public void Question2(drugbanktype drugbank)
{
var path = InitQuestion(2);
var drugQuery = drugbank.drug
.Where(d => d.classification != null);
drugQuery
.SelectMany(d => d.targets
.Select(t => new DrugClassificationAndTargetSubtype(d.classification, d.drugbankid.First(id => id.primary).Value, t.id, "target")))
.ToFile(path, "drug_classification_targets.tsv");
drugQuery
.SelectMany(d => d.transporters
.Select(t => new DrugClassificationAndTargetSubtype(d.classification, d.drugbankid.First(id => id.primary).Value, t.id, "transporter")))
.ToFile(path, "drug_classification_transporters.tsv");
drugQuery
.SelectMany(d => d.enzymes
.Select(t => new DrugClassificationAndTargetSubtype(d.classification, d.drugbankid.First(id => id.primary).Value, t.id, "enzyme")))
.ToFile(path, "drug_classification_enzymes.tsv");
drugQuery
.SelectMany(d => d.carriers
.Select(t => new DrugClassificationAndTargetSubtype(d.classification, d.drugbankid.First(id => id.primary).Value, t.id, "carrier")))
.ToFile(path, "drug_classification_carriers.tsv");
}
public void Question7(drugbanktype drugbank)
{
var path = InitQuestion(7);
var targetTargetLinks = new HashSet <TargetTargetLink>();
TargetTargetLink link;
foreach (var drug in drugbank.drug)
{
foreach (var target1 in drug.targets)
{
foreach (var target2 in drug.targets)
{
if (target1 != target2)
{
link = new TargetTargetLink(target1.id, target2.id);
targetTargetLinks.TryGetValue(link, out TargetTargetLink existingLink);
link = existingLink ?? link;
link.LinkValue += 1;
targetTargetLinks.Add(link);
}
}
}
}
foreach (var targetTargetLink in targetTargetLinks)
{
targetTargetLink.LinkValue /= 2;
}
targetTargetLinks.ToFile(path, "target_target_link.tsv");
}
public void Question8(drugbanktype drugbank)
{
var path = InitQuestion(8);
var drugTargetGoClassifier = drugbank.drug
.SelectMany(d => d.targets
.Where(t => t.polypeptide != null)
.SelectMany(t => t.polypeptide
.SelectMany(p => p.goclassifiers
.Select(g => new DrugTargetGoClassifier(d, t, g))
.Distinct())));
drugTargetGoClassifier.ToFile(path, "drug_target_go_classifiers_with_dates.tsv");
drugbank.drug
.Where(d => d.targets.Length > 1)
.SelectMany(d => d.targets
.Select(t => new DrugTarget(d.drugbankid.First(id => id.primary).Value, t.id)))
.ToFile(path, "multitarget_drug_targets.tsv");
drugbank.drug
.Where(d => d.targets.Length == 1)
.SelectMany(d => d.targets
.Select(t => new DrugTarget(d.drugbankid.First(id => id.primary).Value, t.id)))
.ToFile(path, "singletarget_drug_targets.tsv");
}
public void Question4(drugbanktype drugbank)
{
var path = InitQuestion(4);
drugbank.drug
.SelectMany(d => d.targets
.Select(c => new DrugTargetGroup(d.drugbankid.First(id => id.primary).Value, c.id, d.groups.group)))
.ToFile(path, "drug_targets_groups.tsv");
}
public void Question12(drugbanktype drugbank)
{
var path = InitQuestion(12);
drugbank.drug
.Where(d => d.prices != null)
.SelectMany(d => d.prices
.Select(p => new DrugPrice(d, p)))
.ToFile(path, "drug_prices.tsv");
}
public void Question9(drugbanktype drugbank)
{
var path = InitQuestion(9);
var drugTargetPositions = drugbank.drug
.SelectMany(d => d.targets
.Where(t => t.polypeptide != null)
.SelectMany(t => t.polypeptide
.Select(p => new DrugTargetPosition(d, t.id, p.cellularlocation))));
drugTargetPositions.ToFile(path, "drug_target_positions.tsv");
}
public void Question6(drugbanktype drugbank)
{
var path = InitQuestion(6);
var targets = drugbank.drug
.SelectMany(d => d.targets
.Select(t => new DrugTarget(d.drugbankid.First(id => id.primary).Value, t.id)))
.GroupBy(dt => dt.TargetId)
.Select(group => new { targetId = group.Key, drugs = group.Select(g => g.DrugId) });
var drugDrugLinks = new HashSet <DrugDrugLink>();
DrugDrugLink link;
foreach (var target in targets)
{
foreach (var drug1 in target.drugs)
{
foreach (var drug2 in target.drugs)
{
if (drug1 != drug2)
{
link = new DrugDrugLink(drug1, drug2);
drugDrugLinks.TryGetValue(link, out DrugDrugLink existingLink);
link = existingLink ?? link;
link.LinkValue += 1;
drugDrugLinks.Add(link);
}
}
}
}
foreach (var drugDrugLink in drugDrugLinks)
{
drugDrugLink.LinkValue /= 2;
}
drugDrugLinks.ToFile(path, "drug_drug_link.tsv");
drugbank.drug
.SelectMany(d => d.druginteractions
.Select(i => new DrugInterraction(d.drugbankid.First(id => id.primary).Value, i)))
.ToFile(path, "drug_interactions.tsv");
}
public void Question3(drugbanktype drugbank)
{
var path = InitQuestion(3);
drugbank.drug
.SelectMany(d => d.carriers
.Select(c => new DrugTarget(d.drugbankid.First(id => id.primary).Value, c.id)))
.ToFile(path, "drug_carriers.tsv");
drugbank.drug
.SelectMany(d => d.transporters
.Select(t => new DrugTarget(d.drugbankid.First(id => id.primary).Value, t.id)))
.ToFile(path, "drug_transporters.tsv");
drugbank.drug
.SelectMany(d => d.enzymes
.Select(e => new DrugTarget(d.drugbankid.First(id => id.primary).Value, e.id)))
.ToFile(path, "drug_enzymes.tsv");
}
public void Question1(drugbanktype drugbank)
{
var path = InitQuestion(1);
var drugtargets = drugbank.drug
.SelectMany(d => d.targets
.Select(t => new DrugTarget(d.drugbankid.First(id => id.primary).Value, t.id)));
drugtargets.ToFile(path, "drug_targets.tsv");
var drugTargetsCountQuery = drugbank.drug.Select(d => new { id = d.drugbankid.First(id => id.primary).Value, targetsCount = d.targets.Count() });
var maxTargets = drugTargetsCountQuery.Max(d => d.targetsCount);
var minTargets = drugTargetsCountQuery.Min(d => d.targetsCount);
var drugsWithTargets = drugTargetsCountQuery.Where(d => d.targetsCount == maxTargets);
File.WriteAllLines(Path.Combine(path, "drugs_with_max_targets_count.tsv"), drugsWithTargets.Select(d => d.id).Prepend($"max targets, {maxTargets}"));
drugsWithTargets = drugTargetsCountQuery.Where(d => d.targetsCount == minTargets);
File.WriteAllLines(Path.Combine(path, "drugs_with_min_targets_count.tsv"), drugsWithTargets.Select(d => d.id).Prepend($"min targets, {minTargets}"));
File.WriteAllText(Path.Combine(path, "mean_targets_count.tsv"), drugTargetsCountQuery.Select(d => d.targetsCount).Average().ToString());
}
public void Question10(drugbanktype drugbank)
{
var path = InitQuestion(10);
Console.WriteLine("Enter modifications tsv file path...");
var modsFile = Console.ReadLine();
var mods = File.ReadAllLines(modsFile).Select(l => new Modifications(l));
var targetModifications = drugbank.drug
.SelectMany(d => d.targets
.Where(t => t.polypeptide != null)
.SelectMany(t => t.polypeptide
.Select(p => new TargetModifications(t.id, p.id, p.goclassifiers))));
targetModifications = targetModifications.Join(mods,
t => t.UniprotId,
m => m.UniprotId,
(t, m) => new TargetModifications(t, m));
targetModifications
.ToFile(path, "target_mods.tsv");
}
