public static List <SomaticItem> ParseAnnovarFile(string fileName, Regex reg, string scorePrefix, Func <string, bool> acceptChromosome)
{
var result = new List <SomaticItem>();
var bar = Path.GetFileName(fileName).StringBefore(".");
var annos = new AnnotationFormat("^#").ReadFromFile(fileName);
var headers = File.ReadAllLines(fileName).Where(l => !l.StartsWith("#")).First().Split('\t');
foreach (var ann in annos)
{
//Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene snp138 cosmic70 FILTER INFO FORMAT H_LS-A7-A0D9-01A-31W-A071-09-1 H_LS-A7-A0D9-10A-01W-A071-09-1
var chr = ann.Annotations["Chr"].ToString();
if (!acceptChromosome(chr))
{
continue;
}
var m1 = reg.Match(ann.Annotations[headers[headers.Length - 2]].ToString());
var m1Major = int.Parse(m1.Groups[1].Value);
var m1Minor = int.Parse(m1.Groups[2].Value);
var m2 = reg.Match(ann.Annotations[headers[headers.Length - 1]].ToString());
var m2Major = int.Parse(m2.Groups[1].Value);
var m2Minor = int.Parse(m2.Groups[2].Value);
var isNormalFirst = (((double)m1Minor) / (m1Major + m1Minor)) < (((double)m2Minor) / (m2Major + m2Minor));
var info = ann.Annotations["INFO"].ToString();
var item = new SomaticItem()
{
Sample = bar,
Chrom = chr,
StartPosition = int.Parse(ann.Annotations["Start"].ToString()),
RefAllele = ann.Annotations["Ref"].ToString(),
AltAllele = ann.Annotations["Alt"].ToString(),
NormalMajorCount = isNormalFirst ? m1Major : m2Major,
NormalMinorCount = isNormalFirst ? m1Minor : m2Minor,
TumorMajorCount = isNormalFirst ? m2Major : m1Major,
TumorMinorCount = isNormalFirst ? m2Minor : m1Minor,
Score = double.Parse(info.StringAfter(scorePrefix)),
RefGeneFunc = GetDictionaryValue(ann.Annotations, "Func.refGene", string.Empty),
RefGeneName = GetDictionaryValue(ann.Annotations, "Gene.refGene", string.Empty),
RefGeneExonicFunc = GetDictionaryValue(ann.Annotations, "ExonicFunc.refGene", string.Empty)
};
result.Add(item);
}
return(result);
}
public static List <SomaticItem> ParseGlmvcFile(string fileName, Func <string, bool> acceptChromosome)
{
var result = new List <SomaticItem>();
var bar = Path.GetFileName(fileName).StringBefore(".");
var annos = new AnnotationFormat().ReadFromFile(fileName);
foreach (var ann in annos)
{
var chr = ann.Annotations["chr"].ToString();
if (!acceptChromosome(chr))
{
continue;
}
var fdr = ann.Annotations["brglm_group_fdr"].ToString();
var item = new SomaticItem()
{
Sample = bar,
Chrom = chr,
StartPosition = int.Parse(ann.Annotations["start"].ToString()),
RefAllele = ann.Annotations["major_allele"].ToString(),
AltAllele = ann.Annotations["minor_allele"].ToString(),
NormalMajorCount = int.Parse(ann.Annotations["normal_major_count"].ToString()),
NormalMinorCount = int.Parse(ann.Annotations["normal_minor_count"].ToString()),
TumorMajorCount = int.Parse(ann.Annotations["tumor_major_count"].ToString()),
TumorMinorCount = int.Parse(ann.Annotations["tumor_minor_count"].ToString()),
LogisticScore = ann.Annotations["brglm_score"].ToString(),
LogisticStrand = ann.Annotations["brglm_strand"].ToString(),
LogisticPosition = ann.Annotations["brglm_position"].ToString(),
LogisticGroupFdr = fdr,
Score = -Math.Log(double.Parse(fdr)),
RefGeneFunc = GetDictionaryValue(ann.Annotations, "annovar_Func.refGene", string.Empty),
RefGeneName = GetDictionaryValue(ann.Annotations, "annovar_Gene.refGene", string.Empty),
RefGeneExonicFunc = GetDictionaryValue(ann.Annotations, "annovar_ExonicFunc.refGene", string.Empty),
RefGeneAAChange = GetDictionaryValue(ann.Annotations, "annovar_AAChange.refGene", string.Empty),
};
result.Add(item);
}
return(result);
}
public static List<SomaticItem> ParseAnnovarFile(string fileName, Regex reg, string scorePrefix, Func<string, bool> acceptChromosome)
{
var result = new List<SomaticItem>();
var bar = Path.GetFileName(fileName).StringBefore(".");
var annos = new AnnotationFormat("^#").ReadFromFile(fileName);
var headers = File.ReadAllLines(fileName).Where(l => !l.StartsWith("#")).First().Split('\t');
foreach (var ann in annos)
{
//Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene snp138 cosmic70 FILTER INFO FORMAT H_LS-A7-A0D9-01A-31W-A071-09-1 H_LS-A7-A0D9-10A-01W-A071-09-1
var chr = ann.Annotations["Chr"].ToString();
if (!acceptChromosome(chr))
{
continue;
}
var m1 = reg.Match(ann.Annotations[headers[headers.Length - 2]].ToString());
var m1Major = int.Parse(m1.Groups[1].Value);
var m1Minor = int.Parse(m1.Groups[2].Value);
var m2 = reg.Match(ann.Annotations[headers[headers.Length - 1]].ToString());
var m2Major = int.Parse(m2.Groups[1].Value);
var m2Minor = int.Parse(m2.Groups[2].Value);
var isNormalFirst = (((double)m1Minor) / (m1Major + m1Minor)) < (((double)m2Minor) / (m2Major + m2Minor));
var info = ann.Annotations["INFO"].ToString();
var item = new SomaticItem()
{
Sample = bar,
Chrom = chr,
StartPosition = int.Parse(ann.Annotations["Start"].ToString()),
RefAllele = ann.Annotations["Ref"].ToString(),
AltAllele = ann.Annotations["Alt"].ToString(),
NormalMajorCount = isNormalFirst ? m1Major : m2Major,
NormalMinorCount = isNormalFirst ? m1Minor : m2Minor,
TumorMajorCount = isNormalFirst ? m2Major : m1Major,
TumorMinorCount = isNormalFirst ? m2Minor : m1Minor,
Score = double.Parse(info.StringAfter(scorePrefix)),
RefGeneFunc = GetDictionaryValue(ann.Annotations, "Func.refGene", string.Empty),
RefGeneName = GetDictionaryValue(ann.Annotations, "Gene.refGene", string.Empty),
RefGeneExonicFunc = GetDictionaryValue(ann.Annotations, "ExonicFunc.refGene", string.Empty)
};
result.Add(item);
}
return result;
}
public static List<SomaticItem> ParseGlmvcFile(string fileName, Func<string, bool> acceptChromosome)
{
var result = new List<SomaticItem>();
var bar = Path.GetFileName(fileName).StringBefore(".");
var annos = new AnnotationFormat().ReadFromFile(fileName);
foreach (var ann in annos)
{
var chr = ann.Annotations["chr"].ToString();
if (!acceptChromosome(chr))
{
continue;
}
var fdr = ann.Annotations["brglm_group_fdr"].ToString();
var item = new SomaticItem()
{
Sample = bar,
Chrom = chr,
StartPosition = int.Parse(ann.Annotations["start"].ToString()),
RefAllele = ann.Annotations["major_allele"].ToString(),
AltAllele = ann.Annotations["minor_allele"].ToString(),
NormalMajorCount = int.Parse(ann.Annotations["normal_major_count"].ToString()),
NormalMinorCount = int.Parse(ann.Annotations["normal_minor_count"].ToString()),
TumorMajorCount = int.Parse(ann.Annotations["tumor_major_count"].ToString()),
TumorMinorCount = int.Parse(ann.Annotations["tumor_minor_count"].ToString()),
LogisticScore = ann.Annotations["brglm_score"].ToString(),
LogisticStrand = ann.Annotations["brglm_strand"].ToString(),
LogisticPosition = ann.Annotations["brglm_position"].ToString(),
LogisticGroupFdr = fdr,
Score = -Math.Log(double.Parse(fdr)),
RefGeneFunc = GetDictionaryValue(ann.Annotations, "annovar_Func.refGene", string.Empty),
RefGeneName = GetDictionaryValue(ann.Annotations, "annovar_Gene.refGene", string.Empty),
RefGeneExonicFunc = GetDictionaryValue(ann.Annotations, "annovar_ExonicFunc.refGene", string.Empty),
RefGeneAAChange = GetDictionaryValue(ann.Annotations, "annovar_AAChange.refGene", string.Empty),
};
result.Add(item);
}
return result;
}