--- /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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