public Sequence(CazyItem item)
{
this.Organism = item.Organism;
this.Name = item.ProteinName;
this.FastaUrl = item.UniprotUrl;
this.FastaProtein = item.FastaProtein;
this.Lineage = item.Lineage;
}
public CazyItem GetItemFromSequence()
{
CazyItem item = new CazyItem();
item.Lineage = this.Lineage;
item.UniprotUrl = this.FastaUrl;
item.Organism = this.Organism;
item.ProteinName = this.Name;
return(item);
}
private void GetFastaFormat(CazyItem item)
{
try
{
item.FastaProtein = webClient.DownloadString(uniprotLink + item.UniprotUrl + ".fasta");
}
catch (Exception e)
{
item.FastaProtein = null;
}
}
private void RecItem(HtmlNode node)
{
CazyItem item = new CazyItem();
if (node.Name == "tr")
{
int index = 0;
foreach (var n in node.ChildNodes.Where(x => x.Name != "#text"))
{
if (n.Name == "td")
{
switch (index)
{
case 0: item.ProteinName = n.InnerText.Replace(" ", ""); break;
case 2: item.Organism = ParseOrganismName(n.InnerText); break;
case 4: item.UniprotUrl = n.InnerText.Replace(" ", ""); break;
}
index++;
}
}
if (!String.IsNullOrEmpty(item.UniprotUrl))
{
if (!items.Select(x => x.ProteinName).Contains(item.ProteinName) && !items.Select(x => x.Organism).Contains(item.Organism))
{
if (!String.IsNullOrEmpty(Pattern))
{
GetFastaFormat(item);
GetLineage(item);
if (item.ProteinName.ToUpper().Contains(Pattern.ToUpper()))
{
if (item.FastaProtein != null)
{
items.Add(item);
}
}
}
else
{
GetFastaFormat(item);
GetLineage(item);
if (item.FastaProtein != null)
{
items.Add(item);
}
}
}
}
}
}
private void GetLineage(CazyItem item)
{
try
{
string json = webClient.DownloadString(taxonomyLink + item.Organism);
if (json != "No results.")
{
dynamic jsonDynamic = JsonConvert.DeserializeObject <dynamic>(json);
string lineage = jsonDynamic[0].lineage;
string[] lineageSplit = lineage.Split(new string[] { ";" }, StringSplitOptions.RemoveEmptyEntries);
if (lineageSplit != null && lineageSplit.Any())
{
item.Lineage = lineageSplit.Select(x => x.Replace(" ", "")).Where(x => !String.IsNullOrEmpty(x)).ToList();
}
}
}
catch (Exception e)
{
}
}
