+++ /dev/null
-/*****************************************************************
- * SQUID - a library of functions for biological sequence analysis
- * Copyright (C) 1992-2002 Washington University School of Medicine
- *
- * This source code is freely distributed under the terms of the
- * GNU General Public License. See the files COPYRIGHT and LICENSE
- * for details.
- *****************************************************************/
-
-/* aligneval.c
- *
- * Comparison of multiple alignments. Three functions are
- * provided, using subtly different scoring schemes:
- * CompareMultAlignments() - basic scoring scheme
- * CompareRefMultAlignments() - only certain "canonical" columns
- * are scored
- *
- * The similarity measure is a fractional alignment identity averaged
- * over all sequence pairs. The score for all pairs is:
- * (identically aligned symbols) / (total aligned columns in
- * known alignment)
- *
- * A column c is identically aligned for sequences i, j if:
- * 1) both i,j have a symbol aligned in column c, and the
- * same pair of symbols is aligned somewhere in the test
- * alignment
- * 2) S[i][c] is aligned to a gap in sequence j, and that symbol
- * is aligned to a gap in the test alignment
- * 3) converse of 2)
- *
- *
- * The algorithm is as follows:
- * 1) For each known/test aligned pair of sequences (k1,k2 and t1,t2)
- * construct a list for each sequence, in which for every
- * counted symbol we record the raw index of the symbol in
- * the other sequence that it aligns to, or -1 if it aligns
- * to a gap or uncounted symbol.
- *
- * 2) Compare the list for k1 to the list for t1 and count an identity
- * for each correct alignment.
- *
- * 3) Repeat 2) for comparing k2 to t2. Note that this means correct sym/sym
- * alignments count for 2; correct sym/gap alignments count for 1.
- *
- * 4) The score is (identities from 2 + identities from 3) /
- * (totals from 2 + totals from 3).
- *
- * Written originally for koala's ss2 pairwise alignment package.
- *
- * Sean Eddy, Sun Nov 1 12:45:11 1992
- * SRE, Thu Jul 29 16:47:18 1993: major revision: all functions replaced by new algorithm
- * CVS $Id: aligneval.c,v 1.7 2002/10/09 14:26:09 eddy Exp)
- */
-
-
-#include <stdio.h>
-#include <string.h>
-#include <ctype.h>
-#include "squid.h"
-#include "sre_random.h"
-
-static int make_alilist(char *s1, char *s2, int **ret_s1_list, int *ret_listlen);
-static int make_ref_alilist(int *refcoords, char *k1, char *k2, char *s1, char *s2,
- int **ret_s1_list, int *ret_listlen);
-static int compare_lists(int *k1, int *k2, int *t1, int *t2, int len1, int len2, float *ret_sc);
-
-
-/* Function: ComparePairAlignments
- *
- * Purpose: Calculate and return a number representing how well two different alignments
- * of a pair of sequences compare. The number is, roughly speaking,
- * the fraction of columns which are identically aligned.
- *
- * For all columns c in which either known1[c] or known2[c]
- * is a non-gap, count an identity if those same symbols are
- * aligned somewhere in calc1/calc2. The score is identities/total
- * columns examined. (i.e. fully gapped columns don't count)
- *
- * more explicitly, identities come from:
- * both known and test aligned pairs have the same symbol in the first sequence aligned to
- * a gap in the second sequence;
- * both known and test aligned pairs have the same symbol in the second sequence
- * aligned to a gap in the first sequence;
- * the known alignment has symbols aligned at this column, and the test
- * alignment aligns the same two symbols.
- *
- * Args: known1, known2: trusted alignment of two sequences
- * calc1, calc2: test alignment of two sequences
- *
- * Return: Returns -1.0 on internal failure.
- */
-float
-ComparePairAlignments(char *known1, char *known2, char *calc1, char *calc2)
-{
- int *klist1;
- int *klist2;
- int *tlist1;
- int *tlist2;
- int len1, len2;
- float score;
-
- if (! make_alilist(calc1, calc2, &tlist1, &len1)) return -1.0;
- if (! make_alilist(calc2, calc1, &tlist2, &len2)) return -1.0;
- if (! make_alilist(known1, known2, &klist1, &len1)) return -1.0;
- if (! make_alilist(known2, known1, &klist2, &len2)) return -1.0;
- if (! compare_lists(klist1, klist2, tlist1, tlist2, len1, len2, &score)) return -1.0;
-
- free(klist1);
- free(klist2);
- free(tlist1);
- free(tlist2);
- return score;
-}
-
-
-
-/* Function: CompareRefPairAlignments()
- *
- * Same as above, but the only columns that count are the ones
- * with indices in *refcoord. *refcoord and the known1, known2
- * pair must be in sync with each other (come from the same
- * multiple sequence alignment)
- *
- * Args: ref - 0..alen-1 array of 1 or 0
- * known1,known2 - trusted alignment
- * calc1, calc2 - test alignment
- *
- * Return: the fractional alignment identity on success, -1.0 on failure.
- */
-float
-CompareRefPairAlignments(int *ref, char *known1, char *known2, char *calc1, char *calc2)
-{
- int *klist1;
- int *klist2;
- int *tlist1;
- int *tlist2;
- int len1, len2;
- float score;
-
- if (! make_ref_alilist(ref, known1, known2, calc1, calc2, &tlist1, &len1)) return -1.0;
- if (! make_ref_alilist(ref, known2, known1, calc2, calc1, &tlist2, &len2)) return -1.0;
- if (! make_ref_alilist(ref, known1, known2, known1, known2, &klist1, &len1)) return -1.0;
- if (! make_ref_alilist(ref, known2, known1, known2, known1, &klist2, &len2)) return -1.0;
- if (! compare_lists(klist1, klist2, tlist1, tlist2, len1, len2, &score)) return -1.0;
-
- free(klist1);
- free(klist2);
- free(tlist1);
- free(tlist2);
- return score;
-}
-
-/* Function: make_alilist()
- *
- * Purpose: Construct a list (array) mapping the raw symbols of s1
- * onto the indexes of the aligned symbols in s2 (or -1
- * for gaps in s2). The list (s1_list) will be of the
- * length of s1's raw sequence.
- *
- * Args: s1 - sequence to construct the list for
- * s2 - sequence s1 is aligned to
- * ret_s1_list - RETURN: the constructed list (caller must free)
- * ret_listlen - RETURN: length of the list
- *
- * Returns: 1 on success, 0 on failure
- */
-static int
-make_alilist(char *s1, char *s2, int **ret_s1_list, int *ret_listlen)
-{
- int *s1_list;
- int col; /* column position in alignment */
- int r1, r2; /* raw symbol index at current col in s1, s2 */
-
- /* Malloc for s1_list. It can't be longer than s1 itself; we just malloc
- * for that (and waste a wee bit of space)
- */
- s1_list = (int *) MallocOrDie (sizeof(int) * strlen(s1));
- r1 = r2 = 0;
- for (col = 0; s1[col] != '\0'; col++)
- {
- /* symbol in s1? Record what it's aligned to, and bump
- * the r1 counter.
- */
- if (! isgap(s1[col]))
- {
- s1_list[r1] = isgap(s2[col]) ? -1 : r2;
- r1++;
- }
-
- /* symbol in s2? bump the r2 counter
- */
- if (! isgap(s2[col]))
- r2++;
- }
-
- *ret_listlen = r1;
- *ret_s1_list = s1_list;
- return 1;
-}
-
-
-
-/* Function: make_ref_alilist()
- *
- * Purpose: Construct a list (array) mapping the raw symbols of s1
- * which are under canonical columns of the ref alignment
- * onto the indexes of the aligned symbols in s2 (or -1
- * for gaps in s2 or noncanonical symbols in s2).
- *
- * Args: ref: - array of indices of canonical coords (1 canonical, 0 non)
- * k1 - s1's known alignment (w/ respect to refcoords)
- * k2 - s2's known alignment (w/ respect to refcoords)
- * s1 - sequence to construct the list for
- * s2 - sequence s1 is aligned to
- * ret_s1_list - RETURN: the constructed list (caller must free)
- * ret_listlen - RETURN: length of the list
- *
- * Returns: 1 on success, 0 on failure
- */
-/*ARGSUSED*/
-static int
-make_ref_alilist(int *ref, char *k1, char *k2,
- char *s1, char *s2, int **ret_s1_list, int *ret_listlen)
-{
- int *s1_list;
- int col; /* column position in alignment */
- int r1, r2; /* raw symbol index at current col in s1, s2 */
- int *canons1; /* flag array, 1 if position i in s1 raw seq is canonical */
- int lpos; /* position in list */
-
- /* Allocations. No arrays can exceed the length of their
- * appropriate parent (s1 or s2)
- */
- s1_list = (int *) MallocOrDie (sizeof(int) * strlen(s1));
- canons1 = (int *) MallocOrDie (sizeof(int) * strlen(s1));
-
- /* First we use refcoords and k1,k2 to construct an array of 1's
- * and 0's, telling us whether s1's raw symbol number i is countable.
- * It's countable simply if it's under a canonical column.
- */
- r1 = 0;
- for (col = 0; k1[col] != '\0'; col++)
- {
- if (! isgap(k1[col]))
- {
- canons1[r1] = ref[col] ? 1 : 0;
- r1++;
- }
- }
-
- /* Now we can construct the list. We don't count pairs if the sym in s1
- * is non-canonical.
- * We have to keep separate track of our position in the list (lpos)
- * from our positions in the raw sequences (r1,r2)
- */
- r1 = r2 = lpos = 0;
- for (col = 0; s1[col] != '\0'; col++)
- {
- if (! isgap(s1[col]) && canons1[r1])
- {
- s1_list[lpos] = isgap(s2[col]) ? -1 : r2;
- lpos++;
- }
-
- if (! isgap(s1[col]))
- r1++;
- if (! isgap(s2[col]))
- r2++;
- }
-
- free(canons1);
- *ret_listlen = lpos;
- *ret_s1_list = s1_list;
- return 1;
-}
-
-/* Function: compare_lists()
- *
- * Purpose: Given four alignment lists (k1,k2, t1,t2), calculate the
- * alignment score.
- *
- * Args: k1 - list of k1's alignment to k2
- * k2 - list of k2's alignment to k1
- * t1 - list of t1's alignment to t2
- * t2 - list of t2's alignment to t2
- * len1 - length of k1, t1 lists (same by definition)
- * len2 - length of k2, t2 lists (same by definition)
- * ret_sc - RETURN: identity score of alignment
- *
- * Return: 1 on success, 0 on failure.
- */
-static int
-compare_lists(int *k1, int *k2, int *t1, int *t2, int len1, int len2, float *ret_sc)
-{
- float id;
- float tot;
- int i;
-
- id = tot = 0.0;
- for (i = 0; i < len1; i++)
- {
- tot += 1.0;
- if (t1[i] == k1[i]) id += 1.0;
- }
-
- for ( i = 0; i < len2; i++)
- {
- tot += 1.0;
- if (k2[i] == t2[i]) id += 1.0;
- }
-
- *ret_sc = id / tot;
- return 1;
-}
-
-
-/* Function: CompareMultAlignments
- *
- * Purpose: Invokes pairwise alignment comparison for every possible pair,
- * and returns the average score over all N(N-1) of them or -1.0
- * on an internal failure.
- *
- * Can be slow for large N, since it's quadratic.
- *
- * Args: kseqs - trusted multiple alignment
- * tseqs - test multiple alignment
- * N - number of sequences
- *
- * Return: average identity score, or -1.0 on failure.
- */
-float
-CompareMultAlignments(char **kseqs, char **tseqs, int N)
-{
- int i, j; /* counters for sequences */
- float score;
- float tot_score = 0.0;
- /* do all pairwise comparisons */
- for (i = 0; i < N; i++)
- for (j = i+1; j < N; j++)
- {
- score = ComparePairAlignments(kseqs[i], kseqs[j], tseqs[i], tseqs[j]);
- if (score < 0.0) return -1.0;
- tot_score += score;
- }
- return ((tot_score * 2.0) / ((float) N * ((float) N - 1.0)));
-}
-
-
-
-/* Function: CompareRefMultAlignments()
- *
- * Purpose: Same as above, except an array of reference coords for
- * the canonical positions of the known alignment is also
- * provided.
- *
- * Args: ref : 0..alen-1 array of 1/0 flags, 1 if canon
- * kseqs : trusted alignment
- * tseqs : test alignment
- * N : number of sequences
- *
- * Return: average identity score, or -1.0 on failure
- */
-float
-CompareRefMultAlignments(int *ref, char **kseqs, char **tseqs, int N)
-{
- int i, j; /* counters for sequences */
- float score;
- float tot_score = 0.0;
-
- /* do all pairwise comparisons */
- for (i = 0; i < N; i++)
- for (j = i+1; j < N; j++)
- {
- score = CompareRefPairAlignments(ref, kseqs[i], kseqs[j], tseqs[i], tseqs[j]);
- if (score < 0.0) return -1.0;
- tot_score += score;
- }
- return ((tot_score * 2.0)/ ((float) N * ((float) N - 1.0)));
-}
-
-/* Function: PairwiseIdentity()
- *
- * Purpose: Calculate the pairwise fractional identity between
- * two aligned sequences s1 and s2. This is simply
- * (idents / MIN(len1, len2)).
- *
- * Note how many ways there are to calculate pairwise identity,
- * because of the variety of choices for the denominator:
- * idents/(idents+mismat) has the disadvantage that artifactual
- * gappy alignments would have high "identities".
- * idents/(AVG|MAX)(len1,len2) both have the disadvantage that
- * alignments of fragments to longer sequences would have
- * artifactually low "identities".
- *
- * Original Case sensitive; also, watch out in nucleic acid alignments;
- * U/T RNA/DNA alignments will be counted as mismatches!
- *
- * Clustal Omega patch: Case insensitive and T and U are treated the same
- */
-float
-PairwiseIdentity(char *s1, char *s2)
-{
- int idents; /* total identical positions */
- int len1, len2; /* lengths of seqs */
- int x; /* position in aligned seqs */
-
- idents = len1 = len2 = 0;
- for (x = 0; s1[x] != '\0' && s2[x] != '\0'; x++)
- {
-#ifdef CLUSTALO
- char c1 = toupper(s1[x]);
- char c2 = toupper(s2[x]);
- if (c1=='U')
- c1 = 'T';
- if (c2=='U')
- c2 = 'T';
-
- if (!isgap(c1)) {
- len1++;
- if (c1 == c2)
- idents++;
- }
- if (!isgap(c2))
- len2++;
-#else
- if (!isgap(s1[x])) {
- len1++;
- if (s1[x] == s2[x]) idents++;
- }
- if (!isgap(s2[x])) len2++;
-#endif
- }
- if (len2 < len1) len1 = len2;
- return (len1 == 0 ? 0.0 : (float) idents / (float) len1);
-}
-
-
-
-/* Function: AlignmentIdentityBySampling()
- * Date: SRE, Mon Oct 19 14:29:01 1998 [St. Louis]
- *
- * Purpose: Estimate and return the average pairwise
- * fractional identity of an alignment,
- * using sampling.
- *
- * For use when there's so many sequences that
- * an all vs. all rigorous calculation will
- * take too long.
- *
- * Case sensitive!
- *
- * Args: aseq - aligned sequences
- * L - length of alignment
- * N - number of seqs in alignment
- * nsample - number of samples
- *
- * Returns: average fractional identity, 0..1.
- */
-float
-AlignmentIdentityBySampling(char **aseq, int L, int N, int nsample)
-{
- int x, i, j; /* counters */
- float sum;
-
- if (N < 2) return 1.0;
-
- sum = 0.;
- for (x = 0; x < nsample; x++)
- {
- i = CHOOSE(N);
- do { j = CHOOSE(N); } while (j == i); /* make sure j != i */
- sum += PairwiseIdentity(aseq[i], aseq[j]);
- }
- return sum / (float) nsample;
-}
-
-/* Function: MajorityRuleConsensus()
- * Date: SRE, Tue Mar 7 15:30:30 2000 [St. Louis]
- *
- * Purpose: Given a set of aligned sequences, produce a
- * majority rule consensus sequence. If >50% nonalphabetic
- * (usually meaning gaps) in the column, ignore the column.
- *
- * Args: aseq - aligned sequences, [0..nseq-1][0..alen-1]
- * nseq - number of sequences
- * alen - length of alignment
- *
- * Returns: ptr to allocated consensus sequence.
- * Caller is responsible for free'ing this.
- */
-char *
-MajorityRuleConsensus(char **aseq, int nseq, int alen)
-{
- char *cs; /* RETURN: consensus sequence */
- int count[27]; /* counts for a..z and gaps in a column */
- int idx,apos; /* counters for seq, column */
- int spos; /* position in cs */
- int x; /* counter for characters */
- int sym;
- int max, bestx;
-
- cs = MallocOrDie(sizeof(char) * (alen+1));
-
- for (spos=0,apos=0; apos < alen; apos++)
- {
- for (x = 0; x < 27; x++) count[x] = 0;
-
- for (idx = 0; idx < nseq; idx++)
- {
- if (isalpha(aseq[idx][apos])) {
- sym = toupper(aseq[idx][apos]);
- count[sym-'A']++;
- } else {
- count[26]++;
- }
- }
-
- if ((float) count[26] / (float) nseq <= 0.5) {
- max = bestx = -1;
- for (x = 0; x < 26; x++)
- if (count[x] > max) { max = count[x]; bestx = x; }
- cs[spos++] = (char) ('A' + bestx);
- }
- }
- cs[spos] = '\0';
- return cs;
-}
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