diff -ubrN MUMmer3.20/scripts.orig/exact-tandems.sh MUMmer3.20/scripts/exact-tandems.sh --- MUMmer3.20/scripts.orig/exact-tandems.sh 1970-01-01 01:00:00.000000000 +0100 +++ MUMmer3.20/scripts/exact-tandems.sh 2007-11-12 13:12:31.000000000 +0100 @@ -0,0 +1,34 @@ +#!/bin/sh -e +# +# Find exact tandem repeats in specified file involving an +# exact duplicate of at least the specified length + +usage () { + echo "Usage: `basename $0` " + return 67 # EX_USAGE +} + +if [ $# -ne 2 ] ; then + echo "You provided $# arguments instead of 2." + usage +fi + +filename="$1" +matchlen="$2" + +bindir=__BIN_DIR +scriptdir=__SCRIPT_DIR + +if [ ! -e "$filename" ] ; then + echo "File $filename does not exist." + usage +fi + +echo "Finding matches" +$bindir/repeat-match -t -n $matchlen "$filename" | tail +3 > $$.tmp.matches +# This is default behavior when shell started with -e +# if ($status != 0) exit -1 + +echo "Tandem repeats" +sort -k1n -k2n $$.tmp.matches | awk -f $scriptdir/tandem-repeat.awk +rm -f $$.tmp.matches diff -ubrN MUMmer3.20/scripts.orig/Makefile MUMmer3.20/scripts/Makefile --- MUMmer3.20/scripts.orig/Makefile 2007-07-13 19:06:57.000000000 +0200 +++ MUMmer3.20/scripts/Makefile 2007-11-12 13:15:01.000000000 +0100 @@ -7,9 +7,18 @@ ifndef AUX_BIN_DIR AUX_BIN_DIR := $(CURDIR) endif +ifndef INSTALL_AUX_BIN_DIR +INSTALL_AUX_BIN_DIR := $(AUX_BIN_DIR) +endif ifndef SCRIPT_DIR SCRIPT_DIR := $(CURDIR) endif +ifndef INSTALL_BIN_DIR +INSTALL_BIN_DIR := $(BIN_DIR) +endif +ifndef INSTALL_SCRIPT_DIR +INSTAL_SCRIPT_DIR := $(SCRIPT_DIR) +endif SCRIPT_DIR := $(CURDIR) SED := $(filter /%,$(shell /bin/sh -c 'type sed')) @@ -29,68 +38,24 @@ clean: rm -f *~ - cd $(BIN_DIR); rm -f $(ALL) - - + ( cd $(BIN_DIR); rm -f $(ALL) ) +#-- replace variables by real path names --# -#-- not so PHONY rules --# -exact-tandems: exact-tandems.csh - $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ - -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ - exact-tandems.csh > $(BIN_DIR)/exact-tandems - chmod 755 $(BIN_DIR)/exact-tandems +%: + $(SED) -e 's?__AUX_BIN_DIR?$(INSTALL_AUX_BIN_DIR)?g' \ + -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \ + -e 's?__PERL_PATH?$(PERL)?g' \ + -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \ + $< > $(BIN_DIR)/$@ + chmod 755 $(BIN_DIR)/$@ +exact-tandems: exact-tandems.sh mapview: mapview.pl - $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ - -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ - mapview.pl > $(BIN_DIR)/mapview - chmod 755 $(BIN_DIR)/mapview - mummerplot: mummerplot.pl Foundation.pm - $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ - -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ - mummerplot.pl > $(BIN_DIR)/mummerplot - chmod 755 $(BIN_DIR)/mummerplot - dnadiff: dnadiff.pl Foundation.pm - $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ - -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ - dnadiff.pl > $(BIN_DIR)/dnadiff - chmod 755 $(BIN_DIR)/dnadiff - nucmer: nucmer.pl Foundation.pm - $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ - -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ - -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ - nucmer.pl > $(BIN_DIR)/nucmer - chmod 755 $(BIN_DIR)/nucmer - promer: promer.pl Foundation.pm - $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ - -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ - -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ - promer.pl > $(BIN_DIR)/promer - chmod 755 $(BIN_DIR)/promer - -run-mummer1: run-mummer1.csh - $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ - run-mummer1.csh > $(BIN_DIR)/run-mummer1 - chmod 755 $(BIN_DIR)/run-mummer1 - -run-mummer3: run-mummer3.csh - $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ - run-mummer3.csh > $(BIN_DIR)/run-mummer3 - chmod 755 $(BIN_DIR)/run-mummer3 - +run-mummer1: run-mummer1.sh +run-mummer3: run-mummer3.sh nucmer2xfig: nucmer2xfig.pl - $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ - nucmer2xfig.pl > $(BIN_DIR)/nucmer2xfig - chmod 755 $(BIN_DIR)/nucmer2xfig diff -ubrN MUMmer3.20/scripts.orig/run-mummer1.sh MUMmer3.20/scripts/run-mummer1.sh --- MUMmer3.20/scripts.orig/run-mummer1.sh 1970-01-01 01:00:00.000000000 +0100 +++ MUMmer3.20/scripts/run-mummer1.sh 2007-11-12 13:12:31.000000000 +0100 @@ -0,0 +1,45 @@ +#!/bin/sh -e +# +# **SEVERELY** antiquated script for running the mummer 1 suite +# -r option reverse complements the query sequence, coordinates of the reverse +# matches will be relative to the reversed sequence +# + +usage () { + echo "Usage: `basename $0` [-r]" + return 67 # EX_USAGE +} + +if [ $# -ne 3 -a $# -ne 4 ] ; then + echo "You provided $# arguments." + usage +fi + +ref="$1" +qry="$2" +pfx="$3" +rev="$4" + +bindir=__BIN_DIR + +if [ ! -e "$ref" ] ; then + echo "File for fasta reference $ref does not exist." + usage +fi + +if [ ! -e "$qry" ] ; then + echo "File for fasta query $qry does not exist." + usage +fi + +if [ "$pfx" = "" ] ; then + usage +fi + +echo "Find MUMs" +$bindir/mummer -mum -l 20 "$rev" "$ref" "$qry" | tail +2 > "$pfx".out +echo "Determine gaps" +$bindir/gaps "$ref" "$rev" < "$pfx".out > "$pfx".gaps +echo "Align gaps" +$bindir/mummer-annotate "$pfx".gaps "$qry" > "$pfx".align +mv witherrors.gaps "$pfx".errorsgaps diff -ubrN MUMmer3.20/scripts.orig/run-mummer3.sh MUMmer3.20/scripts/run-mummer3.sh --- MUMmer3.20/scripts.orig/run-mummer3.sh 1970-01-01 01:00:00.000000000 +0100 +++ MUMmer3.20/scripts/run-mummer3.sh 2007-11-12 13:12:31.000000000 +0100 @@ -0,0 +1,47 @@ +#!/bin/sh -e +# +# for running the basic mummer 3 suite, should use nucmer instead when possible +# to avoid the confusing reverse coordinate system of the raw programs. +# +# NOTE: be warned that all reverse matches will then +# be relative to the reverse complement of the query sequence. +# +# Edit this script as necessary to alter the matching and clustering values +# + +usage () { + echo "Usage: `basename $0` " + return 67 # EX_USAGE +} + +if [ $# -ne 3 ] ; then + echo "You provided $# arguments." + usage +fi + +ref="$1" +qry="$2" +pfx="$3" + +bindir=__BIN_DIR + +if [ ! -e "$ref" ] ; then + echo "File for fasta reference $ref does not exist." + usage +fi + +if [ ! -e "$qry" ] ; then + echo "File for fasta query $qry does not exist." + usage +fi + +if [ "$pfx" = "" ] ; then + usage +fi + +echo "Find MUMs" +$bindir/mummer -mumreference -b -l 20 "$ref" "$qry" > "$pfx".out +echo "Determine gaps" +$bindir/mgaps -l 100 -f .12 -s 600 < "$pfx".out > "$pfx".gaps +echo "Align gaps" +$bindir/combineMUMs -x -e .10 -W "$pfx".errorsgaps "$ref" "$qry" "$pfx".gaps > "$pfx".align