public void TestIpiToUniprot()
{
var mapper = new IpiToUniprotMap();
Assert.AreEqual("O95793", mapper.MapToUniprot("IPI0000001")); // The 0th one
Assert.AreEqual("Q28062", mapper.MapToUniprot("IPI1028485")); // The nth one
Assert.AreEqual("IPI1028486", mapper.MapToUniprot("IPI1028486")); // The n+1th nonexistent one
Assert.AreEqual("IPI1027205", mapper.MapToUniprot("IPI1027205")); // A midrange nonexistent one
Assert.AreEqual("Q2V4A8", mapper.MapToUniprot("IPI0657347")); // Somewhere in the middle
Assert.AreEqual("IPI0000000", mapper.MapToUniprot("IPI0000000")); // The -1th nonexistent one
Assert.AreEqual("nonsense", mapper.MapToUniprot("nonsense")); // The really nonexistent one
Assert.AreEqual("O14686", mapper.MapToUniprot("IPI0297859")); // Somewhere in the middle
Assert.AreEqual("P42025", mapper.MapToUniprot("IPI029469")); // Somewhere toward the front
}
/// <summary>
/// Peruse the list of proteins, access webservices as needed to resolve protein metadata.
/// note: best to use this in its own thread since it may block on web access
/// </summary>
/// <param name="proteinsToSearch">the proteins to populate</param>
/// <param name="progressMonitor">For checking operation cancellation</param>
/// <param name="singleBatch">if true, just do one batch and plan to come back later for more</param>
/// <returns>IEnumerable of the proteins it actually populated (some don't need it, some have to wait for a decent web connection)</returns>
public IEnumerable<ProteinSearchInfo> DoWebserviceLookup(IEnumerable<ProteinSearchInfo> proteinsToSearch, IProgressMonitor progressMonitor, bool singleBatch)
{
const int SINGLE_BATCH_SIZE = 500; // If caller has indicated that it wants to do a single batch and return for more later, stop after this many successes
const int ENTREZ_RATELIMIT = 333; // 1/3 second between requests on Entrez
const int UNIPROTKB_RATELIMIT = 10;
var searchOrder = new[]
{
GENINFO_TAG,
ENTREZ_TAG,
UNIPROTKB_TAG // this order matters - we may take entrez results into uniprot for further search
};
var minSearchTermLen = new Dictionary<char, int>
{
{GENINFO_TAG, 3}, // some gi numbers are quite small
{ENTREZ_TAG, 6},
{UNIPROTKB_TAG, 6} // if you feed uniprot a partial search term you get a huge response
};
var ratelimit = new Dictionary<char, int>
{
{GENINFO_TAG, ENTREZ_RATELIMIT}, // search on Entrez, but don't mix with non-GI searches
{ENTREZ_TAG, ENTREZ_RATELIMIT},
{UNIPROTKB_TAG, UNIPROTKB_RATELIMIT}
};
// sort out the various webservices so we can batch up
var proteins = proteinsToSearch.ToArray();
foreach (var prot in proteins)
{
// translate from IPI to Uniprot if needed
var search = prot.GetProteinMetadata().GetPendingSearchTerm().ToUpperInvariant();
if (search.StartsWith("IPI")) // Not L10N
{
if (_ipiMapper == null)
_ipiMapper = new IpiToUniprotMap();
string mapped = _ipiMapper.MapToUniprot(search);
if (mapped == search) // no mapping from that IPI
{
prot.SetWebSearchCompleted(); // no resolution for that IPI value
}
else
{
prot.Accession = mapped; // go ahead and note the Uniprot accession, even though we haven't searched yet
prot.SetWebSearchTerm(new WebSearchTerm(UNIPROTKB_TAG,mapped));
}
}
else if (prot.GetProteinMetadata().GetSearchType() == UNIPROTKB_TAG)
{
// Check for homegrown numbering schemes
long dummy;
if (Int64.TryParse(search, out dummy))
{
prot.SetWebSearchCompleted(); // All numbers, not a Uniprot ID
}
// Some uniprot records just don't have gene info - have we already parsed all there is to know from description?
else if (prot.GetProteinMetadata().HasMissingMetadata())
{
var test = prot.GetProteinMetadata().ChangeGene("test"); // Not L10N
if (!test.HasMissingMetadata()) // We got everything except gene info
{
// Check to see if this is a standard uniprot formatted header, if so assume that GN was ommitted on purpose
if (prot.GetProteinMetadata().Description.Contains(string.Format(" OS={0} ", (prot.GetProteinMetadata().Species)))) // Not L10N
prot.SetWebSearchCompleted(); // There's not going to be any gene info
}
}
}
if (prot.GetProteinMetadata().NeedsSearch())
{
// if you feed uniprot a partial search term you get a huge response
int minLen = minSearchTermLen[prot.GetProteinMetadata().GetSearchType()];
if (prot.GetProteinMetadata().GetPendingSearchTerm().Length < minLen)
{
prot.SetWebSearchCompleted(); // don't attempt it
}
}
if (!(prot.GetProteinMetadata().NeedsSearch()))
{
yield return prot; // doesn't need search, just pass it back unchanged
}
}
_ipiMapper = null; // Done with this now
// CONSIDER(bspratt): Could this be simplified?
var cancelled = false;
var politeStopwatch = new Stopwatch();
var totalSuccessesThisBatch = 0;
politeStopwatch.Start();
var furtherUniprotSearches = new List<ProteinSearchInfo>(); // Uniprot searches that result from intermediate searches
foreach (var searchType in searchOrder)
{
var consecutiveFailures = 0;
var failureCount = 0;
var successCount = 0;
cancelled |= ((progressMonitor != null) && progressMonitor.IsCanceled);
if (cancelled)
break;
var politenessIntervalMsec = ratelimit[searchType];
var batchsizeIncreaseThreshold = 2; // If you can do this many in a row at reduced batchsize, try increasing it
while (true)
{
var idealBatchsize = _maxBatchSize[searchType];
cancelled |= ((progressMonitor != null) && progressMonitor.IsCanceled);
if (cancelled)
break;
var type = searchType;
var furtherUniprotSearchesToProcess = Equals(searchType, UNIPROTKB_TAG)
? furtherUniprotSearches.Where(s => (s.GetProteinMetadata().NeedsSearch())).ToList()
: null;
var searchlist = (furtherUniprotSearchesToProcess != null && furtherUniprotSearchesToProcess.Any())
? furtherUniprotSearchesToProcess
: proteins.Where(s => (s.GetProteinMetadata().NeedsSearch() &&
s.GetProteinMetadata().GetSearchType() == type)).ToList();
if (!searchlist.Any())
break;
// try to batch up requests - reduce batch size if responses are ambiguous
var nextSearch = 0;
var searches = new List<ProteinSearchInfo>();
while ((nextSearch < searchlist.Count) && (searches.Count < _batchsize[searchType]))
{
// Unique sequence length helps a lot in disambiguation
if (searches.All(s => s.SeqLength != searchlist[nextSearch].SeqLength))
searches.Add(searchlist[nextSearch]);
nextSearch++;
}
// Be a good citizen - no more than three hits per second for Entrez
var snoozeMs = politenessIntervalMsec - politeStopwatch.ElapsedMilliseconds;
if (snoozeMs > 0)
Thread.Sleep((int)snoozeMs);
politeStopwatch.Restart();
cancelled |= ((progressMonitor != null) && progressMonitor.IsCanceled);
if (cancelled)
break;
var processed = DoWebserviceLookup(searches, searchType, progressMonitor);
if (processed < 0) // Returns negative on web access error
{
if (processed == -2)
{
// We're creating URLs that are too long
_maxBatchSize[searchType] = Math.Max(1, (int)(_maxBatchSize[searchType] * 0.75));
}
else
{
// Some error, we should just try again later so don't retry now
break;
}
}
var success = false;
foreach (var s in searches)
{
if (s.GetProteinMetadata().GetPendingSearchTerm().Length == 0)
{
yield return s; // We've processed it
if (s.Status == ProteinSearchInfo.SearchStatus.success)
{
success = true;
_successCountAtThisBatchsize[searchType]++;
}
}
else
{
// possibly an Entrez search we wish to further process in Uniprot
var newSearchType = s.GetProteinMetadata().GetSearchType();
if ((newSearchType != searchType) && (Equals(newSearchType, UNIPROTKB_TAG)))
{
success = true; // Entrez search worked, leads us to a UniprotKB search
s.Status = ProteinSearchInfo.SearchStatus.unsearched; // Not yet search as UniprotKB
furtherUniprotSearches.Add(s);
_successCountAtThisBatchsize[searchType]++;
}
else if (_batchsize[searchType] == 1)
{
// No ambiguity is possible at batchsize==1, this one just plain didn't work
s.SetWebSearchCompleted();
yield return s;
}
}
}
// Review the overall history - how is this working out?
foreach (var s in searchlist)
{
if (s.Status == ProteinSearchInfo.SearchStatus.success)
{
successCount++;
totalSuccessesThisBatch++;
consecutiveFailures = 0;
}
else if (s.Status == ProteinSearchInfo.SearchStatus.failure)
{
failureCount++;
consecutiveFailures++;
}
if ((consecutiveFailures > (MAX_CONSECUTIVE_PROTEIN_METATDATA_LOOKUP_FAILURES + successCount)) ||
((failureCount + successCount) > 100 &&
failureCount / (double)(failureCount + successCount) > .5))
{
// We have failed a bunch in a row, or more than half overall. Assume the rest are the same as this streak, and bail.
// That "+ successCount" term above guards against the case where we're a few hundred successes in then
// we hit a bad patch (though this is unlikely - FASTA files tend to be internally consistent).
foreach (var ss in searchlist)
{
if (ss.GetProteinMetadata().GetPendingSearchTerm().Length > 0)
{
ss.NoteSearchFailure();
ss.SetWebSearchCompleted(); // Just tag this as having been tried
yield return ss; // And move on
}
}
break;
}
}
if (success)
{
if ((_successCountAtThisBatchsize[searchType] > batchsizeIncreaseThreshold) && (_batchsize[searchType] < idealBatchsize))
{
_batchsize[searchType] = Math.Min(idealBatchsize, _batchsize[searchType]*2);
_successCountAtThisBatchsize[searchType] = 0;
}
if (singleBatch && (totalSuccessesThisBatch >= SINGLE_BATCH_SIZE))
{ // Probably called from a background loader that's trying to be polite
break; // done with this search type for now, but go on to the next if any (especially for follow-on Uniprot searches)
}
}
else
{
_batchsize[searchType] = Math.Max(1, _batchsize[searchType] / 2);
_successCountAtThisBatchsize[searchType] = 0;
batchsizeIncreaseThreshold = Math.Max(batchsizeIncreaseThreshold, batchsizeIncreaseThreshold * 2); // Get increasingly pessimistic (watch for integer rollover)
}
}
}
}
