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/* BaitFisher (version 1.2.8) a program for designing DNA target enrichment baits
* Copyright 2013-2016 by Christoph Mayer
*
* This source file is part of the BaitFisher-package.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with BaitFisher. If not, see <http://www.gnu.org/licenses/>.
*
*
* For any enquiries send an Email to Christoph Mayer
* c.mayer.zfmk@uni-bonn.de
*
* When publishing work that is based on the results please cite:
* Mayer et al. 2016: BaitFisher: A software package for multi-species target DNA enrichment probe design
*
*/
#include "Csequence_cluster_and_center_sequence.h"
#include "DEBUG_STUFF.h"
using namespace std;
CDistance_Cluster *p_global_distcluster;
bool global_bad_dist_this_range;
void call_back_distance(short i1, short i2, double dist)
{
if (dist < 0)
global_bad_dist_this_range = true;
else
p_global_distcluster->add(i1, i2, dist);
}
void Csequence_loci_cluster_collection::cluster_locus(faststring & region_name, const faststring &filename)
{
// TODO:
// We have to check how many (valid) sequences we have.
// If this number is just 0 or 1, the clustering will fail and we need a workaround.
// The number of valid sequences has been determined in the constructor of this object.
if (number_of_valid_sequences < 2)
{
if (number_of_valid_sequences == 0)
{
if (global_VERBOSITY >= VERBOSITY_MOREWARNINGS)
{
cout << "WARNING: Found 0 valid sequences in bait window in Csequence_loci_cluster_collection::cluster_locus()." << endl;
cout << " Alignment file: " << filename << endl;
cout << " Region/gene name: " << region_name << endl;
cout << " Within gene coordinates: " << pos_start+1 << "-" << pos_end << endl;
}
}
if (number_of_valid_sequences == 1)
{
// TODO: Report this only if
if (global_VERBOSITY >= VERBOSITY_MOREWARNINGS)
{
cout << "Note: Found 1 valid sequence in bait window in Csequence_loci_cluster_collection::cluster_locus(). Clustering will be skipped. Bait will be constructed from single sequence." << endl;
cout << " Alignment file: " << filename << endl;
cout << " Region/gene name: " << region_name << endl;
cout << " Within gene coordinates: " << pos_start+1 << "-" << pos_end << endl;
}
// TODO: Uncomment and adapt:
Csequence_cluster_and_center_sequence empty_cluster_and_center_sequence;
// Add an empty object
list_of_clusters.push_back(empty_cluster_and_center_sequence);
if (global_VERBOSITY > 2000)
{
cout << "Object that will be assigned: *******" << endl;
list_of_clusters.back().print(cout);
cout << "*************************************" << endl;
}
// Fill the object
set<short> seq_set;
unsigned i, N = valid_sequences.size();
for (i=0; i < N; ++i)
{
if (valid_sequences[i])
seq_set.insert(i);
}
list_of_clusters.back().assign(pos_start, pos_end, 0, seq_set, this, msa);
if (global_VERBOSITY > 2000)
{
cout << "Object after having been assigned:***" << endl;
list_of_clusters.back().print(cout);
cout << "*************************************" << endl;
}
} // END if (number_of_valid_sequences == 1)
// Prints data for all clusters in this locus. Center sequences are not computed yet.
if (global_VERBOSITY > 2000)
{
print(cout);
}
return;
} // END if (number_of_valid_sequences < 2)
// Create cluster object:
CDistance_Cluster cluster_object;
// We initialise the global pointer to the cluster_object.
// This pointer is used by the global call_back_distance function,
// which we pass to the CSequences2 class where it is used to
// fill the cluster_object with the distances of the sequences.
p_global_distcluster = &cluster_object;
// One problem exists with the sequences that contain gaps or Ns in the window we investigate.
// The clustering algorithm assumes that all sequence numbers are present during clustering,
// so we cannot skip sequences. So. we have to add distances for all sequences in the sequences objects.
// We also do not want to copy the sequences to a new CSequences2 object. Then we have to keep track
// of the new sequence number, and we have global unique numbers, sequence numbers in the exon,
// sequence numbers in the window.
// The best compromise is to add very large distances to the clustering algorithm and to remove
// the "non-present" sequences after the clustering has been done.
// Due to the large distances we assign to all sequence pairs in which one sequence is not valid, non of
// the invalid sequences will be clustered with any other sequence.
// Valid distances among sequences are in the range 0..1.
// With a larger value we indicate a problem, e.g. Ns or gaps in the sequences.
// In order not to cluster sequences that contain Ns or gaps, we
// set the dist_threshold to a maximum value of 10.
// Distances with a value >10 will not be clustered.
// A good value for distances of sequences that contain gaps or Ns is 100.
// Add distances:
seqs->get_sequences_distances(pos_start, pos_end,
call_back_distance,
valid_sequences, 0);
if (global_VERBOSITY > 3000)
{
cout << "Sorted distances in this cluster object" << endl;
cluster_object.print_sorted(cout);
cout << endl;
}
if (global_VERBOSITY >= 900)
{
// Print filename, region name, within gene/alignment coordinate, maximum sequence distance
// for this starting position/locus.
cout << "Maximum distance:\t" << filename << "\t" << region_name << "\t" << pos_start+1 << "\t"
<< cluster_object.max_distance() << endl;
}
// Do clustering:
cluster_object.run_clustering(dist_threshold);
if (global_VERBOSITY > 900)
{
faststring cluster_string;
cluster_object.get_cluster_string2(cluster_string);
cout << "Clustering string: " << cluster_string << endl;
}
// Retrieve results: Store all valid clusters in the list of clusters "list_of_clusters" of this locus.
set<short> seq_set;
// set<short> seq_set_uniq_numbers;
set<short>::iterator it_set, it_set_end;
double max_dist_in_clu;
short i;
bool valid_cluster;
Csequence_cluster_and_center_sequence empty_cluster_and_center_sequence;
i=0;
// For all clusters at this locus:
while ( cluster_object.get_cluster_by_index(i, seq_set, max_dist_in_clu) )
{
valid_cluster = true;
// Determine whether this is a good set of sequences in this range.
// Bad sequences should never cluster with others with our settings. (distance=100)
// So bad sequences should be clusters with just one sequence.
if (seq_set.size() == 1)
{
it_set = seq_set.begin();
unsigned seq_index = *it_set;
valid_cluster = valid_sequences[seq_index];
}
// else - the cluster must be valid in our setup since clusters with more than 1 element cannot contain bad sequences.
// Do something with the cluster:
// Debug code - more important it shows how to extract
// the resulting clustering data
if (global_VERBOSITY > 3000)
{
it_set = seq_set.begin();
it_set_end = seq_set.end();
cout << "Found cluster: (";
while (it_set != it_set_end)
{
cout << *it_set;
++it_set;
if (it_set != it_set_end)
cout << ",";
}
cout << "):" << max_dist_in_clu;
if (valid_cluster)
cout << endl;
else
cout << "(invalid)" << endl;
}
// Copy the clustering data to the Csequence_loci_cluster_collection data
if (valid_cluster)
{
// Too bad: emplace_back is a C++11 feature
// list_of_clusters.emplace_back(pos_start, pos_end, max_dist_in_clu, seq_set, this);
// Add an empty object
list_of_clusters.push_back(empty_cluster_and_center_sequence);
if (global_VERBOSITY > 2000)
{
cout << "Object that will be assigned: *******" << endl;
list_of_clusters.back().print(cout);
cout << "*************************************" << endl;
}
// Fill the object
list_of_clusters.back().assign(pos_start, pos_end, max_dist_in_clu, seq_set, this, msa);
if (global_VERBOSITY > 2000)
{
cout << "Object after having been assigned:***" << endl;
list_of_clusters.back().print(cout);
cout << "*************************************" << endl;
}
}
++i;
} // END while ( cluster_object.get_cluster_by_index(i, seq_set, max_dist_in_clu) )
// Prints data for all clusters in this locus. Center sequences are not computed yet.
if (global_VERBOSITY > 1000)
{
print(cout);
}
} // END Csequence_loci_cluster_collection::cluster_locus()
///////////////////////////////////////////////////////
///////////////// CLUSTERING //////////////////////////
///////////////////////////////////////////////////////
// Helper functions:
// Indices:
// First index: Row, i.e. sequence
// Second index: Col, i.e. sequence position
void recode_range(char * b, char *e)
{
while (b != e)
{
*b = recode_DNA(*b);
++b;
}
}
void back_recode_range(char * b, char *e)
{
while (b != e)
{
*b = backrecode_DNA(*b);
++b;
}
}
// inline bool is_valid_recode_DNA_range(const char *p1, const char *p2)
// {
// while (p1 != p2)
// {
// if (!is_valid_recode_DNA(*p1))
// return false;
// ++p1;
// }
// return true;
// }
void recode_MSA(char **sequences, int num_taxa, int num_pos)
{
int row;
for (row=0; row < num_taxa; ++row)
{
recode_range(sequences[row], sequences[row]+num_pos);
}
}
// Requires recoded sequences as input.
// The consensus will also be recoded.
////////////////// UPDATED/////////////////
void find_consensus(char **msa, int num_taxa, unsigned pos_start_msa,
unsigned pos_end_msa, char *consensus, char *isAmbig)
{
int row, col, col_in_msa;
char c;
int len = pos_end_msa - pos_start_msa;
for (col=0, col_in_msa = pos_start_msa; col < len; ++col, ++col_in_msa)
{
c = msa[0][col_in_msa]; // Take symbol from row=0
for (row=1; row < num_taxa; ++row)
{
c = c | msa[row][col_in_msa]; // Add all symbols of all other rows.
}
consensus[col] = c;
if (recode_is_DNA_ambig(c) )
{
isAmbig[col] = 1; // Keep track of amibig characters: set isAmbig to true
}
else
{
isAmbig[col] = 0; // Keep track of amibig characters: set isAmbig to false
}
}
}
// ONLY DEBUGGING OUTPUT:
// Should work unchanged. CHECK!!!!
void print_all_variants(char *consensus, char *variant, char *isAmbig, int pos, int len)
{
while (pos < len && !isAmbig[pos])
++pos;
if (pos == len)
{
faststring p = variant;
back_recode_range(p.begin(), p.end());
cout << p << endl;
}
else
{
if (consensus[pos]&1)
{
variant[pos] = 1;
print_all_variants(consensus, variant, isAmbig, pos+1, len);
}
if (consensus[pos]&2)
{
variant[pos] = 2;
print_all_variants(consensus, variant, isAmbig, pos+1, len);
}
if (consensus[pos]&4)
{
variant[pos] = 4;
print_all_variants(consensus, variant, isAmbig, pos+1, len);
}
if (consensus[pos]&8)
{
variant[pos] = 8;
print_all_variants(consensus, variant, isAmbig, pos+1, len);
}
}
} // END find_consensus(..)
// Important: msa, consensus, and variant are expected to be passed as recoded msa.
//
// pos1 ... pos2 is the range to work on. pos2 is the index after the end of the range.
//
////////////////// UPDATED/////////////////
void find_center_sequence_exhaustive(char **msa, char *consensus,
char *variant, char *isAmbig,
int len_variant,
int pos_start, int num_taxa,
int pos_start_msa, int pos_end_msa,
int *distances, faststring &best_variant,
int *p_best_maximum_distance)
{
int i;
int len_remaining = pos_end_msa - pos_start_msa;
int pos_end = pos_start + len_remaining;
// Skip all bases for which isAmbig == 0
while (pos_start < pos_end && !isAmbig[pos_start])
{
++pos_start;
++pos_start_msa;
}
if (pos_start == pos_end)
{
// We have a new variant:
// Check wether this is better than the best we found so far.
// Determine maximum distance:
int m_dist = maximum(distances, distances+num_taxa);
if (global_VERBOSITY > 800)
{
cout << "Current sequence:\nDistance: " << m_dist << endl;
faststring p = variant;
back_recode_range(p.begin(), p.end());
cout << p << endl;
print_container(cout, distances, distances+num_taxa, "distances: ", ":", "\n\n");
}
if (m_dist < *p_best_maximum_distance) // We found a better sequence:
{
// Be careful in the following assignment: "=" does not work here, since variant is not 0 terminated!!!
best_variant.assign(variant, 0, len_variant);
*p_best_maximum_distance = m_dist;
// Some debug output:
if (global_VERBOSITY > 500)
{
cout << "*** New best variant: ***" << endl;
faststring tmp = best_variant;
back_recode_range(tmp.begin(), tmp.end() );
cout << tmp << endl;
cout << "Distance: " << *p_best_maximum_distance << endl << endl;
}
}
}
else
{
int *tmp_dist = new int [num_taxa];
// If we get here, we have an non unique "consensus at pos_start.
// So let us try all variants which are found in the msa.
if (consensus[pos_start]&1)
{
variant[pos_start] = 1;
// Determine new distances:
memcpy(tmp_dist, distances, sizeof(int)*num_taxa);
// Adjust distances for this new base:
for (i=0; i<num_taxa; ++i)
{
if (variant[pos_start] != msa[i][pos_start_msa])
++tmp_dist[i];
}
find_center_sequence_exhaustive(msa, consensus, variant, isAmbig, len_variant,
pos_start+1, num_taxa, pos_start_msa+1, pos_end_msa,
tmp_dist, best_variant, p_best_maximum_distance);
}
if (consensus[pos_start]&2)
{
variant[pos_start] = 2;
// Determine new distances:
memcpy(tmp_dist, distances, sizeof(int)*num_taxa);
// Adjust distances for this new base:
for (i=0; i<num_taxa; ++i)
{
if (variant[pos_start] != msa[i][pos_start_msa])
++tmp_dist[i];
}
find_center_sequence_exhaustive(msa, consensus, variant, isAmbig, len_variant,
pos_start+1, num_taxa, pos_start_msa+1, pos_end_msa,
tmp_dist, best_variant, p_best_maximum_distance);
}
if (consensus[pos_start]&4)
{
variant[pos_start] = 4;
// Determine new distances:
memcpy(tmp_dist, distances, sizeof(int)*num_taxa);
// Adjust distances for this new base:
for (i=0; i<num_taxa; ++i)
{
if (variant[pos_start] != msa[i][pos_start_msa])
++tmp_dist[i];
}
find_center_sequence_exhaustive(msa, consensus, variant, isAmbig, len_variant,
pos_start+1, num_taxa, pos_start_msa+1, pos_end_msa,
tmp_dist, best_variant, p_best_maximum_distance);
}
if (consensus[pos_start]&8)
{
variant[pos_start] = 8;
// Determine new distances:
memcpy(tmp_dist, distances, sizeof(int)*num_taxa);
// Adjust distances for this new base:
for (i=0; i<num_taxa; ++i)
{
if (variant[pos_start] != msa[i][pos_start_msa])
++tmp_dist[i];
}
find_center_sequence_exhaustive(msa, consensus, variant, isAmbig, len_variant,
pos_start+1, num_taxa, pos_start_msa+1, pos_end_msa,
tmp_dist, best_variant, p_best_maximum_distance);
}
delete [] tmp_dist;
} // END else of if (pos1 == pos2)
} // END void find_center_sequence_exhaustive
// distances must be initialised by caller.
void find_center_sequence_heuristic(char **msa, char *consensus,
char *center, char *isAmbig,
unsigned len_center,
unsigned pos_start, unsigned num_taxa,
unsigned pos_start_msa, unsigned pos_end_msa,
unsigned *distances,
unsigned *p_best_maximum_distance)
{
static char recode_A = recode_DNA('A');
static char recode_C = recode_DNA('C');
static char recode_G = recode_DNA('G');
static char recode_T = recode_DNA('T');
unsigned len_remaining = pos_end_msa - pos_start_msa;
unsigned pos_end = pos_start + len_remaining;
// pos_start walks through isAmbig and consensus.
// pos_start_msa walks through the msa.
// The following static variables are initialised only when calling this function for the first time.
static unsigned max_num_taxa = 20;
static unsigned *dist_A = new unsigned [max_num_taxa];
static unsigned *dist_C = new unsigned [max_num_taxa];
static unsigned *dist_G = new unsigned [max_num_taxa];
static unsigned *dist_T = new unsigned [max_num_taxa];
if (num_taxa > max_num_taxa)
{
max_num_taxa = num_taxa; // max_num_taxa takes on the new maximum value. It will be used as size when reallocating new arrays.
if (dist_A != NULL)
{
delete [] dist_A;
delete [] dist_C;
delete [] dist_G;
delete [] dist_T;
dist_A = new unsigned [max_num_taxa];
dist_C = new unsigned [max_num_taxa];
dist_G = new unsigned [max_num_taxa];
dist_T = new unsigned [max_num_taxa];
}
}
unsigned distances_sum_squares;
unsigned dist_A_sum_squares;
unsigned dist_C_sum_squares;
unsigned dist_G_sum_squares;
unsigned dist_T_sum_squares;
// unsigned dist_max_A;
// unsigned dist_max_C;
// unsigned dist_max_G;
// unsigned dist_max_T;
// unsigned dist_max;
unsigned j;
// Search for first non-invariant site:
while (pos_start < pos_end && !isAmbig[pos_start])
{
++pos_start;
++pos_start_msa;
}
if (pos_start == pos_end) // This is the case if all sites are invariant.
{
return;
}
// pos_start is first non-invariant site:
{
unsigned A=0, C=0, G=0, T=0;
char c;
for (j=0; j<num_taxa; ++j)
{
if (msa[j][pos_start_msa] == recode_A )
++A;
else if (msa[j][pos_start_msa] == recode_C )
++C;
else if (msa[j][pos_start_msa] == recode_G )
++G;
else if (msa[j][pos_start_msa] == recode_T )
++T;
}
if (A > C)
{
if (G > T)
{
if (A > G)
c = recode_A;
else
c = recode_G;
}
else // (G <= T)
{
if (A > T)
c = recode_A;
else
c = recode_T;
}
}
else // (A <= C)
{
if (G > T)
{
if (C > G)
c = recode_C;
else
c = recode_G;
}
else // (G <= T)
{
if (C > T)
c = recode_C;
else
c = recode_T;
}
}
center[pos_start] = c; // First position has been determined.
distances_sum_squares = 0;
// dist_max = 0;
for (j=0; j<num_taxa; ++j)
{
if (center[pos_start] != msa[j][pos_start_msa])
++distances[j];
distances_sum_squares += distances[j]*distances[j];
// if (dist_max < distances[j])
// dist_max = distances[j];
}
} // pos_start is first non-invariant site:
++pos_start;
++pos_start_msa;
while (pos_start < pos_end)
{
if (isAmbig[pos_start]) // He now search for best nucleotide in center.
{
// Try 'A'
if (consensus[pos_start]&recode_A)
{
memcpy(dist_A, distances, sizeof(unsigned)*num_taxa);
center[pos_start] = recode_A;
dist_A_sum_squares = 0;
for (j=0; j<num_taxa; ++j)
{
if (center[pos_start] != msa[j][pos_start_msa])
++dist_A[j];
dist_A_sum_squares += dist_A[j]*dist_A[j];
}
}
else
dist_A_sum_squares = -1u;
// END // Try 'A'
// Try 'C'
if (consensus[pos_start]&recode_C)
{
memcpy(dist_C, distances, sizeof(unsigned)*num_taxa);
center[pos_start] = recode_C;
dist_C_sum_squares = 0;
for (j=0; j<num_taxa; ++j)
{
if (center[pos_start] != msa[j][pos_start_msa])
++dist_C[j];
dist_C_sum_squares += dist_C[j]*dist_C[j];
}
}
else
dist_C_sum_squares = -1u;
// END // Try 'C'
// Try 'G'
if (consensus[pos_start]&recode_G)
{
memcpy(dist_G, distances, sizeof(unsigned)*num_taxa);
center[pos_start] = recode_G;
dist_G_sum_squares = 0;
for (j=0; j<num_taxa; ++j)
{
if (center[pos_start] != msa[j][pos_start_msa])
++dist_G[j];
dist_G_sum_squares += dist_G[j]*dist_G[j];
}
}
else
dist_G_sum_squares = -1u;
// END // Try 'G'
// Try 'T'
if (consensus[pos_start]&recode_T)
{
memcpy(dist_T, distances, sizeof(unsigned)*num_taxa);
center[pos_start] = recode_T;
dist_T_sum_squares = 0;
for (j=0; j<num_taxa; ++j)
{
if (center[pos_start] != msa[j][pos_start_msa])
++dist_T[j];
dist_T_sum_squares += dist_T[j]*dist_T[j];
}
}
else
dist_T_sum_squares = -1u;
// END // Try 'T'
// Which "Try" is the best?
{
// Smallest dist_x_sum_squares is the best:
if (dist_A_sum_squares < dist_C_sum_squares) // A is better than C
{
if (dist_G_sum_squares < dist_T_sum_squares) // G is better than T
{
if (dist_A_sum_squares < dist_G_sum_squares) // A is better than G
{
// A is the best:
center[pos_start] = recode_A;
memcpy(distances, dist_A, sizeof(unsigned)*num_taxa);
}
else
{
// G is the best:
center[pos_start] = recode_G;
memcpy(distances, dist_G, sizeof(unsigned)*num_taxa);
}
}
else // T is better than or equal to G
{
if (dist_A_sum_squares < dist_T_sum_squares) // A is better than T
{
// A is the best
center[pos_start] = recode_A;
memcpy(distances, dist_A, sizeof(unsigned)*num_taxa);
}
else
{
// T is the best
center[pos_start] = recode_T;
memcpy(distances, dist_T, sizeof(unsigned)*num_taxa);
}
}
}
else // C is better than or equal to A
{
if (dist_G_sum_squares < dist_T_sum_squares) // G is better than T
{
if (dist_C_sum_squares < dist_G_sum_squares) // C is better than G
{
// C is the best:
center[pos_start] = recode_C;
memcpy(distances, dist_C, sizeof(unsigned)*num_taxa);
}
else
{
// G is the best:
center[pos_start] = recode_G;
memcpy(distances, dist_G, sizeof(unsigned)*num_taxa);
}
}
else // T is better than or equal to G
{
if (dist_C_sum_squares < dist_T_sum_squares) // C is better than T
{
// C is the best
center[pos_start] = recode_C;
memcpy(distances, dist_C, sizeof(unsigned)*num_taxa);
}
else
{
// T is the best
center[pos_start] = recode_T;
memcpy(distances, dist_T, sizeof(unsigned)*num_taxa);
}
}
} // END C is better than or equal to A
} // END Which "Try" is the best?
} // END ELSE (!isAmbig[pos_start])
++pos_start;
++pos_start_msa;
} // END while (pos_start < pos_end)
// We have the greedy center sequence.
*p_best_maximum_distance = maximum(distances, distances+num_taxa);
} // END find_center_sequence_heuristic
// TODO ///////////////////
// Requires:
// Multiple sequence alignment that is already recoded.
// References to (empty) faststrings for the center.
// Number of taxa
// Start and end indices of range for which the center sequence shall be computed.
// The center sequence is returned in recoded form.
void find_center_sequence_for_msa_exhaustive(char **msa, faststring ¢er_seq,
int num_taxa,
int pos_start_msa, int pos_end_msa,
double &mdist)
{
faststring cons;
faststring isAmbig;
faststring variant;
faststring best_variant;
int best_maximum_distance = INT_MAX;
// The equality len_variant = pos_end - pos_start is only valid before ever incrementing
// pos_start, which is always true in this function.
int len_variant = pos_end_msa - pos_start_msa;
int pos_start = 0;
// int pos_end = len_variant;
cons.assign(len_variant, ' ');
isAmbig.assign(len_variant, ' ');
// Here we can pass .data() since we do not assign it
find_consensus(msa, num_taxa, pos_start_msa, pos_end_msa, cons.begin(), isAmbig.begin() );
variant = cons;
int *dist_array = new int [num_taxa];
memset(dist_array, 0, num_taxa*sizeof(int));
// for (i=0; i< num_taxa; ++i)
// {
// dist_array[i] = 0;
// }
// print_all_variants(cons.data(), variant.data(), isAmbig.data(), 0, len);
// if (global_VERBOSITY > 5)
// {
// cout << "Start time: " << time(NULL) << endl;
// }
find_center_sequence_exhaustive(msa, cons.data(), variant.data(), isAmbig.data(),
len_variant,
pos_start, num_taxa,
pos_start_msa, pos_end_msa,
dist_array, best_variant,
&best_maximum_distance);
// if (global_VERBOSITY > 5)
// {
// cout << "End time: " << time(NULL) << endl;
// }
center_seq = best_variant;
// TODO remove if is clear this cannot happen
if (len_variant == 0)
{
cerr << "ERROR: len_variant == 0 in find_center_sequence_for_msa_exhaustive. Please report this bug." << endl;
exit(-54);
}
mdist = (double)best_maximum_distance/len_variant;
delete [] dist_array;
//
// back_recode_range(center_seq.begin(), center_seq.end() );
} // END find_center_sequence_for_msa_exhaustive
// Requires:
// Multiple sequence alignment that is already recoded.
// References to (empty) faststrings for the center.
// Number of taxa
// Start and end indices of range for which the center sequence shall be computed.
// The center sequence is returned in recoded form.
void find_center_sequence_for_msa_heuristic(char **msa, faststring ¢er_seq,
int num_taxa,
int pos_start_msa, int pos_end_msa,
double &mdist)
{
faststring cons;
faststring isAmbig;
faststring variant;
unsigned best_maximum_distance = 0;
// The equality len_variant = pos_end - pos_start is only valid before ever incrementing
// pos_start, which is always true in this function.
unsigned len_variant = pos_end_msa - pos_start_msa;
unsigned pos_start = 0;
// unsigned pos_end = len_variant;
cons.assign(len_variant, ' ');
isAmbig.assign(len_variant, ' ');
// Here we can pass .data() since we do not assign it
find_consensus(msa, num_taxa, pos_start_msa, pos_end_msa, cons.begin(), isAmbig.begin() );
variant = cons;
unsigned *dist_array = new unsigned [num_taxa];
memset(dist_array, 0, num_taxa*sizeof(int));
// for (i=0; i< num_taxa; ++i)
// {
// dist_array[i] = 0;
// }
// print_all_variants(cons.data(), variant.data(), isAmbig.data(), 0, len);
// if (global_VERBOSITY > 5)
// {
// cout << "Start time: " << time(NULL) << endl;
// }
find_center_sequence_heuristic(msa, cons.data(), variant.data(), isAmbig.data(),
len_variant,
pos_start, num_taxa,
pos_start_msa, pos_end_msa,
dist_array, &best_maximum_distance);
// if (global_VERBOSITY > 5)
// {
// cout << "End time: " << time(NULL) << endl;
// }
// for (i=0; i< num_taxa; ++i)
// {
// if (dist_array[i] > best_maximum_distance)
// best_maximum_distance = dist_array[i];
// }
// best_maximum_distance = maximum(distances, distances+num_taxa);
center_seq = variant;
// TODO remove is clear this cannot happen
if (len_variant == 0)
{
cerr << "ERROR: len_variant == 0 in find_center_sequence_for_msa_heuristic. Please report this bug." << endl;
exit(-55);
}
mdist = (double)best_maximum_distance/len_variant;
if (global_VERBOSITY > 100)
{
cout << "Reporting mdist for a center sequence with starting position: " << pos_start << " " << mdist << endl;
}
//
// back_recode_range(center_seq.begin(), center_seq.end() );
delete [] dist_array;
} // END find_center_sequence_for_msa_heuristic
void Csequence_cluster_and_center_sequence::compute_center(char center_computation_mode)
{
// The msa is prepared for the center algorithm:
// We still need: the "consensus" and the "ambig" strings.
int num_sequences = taxon_set.size();
// if (global_VERBOSITY > 5)
// {
// cout << "Computing center sequence: " << endl << flush;
// }
if (num_sequences == 1)
{
center_sequence.assign(msa[0]+pos_start, msa[0]+pos_end);
max_dist_bait_to_msa = 0;
}
else // We have to compute a center sequence:
{
if (center_computation_mode == 0) // exhaustive
{
find_center_sequence_for_msa_exhaustive(msa, center_sequence, num_sequences, pos_start, pos_end, max_dist_bait_to_msa);
}
else if (center_computation_mode == 1) // heuristic
{
find_center_sequence_for_msa_heuristic(msa, center_sequence, num_sequences, pos_start, pos_end, max_dist_bait_to_msa);
}
else // Comparison mode
{
std::set<short>::iterator it;
it = taxon_set.begin();
{
unsigned i;
cout << "The MSA for the result below:" << endl;
cout << "Time: " << time(NULL) << endl;
for (i=0; i<taxon_set.size(); ++i, ++it)
{
faststring tmp( msa[i]+pos_start, msa[i]+pos_end);
back_recode_range(tmp.begin(), tmp.end());
cout.width(4);
cout << *it << ":" << tmp << std::endl;
}
}
unsigned t1, t2, t3;
faststring c1, c2;
double md1, md2;
t1 = time(NULL);
find_center_sequence_for_msa_exhaustive(msa, c1, num_sequences, pos_start, pos_end, md1);
t2 = time(NULL);
find_center_sequence_for_msa_heuristic(msa, c2, num_sequences, pos_start, pos_end, md2);
t3 = time(NULL);
// This assignment must come before back recoding c1.
// Otherwise we back recode twice, which is not correct.
center_sequence = c1;
back_recode_range(c1.begin(), c1.end());
back_recode_range(c2.begin(), c2.end());
cout << "Cent1: " << c1 << endl;
cout << "max_dist1: " << md1 << endl;
cout << "Tdiff1: " << t2-t1 << endl;
cout << "Cent2: " << c2 << endl;
cout << "max_dist2: " << md2 << endl;
cout << "Tdiff2: " << t3-t2 << endl;
max_dist_bait_to_msa = md1;
if (md1 != md2)
{
cout << "Deviating distances found: " << md2-md1 << " " << (md2-md1)*120 << endl;
}
else
{
cout << "Same distance." << endl;
}
} // END else // Comparison mode
} // END else // We have to compute a center sequence:
// cout << "LOG: pos: " << pos_start << " mis " << max_dist_bait_to_msa*120 << endl;
// We have to back recode the center sequence:
back_recode_range(center_sequence.begin(), center_sequence.end() );
if (!center_sequence.empty())
{
unsigned CG, AT;
CG_AT_content_in_region(center_sequence.begin_str(), center_sequence.end_str(), AT, CG);
double dCG=CG, dAT=AT;
CG_content = (dCG / (dCG+dAT));
}
}
void Csequence_loci_cluster_collection::compute_center_for_all_clusters(char center_computation_mode)
{
std::list<Csequence_cluster_and_center_sequence>::iterator it_list = list_of_clusters.begin();
std::list<Csequence_cluster_and_center_sequence>::iterator it_list_end = list_of_clusters.end();
// unsigned t1, t2;
while (it_list != it_list_end)
{
// t1 = time(NULL);
// cout << "T1: " << t1 << endl;
it_list->compute_center(center_computation_mode);
// t2 = time(NULL);
// cout << "T2: " << t2 << endl;
// cout << "Tdiff: " << t2-t1 << endl;
if (!it_list->center_computed() )
{
cerr << "ERROR: Internal error: Center sequence not computed even though it was requested! Number of sequences in cluster: " << it_list->get_number_of_elements_in_cluster() << endl;
}
++it_list;
}
}
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