private static void ParseLocation(XElement locEle, ISequenceRegion loc)
{
loc.Seqname = locEle.Attribute("seqname").Value;
loc.Start = long.Parse(locEle.Attribute("start").Value);
loc.End = long.Parse(locEle.Attribute("end").Value);
loc.Strand = locEle.Attribute("strand").Value[0];
}
public SequenceRegion(ISequenceRegion source)
{
this.Seqname = source.Seqname;
this.Start = source.Start;
this.End = source.End;
this.Name = source.Name;
this.Strand = source.Strand;
this.Sequence = source.Sequence;
}
public bool HasOverlap(ISequenceRegion loc)
{
if (loc == null)
{
return(false);
}
return(this.Contains(loc.Start) || loc.Contains(this.Start));
}
public GtfItem(ISequenceRegion source)
: this()
{
this.Name = source.Name;
this.Seqname = source.Seqname;
this.Start = source.Start;
this.End = source.End;
this.Strand = source.Strand;
this.Sequence = source.Sequence;
}
public static long Offset(this ISequenceRegion actual, ISequenceRegion reference)
{
if (reference.Strand == '-')
{
return(reference.End - actual.End);
}
else
{
return(actual.Start - reference.Start);
}
}
public static string GetDisplayName(this ISequenceRegion sr)
{
if (!string.IsNullOrEmpty(sr.Sequence))
{
return(sr.Name + ":" + sr.Sequence);
}
else
{
return(sr.Name);
}
}
/// <summary>
/// Check if two regions are container-containee. If one contains two, return 1. If two contains one, return -1. Otherwise return 0.
/// </summary>
/// <param name="one">first region</param>
/// <param name="two">second region</param>
/// <returns>result</returns>
public static int Contains(this ISequenceRegion one, ISequenceRegion two)
{
if (one.Length >= two.Length)
{
if (one.Start <= two.Start && one.End >= two.End)
{
return(1);
}
return(0);
}
if (two.Start <= one.Start && two.End >= one.End)
{
return(-1);
}
return(0);
}
public static double OverlapPercentage(this ISequenceRegion one, ISequenceRegion two)
{
if (!one.Seqname.Equals(two.Seqname))
{
return(0.0);
}
ISequenceRegion first, second;
if (one.Start < two.Start || (one.Start == two.Start && one.End > two.End))
{
first = one;
second = two;
}
else
{
first = two;
second = one;
}
//no-overlap
if (first.End < second.Start)
{
return(0.0);
}
//contain
if (first.End >= second.End)
{
return(1.0);
}
//overlap
var overlap = first.End - second.Start + 1.0;
return(overlap / Math.Min(first.Length, second.Length));
}
public FeatureLocation(ISequenceRegion source)
: base(source)
{
this.SamLocations = new List<FeatureSamLocation>();
}
public FeatureLocation(ISequenceRegion source)
: base(source)
{
this.SamLocations = new List <FeatureSamLocation>();
}
public GtfItem(ISequenceRegion source)
: this()
{
this.Name = source.Name;
this.Seqname = source.Seqname;
this.Start = source.Start;
this.End = source.End;
this.Strand = source.Strand;
this.Sequence = source.Sequence;
}
public void Union(ISequenceRegion loc)
{
this.Start = Math.Min(this.Start, loc.Start);
this.End = Math.Max(this.End, loc.End);
}
/// <summary>
/// Get location using chrom:start-end:strand format
/// </summary>
/// <param name="sr"></param>
/// <returns></returns>
public static string GetLocation(this ISequenceRegion sr)
{
return(string.Format("{0}:{1}-{2}:{3}", sr.Seqname, sr.Start, sr.End, sr.Strand));
}
public static bool Overlap(this ISequenceRegion one, ISequenceRegion two, double minPercentage)
{
var perc = OverlapPercentage(one, two);
return(perc > 0 && perc >= minPercentage);
}
public static void UnionWith(this ISequenceRegion loc, ISequenceRegion item)
{
loc.Start = Math.Min(loc.Start, item.Start);
loc.End = Math.Max(loc.End, item.End);
}
/// <summary>
/// Get name and location using (name)chrom:start-end:strand format
/// </summary>
/// <param name="sr"></param>
/// <returns></returns>
public static string GetNameLocation(this ISequenceRegion sr)
{
return(string.Format("({0}){1}", sr.Name, sr.GetLocation()));
}
