| { | ||
| var inheritances = new HashSet<string>(); | ||
| if (string.IsNullOrEmpty(inheritance)) return inheritances; | ||
|
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| var contents = inheritance.Split(','); | ||
| foreach (var content in contents) | ||
| { | ||
| var trimmedContent = content.Trim(' '); | ||
| inheritances.Add(trimmedContent); | ||
| } | ||
|
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| return inheritances; | ||
| } | ||
|
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| private static void ParsePhenotypeMapping(string phenotypeGroup, out string phenotype, out OmimEntry.Comments comments) | ||
| { | ||
| phenotypeGroup = phenotypeGroup.Trim(' '); | ||
| phenotype = phenotypeGroup.TrimStart('?', '{', '[').TrimEnd('}', ']'); | ||
| comments = OmimEntry.Comments.unknown; | ||
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| if (phenotypeGroup.Substring(0, 2).Contains("?")) | ||
| { | ||
| comments = OmimEntry.Comments.unconfirmed_or_possibly_spurious_mapping; | ||
| } | ||
| else | ||
| { | ||
| if (phenotypeGroup.StartsWith("{")) | ||
| { | ||
| comments = OmimEntry.Comments.contribute_to_susceptibility_to_multifactorial_disorders_or_to_susceptibility_to_infection; | ||
| }else if (phenotypeGroup.StartsWith("[")) | ||
| { | ||
| comments = OmimEntry.Comments.nondiseases; | ||
| } | ||
|
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| } | ||
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| } | ||
|
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| private static bool IsHeader(string line) | ||
| { | ||
| return line.StartsWith("# Chromosome"); | ||
| } | ||
|
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| private static bool IsContentLine(string line) | ||
| { | ||
| return !line.StartsWith("#"); | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| using System; | ||
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| namespace SAUtils | ||
| { | ||
| class Program | ||
| { | ||
| static void Main(string[] args) | ||
| { | ||
| Console.WriteLine("Hello World!"); | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| <Project Sdk="Microsoft.NET.Sdk"> | ||
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| <PropertyGroup> | ||
| <OutputType>Exe</OutputType> | ||
| <TargetFramework>netcoreapp1.1</TargetFramework> | ||
| </PropertyGroup> | ||
|
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| <ItemGroup> | ||
| <ProjectReference Include="..\VariantAnnotation\VariantAnnotation.csproj" /> | ||
| </ItemGroup> | ||
|
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| </Project> |