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#include "myutils.h"
#include "chime.h"
#include "seqdb.h"
#include "dp.h"
#include "ultra.h"
#include "hspfinder.h"
#include <algorithm>
#include <set>
bool SearchChime(Ultra &U, const SeqData &QSD, float QAb,
const AlnParams &AP, const AlnHeuristics &AH, HSPFinder &HF,
float MinFractId, ChimeHit2 &Hit);
FILE *g_fUChime;
FILE *g_fUChimeAlns;
const vector<float> *g_SortVecFloat;
bool g_UchimeDeNovo = false;
void Usage()
{
printf("\n");
printf("UCHIME %s by Robert C. Edgar\n", MY_VERSION);
printf("http://www.drive5.com/uchime\n");
printf("\n");
printf("This software is donated to the public domain\n");
printf("\n");
printf(
#include "help.h"
);
}
void SetBLOSUM62()
{
Die("SetBLOSUM62 not implemented");
}
void ReadSubstMx(const string &/*FileName*/, Mx<float> &/*Mxf*/)
{
Die("ReadSubstMx not implemented");
}
void LogAllocs()
{
/*empty*/
}
static bool CmpDescVecFloat(unsigned i, unsigned j)
{
return (*g_SortVecFloat)[i] > (*g_SortVecFloat)[j];
}
void Range(vector<unsigned> &v, unsigned N)
{
v.clear();
v.reserve(N);
for (unsigned i = 0; i < N; ++i)
v.push_back(i);
}
void SortDescending(const vector<float> &Values, vector<unsigned> &Order)
{
StartTimer(Sort);
const unsigned N = SIZE(Values);
Range(Order, N);
g_SortVecFloat = &Values;
sort(Order.begin(), Order.end(), CmpDescVecFloat);
EndTimer(Sort);
}
float GetAbFromLabel(const string &Label)
{
vector<string> Fields;
Split(Label, Fields, '/');
const unsigned N = SIZE(Fields);
for (unsigned i = 0; i < N; ++i)
{
const string &Field = Fields[i];
if (Field.substr(0, 3) == "ab=")
{
string a = Field.substr(3, string::npos);
return (float) atof(a.c_str());
}
}
if (g_UchimeDeNovo)
Die("Missing abundance /ab=xx/ in label >%s", Label.c_str());
return 0.0;
}
int main(int argc, char *argv[])
{
MyCmdLine(argc, argv);
if (argc < 2)
{
Usage();
return 0;
}
if (opt_version)
{
printf("uchime v" MY_VERSION ".%s\n", SVN_VERSION);
return 0;
}
printf("uchime v" MY_VERSION ".%s\n", SVN_VERSION);
printf("by Robert C. Edgar\n");
printf("http://drive5.com/uchime\n");
printf("This code is donated to the public domain.\n");
printf("\n");
if (!optset_w)
opt_w = 8;
float MinFractId = 0.95f;
if (optset_id)
MinFractId = (float) opt_id;
Log("%8.2f minh\n", opt_minh);
Log("%8.2f xn\n", opt_xn);
Log("%8.2f dn\n", opt_dn);
Log("%8.2f xa\n", opt_xa);
Log("%8.2f mindiv\n", opt_mindiv);
Log("%8u maxp\n", opt_maxp);
if (opt_input == "" && opt_uchime != "")
opt_input = opt_uchime;
if (opt_input == "")
Die("Missing --input");
g_UchimeDeNovo = (opt_db == "");
if (opt_uchimeout != "")
g_fUChime = CreateStdioFile(opt_uchimeout);
if (opt_uchimealns != "")
g_fUChimeAlns = CreateStdioFile(opt_uchimealns);
SeqDB Input;
SeqDB DB;
Input.FromFasta(opt_input);
if (!Input.IsNucleo())
Die("Input contains amino acid sequences");
const unsigned QuerySeqCount = Input.GetSeqCount();
vector<unsigned> Order;
for (unsigned i = 0; i < QuerySeqCount; ++i)
Order.push_back(i);
if (g_UchimeDeNovo)
{
vector<float> Abs;
for (unsigned i = 0; i < QuerySeqCount; ++i)
{
const char *Label = Input.GetLabel(i);
float Ab = GetAbFromLabel(Label);
Abs.push_back(Ab);
}
SortDescending(Abs, Order);
DB.m_IsNucleoSet = true;
DB.m_IsNucleo = true;
}
else
{
DB.FromFasta(opt_db);
if (!DB.IsNucleo())
Die("Database contains amino acid sequences");
}
vector<ChimeHit2> Hits;
unsigned HitCount = 0;
for (unsigned i = 0; i < QuerySeqCount; ++i)
{
unsigned QuerySeqIndex = Order[i];
SeqData QSD;
Input.GetSeqData(QuerySeqIndex, QSD);
float QAb = -1.0;
if (g_UchimeDeNovo)
QAb = GetAbFromLabel(QSD.Label);
ChimeHit2 Hit;
AlnParams &AP = *(AlnParams *) 0;
AlnHeuristics &AH = *(AlnHeuristics *) 0;
HSPFinder &HF = *(HSPFinder *) 0;
bool Found = SearchChime(DB, QSD, QAb, AP, AH, HF, MinFractId, Hit);
if (Found)
++HitCount;
else
{
if (g_UchimeDeNovo)
DB.AddSeq(QSD.Label, QSD.Seq, QSD.L);
}
WriteChimeHit(g_fUChime, Hit);
ProgressStep(i, QuerySeqCount, "%u/%u chimeras found (%.1f%%)", HitCount, i, Pct(HitCount, i+1));
}
Log("\n");
Log("%s: %u/%u chimeras found (%.1f%%)\n",
opt_input.c_str(), HitCount, QuerySeqCount, Pct(HitCount, QuerySeqCount));
CloseStdioFile(g_fUChime);
CloseStdioFile(g_fUChimeAlns);
ProgressExit();
return 0;
}
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