[med-svn] [Git][med-team/mafft][upstream] New upstream version 7.471
Michael R. Crusoe
gitlab at salsa.debian.org
Wed Jul 8 15:05:46 BST 2020
Michael R. Crusoe pushed to branch upstream at Debian Med / mafft
Commits:
5f66d725 by Michael R. Crusoe at 2020-07-08T15:48:51+02:00
New upstream version 7.471
- - - - -
6 changed files:
- core/addsingle.c
- core/disttbfast.c
- core/mafft.tmpl
- core/makedirectionlist.c
- core/mltaln.h
- readme
Changes:
=====================================
core/addsingle.c
=====================================
@@ -2878,6 +2878,30 @@ static void smoothing1( int njob, int nadd, int lenfull, char **seq, Blocktoreal
// for( i=0; i<lenfull+1; i++ ) fprintf( stderr, "i=%d, nnewres=%d, start=%d, end=%d\n", i, realign[i].nnewres, realign[i].start, realign[i].end );
}
+static double ratioambiguouscolumn_simple( char **s, int n, int l )
+{
+ int i, j;
+ int nunambiguous;
+ int nambiguous;
+ if( dorp == 'd' )
+ nunambiguous = 4;
+ else
+ nunambiguous = 6;
+
+ nambiguous = 0;
+ for( i=0; i<l; i++ )
+ {
+ for( j=0; j<n; j++ )
+ if( amino_grp[(int)s[j][i]] < nunambiguous )
+ break;
+ if( j == n )
+ nambiguous += 1;
+ }
+
+ reporterr( "nambiguous = %d / %d, ratio=%f\n", nambiguous, l, (double)nambiguous / l );
+ return( (double)nambiguous / l );
+}
+
int main( int argc, char *argv[] )
{
static int *nlen;
@@ -3270,6 +3294,17 @@ int main( int argc, char *argv[] )
commongappick( norg, seq );
lenfull = strlen( seq[0] );
+ if( ratioambiguouscolumn_simple( seq, norg, lenfull ) > 0.03 )
+ {
+ fprintf( stderr, "################################################################################\n" );
+ fprintf( stderr, "# \n" );
+ fprintf( stderr, "# The reference MSA has >3%% ambiguous columns.\n" );
+ fprintf( stderr, "# Please prepare a better reference.\n" );
+ fprintf( stderr, "# \n" );
+ fprintf( stderr, "################################################################################\n" );
+ exit( 1 );
+ }
+
if( keeplength && mapout )
{
addbk = (char **)calloc( nadd+1, sizeof( char * ) );
@@ -3701,6 +3736,9 @@ int main( int argc, char *argv[] )
+ if( commonIP ) FreeIntMtx( commonIP );
+ commonIP = NULL;
+ A__align( NULL, 0, 0, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
FreeIntMtx( newgaplist_o );
FreeIntVec( newgaplist_compact );
FreeIntVec( posmap );
=====================================
core/disttbfast.c
=====================================
@@ -8,7 +8,7 @@
#define SCOREOUT 0
#define SKIP 1
-#define ITERATIVECYCLE 1
+#define ITERATIVECYCLE 2
#define END_OF_VEC -1
@@ -2408,7 +2408,7 @@ static int dooneiteration( int *nlen, char **aseq, int nadd, char *mergeoralign,
{
int l, ll, len1, len2, i, j;
int clus1, clus2;
- double pscore, tscore;
+ double pscore;
char *indication1 = NULL, *indication2 = NULL;
double *effarr1 = NULL;
double *effarr2 = NULL;
@@ -2422,7 +2422,9 @@ static int dooneiteration( int *nlen, char **aseq, int nadd, char *mergeoralign,
int **localmem = NULL;
double **cpmxchild0, **cpmxchild1;
double orieff1, orieff2;
+ double oscore, nscore;
ExtAnch *pairanch;
+ char **oseq1, **oseq2;
#if SKIP
int **skiptable1 = NULL, **skiptable2 = NULL;
#endif
@@ -2470,7 +2472,6 @@ static int dooneiteration( int *nlen, char **aseq, int nadd, char *mergeoralign,
// writePre( njob, name, nlen, aseq, 0 );
- tscore = 0.0;
for( ll=0; ll<njob*ITERATIVECYCLE; ll++ )
{
l = ll % njob;
@@ -2516,8 +2517,14 @@ static int dooneiteration( int *nlen, char **aseq, int nadd, char *mergeoralign,
// clus2 = fastconjuction_noweight( topol[l][1], aseq, mseq2, effarr2, indication2 );
#endif
- newgapstr = "-";
+ intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, strlen( mseq1[0] ), &oscore );
+ oseq1 = AllocateCharMtx( 1, len1+1 );
+ oseq2 = AllocateCharMtx( njob-1, len2+1 );
+ for( i=0; i<clus1; i++ ) strcpy( oseq1[i], mseq1[i] );
+ for( i=0; i<clus2; i++ ) strcpy( oseq2[i], mseq2[i] );
+
+ newgapstr = "-";
commongappick( clus2, mseq2 );
commongappick( clus1, mseq1 );
@@ -2633,10 +2640,18 @@ static int dooneiteration( int *nlen, char **aseq, int nadd, char *mergeoralign,
ErrorExit( "ERROR IN SOURCE FILE" );
}
}
+ intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, strlen( mseq1[0] ), &nscore );
#if SCOREOUT
reporterr( "score = %10.2f\n", pscore );
#endif
- tscore += pscore;
+ if( nscore < oscore )
+ {
+ for( i=0; i<clus1; i++ ) strcpy( mseq1[i], oseq1[i] );
+ for( i=0; i<clus2; i++ ) strcpy( mseq2[i], oseq2[i] );
+ }
+ FreeCharMtx( oseq1 );
+ FreeCharMtx( oseq2 );
+
nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
// writePre( njob, name, nlen, aseq, 0 );
@@ -2667,9 +2682,6 @@ static int dooneiteration( int *nlen, char **aseq, int nadd, char *mergeoralign,
}
-#if SCOREOUT
- reporterr( "totalscore = %10.2f\n\n", tscore );
-#endif
Falign( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
Falign_udpari_long( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL );
Falign_givenanchors( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL );
=====================================
core/mafft.tmpl
=====================================
@@ -1,7 +1,7 @@
#! /bin/bash
er=0;
myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v7.467 (2020/May/14)"; export version
+version="v7.471 (2020/Jul/3)"; export version
LANG=C; export LANG
os=`uname`
progname=`basename "$0"`
@@ -1077,11 +1077,19 @@ function removetmpfile() { # for MPI
cat "$anchorfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_externalanchors"
SAVEIFS=$IFS
- IFS='\n'
- filelist="$1\n$addfile\n$scorematrix\n$mergetable\n$treeinfile\n$seedtablefile\n$laraparams\n$pdblist\n$ownlist"
+# Fixed a bug: 'n' was misinterpreted as delimiter, 2020/Jun/19
+ IFS=$'\n'
+ filelist="$1
+$addfile
+$scorematrix
+$mergetable
+$treeinfile
+$seedtablefile
+$laraparams
+$pdblist
+$ownlist"
for f in $filelist; do
- # $f="" demo mudani file ga hashiru.
- file "$f" 2>/dev/null | grep "UTF-[13][62]" >& /dev/null && printf "$f: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1;
+ file "$f" 2>/dev/null | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$f: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1;
done
IFS=$SAVEIFS
@@ -1095,7 +1103,7 @@ function removetmpfile() { # for MPI
shift
if [ -r "$1" ]; then
cat "$1" | tr "\r" "\n" > "$TMPFILE/seed$#"
- file "$1" | grep "UTF-[13][62]" >& /dev/null && printf "$1: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1;
+ file "$1" | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$1: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1;
else
echo "$0": Cannot open "$1". 1>&2
echo "" 1>&2
=====================================
core/makedirectionlist.c
=====================================
@@ -8,7 +8,7 @@
#define END_OF_VEC -1
-int nadd;
+//int nadd;
double thresholdtorev;
int dodp;
int addfragment;
=====================================
core/mltaln.h
=====================================
@@ -36,7 +36,7 @@
-#define VERSION "7.467"
+#define VERSION "7.471"
#define SHOWVERSION reporterr( "%s (%s) Version " VERSION "\nalg=%c, model=%s, amax=%3.1f\n%d thread(s)\n\n", progName( argv[0] ), (dorp=='d')?"nuc":((nblosum==-2)?"text":"aa"), alg, modelname, specificityconsideration, nthread )
#define FFT_THRESHOLD 80
=====================================
readme
=====================================
@@ -1,6 +1,6 @@
-----------------------------------------------------------------------
MAFFT: a multiple sequence alignment program
- version 7.467, 2020/May/14
+ version 7.471, 2020/Jul/3
http://mafft.cbrc.jp/alignment/software/
katoh at ifrec.osaka-u.ac.jp
View it on GitLab: https://salsa.debian.org/med-team/mafft/-/commit/5f66d7255cb705102ae70cc916191899eddfbba7
--
View it on GitLab: https://salsa.debian.org/med-team/mafft/-/commit/5f66d7255cb705102ae70cc916191899eddfbba7
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