[med-svn] [Git][med-team/pftools][master] 2 commits: Refresh patches
Andreas Tille
gitlab at salsa.debian.org
Wed Nov 25 09:09:11 GMT 2020
Andreas Tille pushed to branch master at Debian Med / pftools
Commits:
ccf4cd8e by Andreas Tille at 2020-11-25T09:47:51+01:00
Refresh patches
- - - - -
12d78f5f by Andreas Tille at 2020-11-25T09:49:16+01:00
Upstream switched to cmake
- - - - -
11 changed files:
- debian/changelog
- debian/control
- − debian/patches/build_gtop.patch
- − debian/patches/fix_install.patch
- − debian/patches/fix_path_in_test_script.patch
- − debian/patches/fix_test_output.patch
- − debian/patches/gcc10.patch
- − debian/patches/getopt_for_pgdump.patch
- − debian/patches/hardening.patch
- debian/patches/series
- debian/patches/spelling.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -14,6 +14,7 @@ pftools (3.2.6-1) UNRELEASED; urgency=medium
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
+ * Upstream switched to cmake
-- Andreas Tille <tille at debian.org> Tue, 24 Nov 2020 21:17:21 +0100
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
gfortran,
- autoconf-archive
+ cmake
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/pftools
Vcs-Git: https://salsa.debian.org/med-team/pftools.git
=====================================
debian/patches/build_gtop.patch deleted
=====================================
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 21 Mar 2017 22:14:51 +0100
-Description: Build gtop as well since it is used in test suite
-
---- a/src/Fortran/Makefile.am
-+++ b/src/Fortran/Makefile.am
-@@ -1,5 +1,7 @@
--bin_PROGRAMS = htop ptoh ptof pfw 2ft 6ft psa2msa pfscan pfmake pfscale pfsearch
-+bin_PROGRAMS = gtop htop ptoh ptof pfw 2ft 6ft psa2msa pfscan pfmake pfscale pfsearch
-
-+gtop_SOURCES = gtop.f
-+gtop_LDADD = io.o
- htop_SOURCES = htop.f
- ptoh_SOURCES = ptoh.f
- ptof_SOURCES = ptof.f
=====================================
debian/patches/fix_install.patch deleted
=====================================
@@ -1,71 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 21 Mar 2017 22:14:51 +0100
-Description: Do not request user input
-
---- a/install_pftools.sh
-+++ b/install_pftools.sh
-@@ -67,19 +67,13 @@ echo "Make sure you have write permissio
- echo
-
- # Get package directory
--echo -n "Where should the pftools package be installed ? [ $pkgDir ] "
--read userInput
--pkgDir=${userInput:-$pkgDir}
-+pkgDir=$DESTDIR/usr/lib/pftools
-
- # Get binary directory
--echo -n "Where should the pftools executables be installed ? [ $binDir ] "
--read userInput
--binDir=${userInput:-$binDir}
-+binDir=$DESTDIR/usr/bin
-
- # Get man page directory
--echo -n "Where should the pftools man pages be installed ? [ $manDir ] "
--read userInput
--manDir=${userInput:-$manDir}
-+manDir=$DESTDIR/usr/share/man
-
- # Test and remove package directory
- if [ -d $pkgDir ]; then
-@@ -113,41 +107,17 @@ done
-
- # Test and create binary directory
- if [ ! -d $binDir ]; then
-- echo
-- echo "Binary directory $binDir does not exist."
-- echo "Create directory $binDir ? [ y/n ] "
-- read -s -n 1 userInput
-- if [ "$userInput" == 'y' ]; then
-- echo -n " Creating directory $binDir ... "
- mkdir -p $binDir 2>/dev/null || Fatal "Failed to create $binDir";
-- echo "OK"
-- else
-- Fatal "... aborting."
-- fi
- fi
-
- # Test and create man directory
- if [ ! -d $manDir ]; then
-- echo
-- echo "Man page directory $manDir does not exist."
-- echo "Create directory $manDir ? [ y/n ] "
-- read -s -n 1 userInput
-- if [ "$userInput" == 'y' ]; then
-- echo -n " Creating directory $manDir ... "
- mkdir -p $manDir 2>/dev/null || Fatal "Failed to create $manDir";
-- echo "OK"
-- else
-- Fatal "... aborting."
-- fi
- fi
-
- # Test and create man1 and man5 directories
- for subDir in ${manDir}/man1 ${manDir}/man5; do
-- if [ ! -d $subDir ]; then
-- echo -n " Creating directory $subDir ... "
- mkdir -p $subDir 2>/dev/null || Fatal "Failed to create $subDir";
-- echo "OK"
-- fi
- done
-
- # Copy package files to package directory
=====================================
debian/patches/fix_path_in_test_script.patch deleted
=====================================
@@ -1,90 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 21 Mar 2017 22:14:51 +0100
-Description: Since executables do not reside in the same dir with the data the
- relative PATH to the current dir is just wrong. This patch removes any PATH
- of the executables and simply assumes that PATH is properly set (which is done
- in debian/rules)
-
---- a/data/test.sh
-+++ b/data/test.sh
-@@ -1,54 +1,54 @@
- #!/bin/sh
- echo "#----------------------------------------------------------------------#"
--echo "# pftools test 1: ./pfsearch -f sh3.prf sh3.seq C=6.0"
-+echo "# pftools test 1: pfsearch -f sh3.prf sh3.seq C=6.0"
- echo "#----------------------------------------------------------------------#"
--./pfsearch -f sh3.prf sh3.seq C=6.0
-+pfsearch -f sh3.prf sh3.seq C=6.0
- echo "#----------------------------------------------------------------------#"
--echo "# pftools test 2: ./pfsearch -bx ecp.prf CVPBR322 | ./psa2msa -du"
-+echo "# pftools test 2: pfsearch -bx ecp.prf CVPBR322 | psa2msa -du"
- echo "#----------------------------------------------------------------------#"
--./pfsearch -bx ecp.prf CVPBR322 | ./psa2msa -du
-+pfsearch -bx ecp.prf CVPBR322 | psa2msa -du
- echo "#----------------------------------------------------------------------#"
--echo "# pftools test 3: ./pfscan -s GTPA_HUMAN prosite13.prf"
-+echo "# pftools test 3: pfscan -s GTPA_HUMAN prosite13.prf"
- echo "#----------------------------------------------------------------------#"
--./pfscan -s GTPA_HUMAN prosite13.prf
-+pfscan -s GTPA_HUMAN prosite13.prf
- echo "#----------------------------------------------------------------------#"
--echo "# pftools test 4: ./pfscan -by CVPBR322 ecp.prf L=2"
-+echo "# pftools test 4: pfscan -by CVPBR322 ecp.prf L=2"
- echo "#----------------------------------------------------------------------#"
--./pfscan -by CVPBR322 ecp.prf L=2
-+pfscan -by CVPBR322 ecp.prf L=2
- echo "#----------------------------------------------------------------------#"
--echo "# pftools test 5: ./gtop sh3.gpr F=50 | ./pfsearch -far - sh3.seq"
-+echo "# pftools test 5: gtop sh3.gpr F=50 | pfsearch -far - sh3.seq"
- echo "# | sort -nr"
- echo "#----------------------------------------------------------------------#"
--./gtop sh3.gpr F=50 | ./pfsearch -far - sh3.seq | sort -nr
-+gtop sh3.gpr F=50 | pfsearch -far - sh3.seq | sort -nr
- echo "#----------------------------------------------------------------------#"
--echo "# pftools test 6: ./htop pfam_sh3.hmm | ./pfsearch -f - sh3.seq"
-+echo "# pftools test 6: htop pfam_sh3.hmm | pfsearch -f - sh3.seq"
- echo " | sort -nr"
- echo "#----------------------------------------------------------------------#"
--./htop pfam_sh3.hmm | ./pfsearch -f - sh3.seq | sort -nr
-+htop pfam_sh3.hmm | pfsearch -f - sh3.seq | sort -nr
- echo "#----------------------------------------------------------------------#"
--echo "# pftools test 7: ./pfw sh3.msf N=1000 |"
--echo "# ./pfmake -b - blosum45.cmp H=0.6"
-+echo "# pftools test 7: pfw sh3.msf N=1000 |"
-+echo "# pfmake -b - blosum45.cmp H=0.6"
- echo "#----------------------------------------------------------------------#"
--./pfw sh3.msf N=1000 | ./pfmake -b - blosum45.cmp H=0.6
-+pfw sh3.msf N=1000 | pfmake -b - blosum45.cmp H=0.6
- echo "#----------------------------------------------------------------------#"
--echo "# pftools test 8:./ptoh ecp.prf L=1.15"
-+echo "# pftools test 8: ptoh ecp.prf L=1.15"
- echo "#----------------------------------------------------------------------#"
--./ptoh ecp.prf L=1.15
-+ptoh ecp.prf L=1.15
- echo "#----------------------------------------------------------------------#"
--echo "# pftools test 9: ./pfscale score.lis N=14147368 P=0.0001"
-+echo "# pftools test 9: pfscale score.lis N=14147368 P=0.0001"
- echo "# Q=0.000001 | sed -n 1,25p"
- echo "#----------------------------------------------------------------------#"
--./pfscale score.lis N=14147368 P=0.0001 Q=0.000001 | sed -n 1,25p
-+pfscale score.lis N=14147368 P=0.0001 Q=0.000001 | sed -n 1,25p
- echo "#----------------------------------------------------------------------#"
--echo "# pftools test 10: ./pfsearch -y coils.prf MYSA_HUMAN"
-+echo "# pftools test 10: pfsearch -y coils.prf MYSA_HUMAN"
- echo "#----------------------------------------------------------------------#"
--./pfsearch -y coils.prf MYSA_HUMAN
-+pfsearch -y coils.prf MYSA_HUMAN
- echo "#----------------------------------------------------------------------#"
--echo "# pftools test 11: /bin/rm sh3.fsp"
--echo "# ./ptof -r sh3.prf F=-1.2 I=0.6 X=-1.5 B=-0.5 >sh3.fsp"
--echo "# ./2ft < R76849.seq | ./pfsearch -fy sh3.fsp - C=5.0"
--echo "# /bin/rm sh3.fsp"
-+echo "# pftools test 11: rm sh3.fsp"
-+echo "# ptof -r sh3.prf F=-1.2 I=0.6 X=-1.5 B=-0.5 >sh3.fsp"
-+echo "# 2ft < R76849.seq | pfsearch -fy sh3.fsp - C=5.0"
-+echo "# rm sh3.fsp"
- echo "#----------------------------------------------------------------------#"
--/bin/rm sh3.fsp; ./ptof -r sh3.prf F=-1.2 I=0.6 X=-1.5 B=-0.5 > sh3.fsp ; ./2ft < R76849.seq | ./pfsearch -fy sh3.fsp - C=5.0; /bin/rm sh3.fsp
-+rm sh3.fsp; ptof -r sh3.prf F=-1.2 I=0.6 X=-1.5 B=-0.5 > sh3.fsp ; 2ft < R76849.seq | pfsearch -fy sh3.fsp - C=5.0; rm sh3.fsp
-
-
=====================================
debian/patches/fix_test_output.patch deleted
=====================================
@@ -1,445 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 21 Mar 2017 22:14:51 +0100
-Description: The test output seems to be created with pftools 2.3 and the
- output format has changed in version 3. This patch adapts to slight
- formatting changes (as well as the dropped PATH from test script).
- .
- Note: There are more relevant differences than just spacing which are
- not fixed in this patch.
-
---- a/data/test.out
-+++ b/data/test.out
-@@ -1,169 +1,169 @@
- #----------------------------------------------------------------------#
--# pftools test 1: ./pfsearch -f sh3.prf sh3.seq C=6.0
-+# pftools test 1: pfsearch -f sh3.prf sh3.seq C=6.0
- #----------------------------------------------------------------------#
-- 8.455 459 pos. 1 - 39 sp|P03949|ABL1_CAEEL TYROSINE-PROTEIN KINASE ABL-1 (EC 2.7.1.112) (FRAGMENT).
-- 14.973 857 pos. 61 - 121 sp|P00519|ABL1_HUMAN PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL (EC 2.7.1.112) (P150) (C-ABL).
-- 12.958 734 pos. 43 - 107 sp|P39969|BEB1_YEAST BEB1 PROTEIN.
-- 13.499 767 pos. 58 - 128 sp|P04821|CC25_YEAST CELL DIVISION CONTROL PROTEIN 25.
-- 10.043 556 pos. 100 - 161 sp|Q02640|CICX_HUMAN DIHYDROPRYRIDINE-SENSITIVE L-TYPE, BRAIN CALCIUM CHANNEL BETA-1-B1 SUBUNIT.
-- 11.812 664 pos. 279 - 341 sp|P20936|GTPA_HUMAN GTPASE-ACTIVATING PROTEIN (GAP) (RAS P21 PROTEIN ACTIVATOR).
-- 10.289 571 pos. 114 - 175 sp|Q08289|MSAB_HUMAN LAMBERT-EATON MYASTHENIC SYNDROME ANTIGEN B (MYSB).
-- 18.100 1048 pos. 1053 - 1111 sp|P34092|MYSB_DICDI MYOSIN IB HEAVY CHAIN.
-- 15.316 878 pos. 156 - 215 sp|P14598|NCF1_HUMAN NEUTROPHIL CYTOSOL FACTOR 1 (NCF-1) (NCF-47K) (47 KD AUTOSOMAL CHRONIC GRANU
-- 12.238 690 pos. 226 - 285 sp|P14598|NCF1_HUMAN NEUTROPHIL CYTOSOL FACTOR 1 (NCF-1) (NCF-47K) (47 KD AUTOSOMAL CHRONIC GRANU
-- 16.315 939 pos. 2 - 61 sp|P16333|NCK_HUMAN CYTOPLASMIC PROTEIN NCK.
-- 15.284 876 pos. 115 - 165 sp|P16333|NCK_HUMAN CYTOPLASMIC PROTEIN NCK.
-- 17.036 983 pos. 190 - 252 sp|P16333|NCK_HUMAN CYTOPLASMIC PROTEIN NCK.
-- 13.384 760 pos. 3 - 79 sp|P23727|P85A_BOVIN PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT (PI3-KINASE P85-ALPHA
-- 15.464 887 pos. 769 - 829 sp|P16885|PIP5_HUMAN 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE GAMMA 2 (EC 3.1.4.
-- 15.382 882 pos. 24 - 86 sp|P40996|SCD2_SCHPO SCD2 PROTEIN.
-- 11.992 675 pos. 123 - 185 sp|P40996|SCD2_SCHPO SCD2 PROTEIN.
-- 16.889 974 pos. 1 - 58 sp|P29355|SEM5_CAEEL SEX MUSCLE ABNORMAL PROTEIN 5.
-- 18.837 1093 pos. 154 - 213 sp|P29355|SEM5_CAEEL SEX MUSCLE ABNORMAL PROTEIN 5.
-- 20.295 1182 pos. 80 - 141 sp|P00523|SRC_CHICK PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC (EC 2.7.1.112) (P60-SRC).
-- 10.764 600 pos. 1 - 60 sp|P26674|STE6_SCHPO STE6 PROTEIN.
-- 11.796 663 pos. 617 - 660 sp|P15498|VAV_HUMAN VAV ONCOGENE.
-- 17.560 1015 pos. 783 - 843 sp|P15498|VAV_HUMAN VAV ONCOGENE.
-- 18.542 1075 pos. 314 - 373 sp|P43603|YFJ4_YEAST HYPOTHETICAL 40.4 KD PROTEIN IN PES4-HIS2 INTERGENIC REGION.
-- 13.089 742 pos. 493 - 555 sp|P38822|YHR4_YEAST HYPOTHETICAL 71.2 KD PROTEIN IN CDC12-ORC6 INTERGENIC REGION.
-- 13.695 779 pos. 577 - 633 sp|P38822|YHR4_YEAST HYPOTHETICAL 71.2 KD PROTEIN IN CDC12-ORC6 INTERGENIC REGION.
-- 9.323 512 pos. 504 - 572 sp|Q07157|ZO1_HUMAN TIGHT JUNCTION PROTEIN ZO-1.
-+ 8.455 459 pos. 1 - 39 sp|P03949|ABL1_CAEEL TYROSINE-PROTEIN KINASE ABL-1 (EC 2.7.1.112) (FRAGMENT).
-+ 14.973 857 pos. 61 - 121 sp|P00519|ABL1_HUMAN PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL (EC 2.7.1.112) (P150) (C-ABL).
-+ 12.958 734 pos. 43 - 107 sp|P39969|BEB1_YEAST BEB1 PROTEIN.
-+ 13.499 767 pos. 58 - 128 sp|P04821|CC25_YEAST CELL DIVISION CONTROL PROTEIN 25.
-+ 10.043 556 pos. 100 - 161 sp|Q02640|CICX_HUMAN DIHYDROPRYRIDINE-SENSITIVE L-TYPE, BRAIN CALCIUM CHANNEL BETA-1-B1 SUBUNIT.
-+ 11.812 664 pos. 279 - 341 sp|P20936|GTPA_HUMAN GTPASE-ACTIVATING PROTEIN (GAP) (RAS P21 PROTEIN ACTIVATOR).
-+ 10.289 571 pos. 114 - 175 sp|Q08289|MSAB_HUMAN LAMBERT-EATON MYASTHENIC SYNDROME ANTIGEN B (MYSB).
-+ 18.100 1048 pos. 1053 - 1111 sp|P34092|MYSB_DICDI MYOSIN IB HEAVY CHAIN.
-+ 15.316 878 pos. 156 - 215 sp|P14598|NCF1_HUMAN NEUTROPHIL CYTOSOL FACTOR 1 (NCF-1) (NCF-47K) (47 KD AUTOSOMAL CHRONIC GRANU
-+ 12.238 690 pos. 226 - 285 sp|P14598|NCF1_HUMAN NEUTROPHIL CYTOSOL FACTOR 1 (NCF-1) (NCF-47K) (47 KD AUTOSOMAL CHRONIC GRANU
-+ 16.315 939 pos. 2 - 61 sp|P16333|NCK_HUMAN CYTOPLASMIC PROTEIN NCK.
-+ 15.284 876 pos. 115 - 165 sp|P16333|NCK_HUMAN CYTOPLASMIC PROTEIN NCK.
-+ 17.036 983 pos. 190 - 252 sp|P16333|NCK_HUMAN CYTOPLASMIC PROTEIN NCK.
-+ 13.384 760 pos. 3 - 79 sp|P23727|P85A_BOVIN PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT (PI3-KINASE P85-ALPHA
-+ 15.464 887 pos. 769 - 829 sp|P16885|PIP5_HUMAN 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE GAMMA 2 (EC 3.1.4.
-+ 15.382 882 pos. 24 - 86 sp|P40996|SCD2_SCHPO SCD2 PROTEIN.
-+ 11.992 675 pos. 123 - 185 sp|P40996|SCD2_SCHPO SCD2 PROTEIN.
-+ 16.889 974 pos. 1 - 58 sp|P29355|SEM5_CAEEL SEX MUSCLE ABNORMAL PROTEIN 5.
-+ 18.837 1093 pos. 154 - 213 sp|P29355|SEM5_CAEEL SEX MUSCLE ABNORMAL PROTEIN 5.
-+ 20.295 1182 pos. 80 - 141 sp|P00523|SRC_CHICK PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC (EC 2.7.1.112) (P60-SRC).
-+ 10.764 600 pos. 1 - 60 sp|P26674|STE6_SCHPO STE6 PROTEIN.
-+ 11.796 663 pos. 617 - 660 sp|P15498|VAV_HUMAN VAV ONCOGENE.
-+ 17.560 1015 pos. 783 - 843 sp|P15498|VAV_HUMAN VAV ONCOGENE.
-+ 18.542 1075 pos. 314 - 373 sp|P43603|YFJ4_YEAST HYPOTHETICAL 40.4 KD PROTEIN IN PES4-HIS2 INTERGENIC REGION.
-+ 13.089 742 pos. 493 - 555 sp|P38822|YHR4_YEAST HYPOTHETICAL 71.2 KD PROTEIN IN CDC12-ORC6 INTERGENIC REGION.
-+ 13.695 779 pos. 577 - 633 sp|P38822|YHR4_YEAST HYPOTHETICAL 71.2 KD PROTEIN IN CDC12-ORC6 INTERGENIC REGION.
-+ 9.323 512 pos. 504 - 572 sp|Q07157|ZO1_HUMAN TIGHT JUNCTION PROTEIN ZO-1.
- #----------------------------------------------------------------------#
--# pftools test 2: ./pfsearch -bx ecp.prf CVPBR322 | ./psa2msa -du
-+# pftools test 2: pfsearch -bx ecp.prf CVPBR322 | psa2msa -du
- #----------------------------------------------------------------------#
-->CVPBR322_1 63.920 271 pos. 1 - 41 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_1 63.920 271 pos. 1 - 41 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- TTCTCATGTTTGACAGCTTATCATC----GATAAGCTTTAATGCG
-->CVPBR322_2 45.534 240 pos. 25 - 65 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_2 45.534 240 pos. 25 - 65 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- CGATAAGCTTTAATGCGGTAGTTTA----TCACAGTTAAATTGCT
-->CVPBR322_3 55.617 257 pos. 1589 - 1629 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_3 55.617 257 pos. 1589 - 1629 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- CAACATGAATGGTCTTCGGTTTCCG----TGTTTCGTAAAGTCTG
-->CVPBR322_4 46.720 242 pos. 2274 - 2314 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_4 46.720 242 pos. 2274 - 2314 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- CAGATTGTACTGAGAGTGCACCATA----TGCGGTGTGAAATACC
-->CVPBR322_5 48.500 245 pos. 2296 - 2340 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_5 48.500 245 pos. 2296 - 2340 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- ATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACC
-->CVPBR322_6 64.513 272 pos. 2931 - 2972 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_6 64.513 272 pos. 2931 - 2972 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- ACAGAGTTCTTGAAGTGGTGGCCTA---ACTACGGCTACACTAGA
-->CVPBR322_7 50.872 249 pos. 3207 - 3246 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_7 50.872 249 pos. 3207 - 3246 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- AAAAGGATCTTCACCTAGATCCTTT-----TAAATTAAAAATGAA
-->CVPBR322_8 45.534 240 pos. 3233 - 3274 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_8 45.534 240 pos. 3233 - 3274 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- AAATTAAAAATGAAGTTTTAAATCA---ATCTAAAGTATATATGA
-->CVPBR322_9 53.244 253 pos. 3240 - 3284 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_9 53.244 253 pos. 3240 - 3284 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- AAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGG
-->CVPBR322_10 52.058 251 pos. 3350 - 3391 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_10 52.058 251 pos. 3350 - 3391 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- CATAGTTGCCTGACTCCCCGTCGTG---TAGATAACTACGATACG
-->CVPBR322_11 53.837 254 pos. 3788 - 3828 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_11 53.837 254 pos. 3788 - 3828 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- ACTGCATAATTCTCTTACTGTCATG----CCATCCGTAAGATGCT
-->CVPBR322_12 46.127 241 pos. 3796 - 3836 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_12 46.127 241 pos. 3796 - 3836 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- ATTCTCTTACTGTCATGCCATCCGT----AAGATGCTTTTCTGTG
-->CVPBR322_13 56.210 258 pos. 4133 - 4173 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_13 56.210 258 pos. 4133 - 4173 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- ACGGAAATGTTGAATACTCATACTC----TTCCTTTTTCAATATT
-->CVPBR322_14 53.244 253 pos. 4166 - 4207 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_14 53.244 253 pos. 4166 - 4207 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- TCAATATTATTGAAGCATTTATCAG---GGTTATTGTCTCATGAG
-->CVPBR322_15 52.058 251 pos. 4187 - 4227 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_15 52.058 251 pos. 4187 - 4227 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- TCAGGGTTATTGTCTCATGAGCGGA----TACATATTTGAATGTA
-->CVPBR322_16 56.803 259 pos. 4273 - 4312 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_16 56.803 259 pos. 4273 - 4312 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- AAGTGCCACCTGACGTCTAAGAAAC-----CATTATTATCATGAC
-->CVPBR322_17 47.906 244 pos. 4291 - 4331 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_17 47.906 244 pos. 4291 - 4331 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- AAGAAACCATTATTATCATGACATT----AACCTATAAAAATAGG
-->CVPBR322_18 47.906 244 pos. 4299 - 4342 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_18 47.906 244 pos. 4299 - 4342 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- ATTATTATCATGACATTAACCTATA-AAAATAGGCGTATCACGAG
-->CVPBR322_19 50.279 248 pos. 4348 - 4308 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_19 50.279 248 pos. 4348 - 4308 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- AAGGGCCTCGTGATACGCCTATTTT----TATAGGTTAATGTCAT
-->CVPBR322_20 47.906 244 pos. 4336 - 4296 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_20 47.906 244 pos. 4336 - 4296 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- ATACGCCTATTTTTATAGGTTAATG----TCATGATAATAATGGT
-->CVPBR322_21 50.279 248 pos. 4323 - 4283 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_21 50.279 248 pos. 4323 - 4283 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- TATAGGTTAATGTCATGATAATAAT----GGTTTCTTAGACGTCA
-->CVPBR322_22 52.651 252 pos. 4232 - 4192 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_22 52.651 252 pos. 4232 - 4192 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- CTAAATACATTCAAATATGTATCCG----CTCATGAGACAATAAC
-->CVPBR322_23 50.872 249 pos. 4178 - 4135 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_23 50.872 249 pos. 4178 - 4135 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- TCAATAATATTGAAAAAGGAAGAGT-ATGAGTATTCAACATTTCC
-->CVPBR322_24 46.127 241 pos. 3954 - 3913 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_24 46.127 241 pos. 3954 - 3913 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- TGAGCACTTTTAAAGTTCTGCTATG---TGGCGCGGTATTATCCC
-->CVPBR322_25 46.720 242 pos. 3861 - 3821 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_25 46.720 242 pos. 3861 - 3821 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- ATGACTTGGTTGAGTACTCACCAGT----CACAGAAAAGCATCTT
-->CVPBR322_26 45.534 240 pos. 3569 - 3529 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_26 45.534 240 pos. 3569 - 3529 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- ACTACTTACTCTAGCTTCCCGGCAA----CAATTAATAGACTGGA
-->CVPBR322_27 47.313 243 pos. 3464 - 3420 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_27 47.313 243 pos. 3464 - 3420 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- TGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGC
-->CVPBR322_28 54.431 255 pos. 3301 - 3261 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_28 54.431 255 pos. 3301 - 3261 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- CATTGGTAACTGTCAGACCAAGTTT----ACTCATATATACTTTA
-->CVPBR322_29 51.465 250 pos. 3273 - 3232 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_29 51.465 250 pos. 3273 - 3232 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- CATATATACTTTAGATTGATTTAAA---ACTTCATTTTTAATTTA
-->CVPBR322_30 45.534 240 pos. 3267 - 3225 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_30 45.534 240 pos. 3267 - 3225 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- TACTTTAGATTGATTTAAAACTTCA--TTTTTAATTTAAAAGGAT
-->CVPBR322_31 46.127 241 pos. 3250 - 3210 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_31 46.127 241 pos. 3250 - 3210 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- AAACTTCATTTTTAATTTAAAAGGA----TCTAGGTGAAGATCCT
-->CVPBR322_32 53.244 253 pos. 3216 - 3173 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_32 53.244 253 pos. 3216 - 3173 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- AGATCCTTTTTGATAATCTCATGAC-CAAAATCCCTTAACGTGAG
-->CVPBR322_33 60.362 265 pos. 3131 - 3091 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_33 60.362 265 pos. 3131 - 3091 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- AGGATCTTCTTGAGATCCTTTTTTT----CTGCGCGTAATCTGCT
-->CVPBR322_34 47.313 243 pos. 2318 - 2274 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_34 47.313 243 pos. 2318 - 2274 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- GTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTG
-->CVPBR322_35 58.582 262 pos. 85 - 41 J01749|CVPBR322 Cloning vector pBR322, complete genome.
-+>CVPBR322_35 58.582 262 pos. 85 - 41 J01749|CVPBR322 Cloning vector pBR322, complete genome.
- ACACGGTGCCTGACTGCGTTAGCAATTTAACTGTGATAAACTACC
- #----------------------------------------------------------------------#
--# pftools test 3: ./pfscan -s GTPA_HUMAN prosite13.prf
-+# pftools test 3: pfscan -s GTPA_HUMAN prosite13.prf
- #----------------------------------------------------------------------#
-->C2_DOMAIN_2 10.353 680 pos. 594 - 676 PS50004|C2_DOMAIN_2 C2-domain profile.
-+>C2_DOMAIN_2 10.353 680 pos. 594 - 676 PS50004|C2_DOMAIN_2 C2-domain profile.
- SSLVLHIEEAHKLPVKHFTNPYCNIYLNSVQVAKTHAREGQNPVWSEEFVFDDLPPDINR
- FEITLSNKTKKSKDPDILFMRCQ
-->PH_DOMAIN 16.616 659 pos. 474 - 577 PS50003|PH_DOMAIN PH domain profile.
-+>PH_DOMAIN 16.616 659 pos. 474 - 577 PS50003|PH_DOMAIN PH domain profile.
- NIVKKGYLLKKGKGKRWKNLYFILEGSDAQLIYFESEKRATKPKGLIDLSVCSVYVVHDS
- LFGRPNCFQIVVQHFSEEHYIFYFAGETPEQAEDWMKGLQAFCN
-->SH2_1 21.898 1450 pos. 181 - 272 PS50001|SH2 Src homology 2 (SH2) domain profile.
-+>SH2_1 21.898 1450 pos. 181 - 272 PS50001|SH2 Src homology 2 (SH2) domain profile.
- WYHGKLDRTIAEERLRQAGKSGSYLIRESDRRPGSFVLSFLSQMNVVNHFRIIAMCGDYY
- IGGRRFSSLSDLIGYYSHVSCLLKGEKLLYPV
-->SH2_2 20.059 1326 pos. 351 - 441 PS50001|SH2 Src homology 2 (SH2) domain profile.
-+>SH2_2 20.059 1326 pos. 351 - 441 PS50001|SH2 Src homology 2 (SH2) domain profile.
- WFHGKISKQEAYNLLMTVGQVCSFLVRPSDNTPGDYSLYFRTNENIQRFKICPTPNNQFM
- MGGRYYNSIGDIIDHYRKEQIVEGYYLKEPV
-->SH3 11.812 664 pos. 279 - 341 PS50002|SH3 Src homology 3 (SH3) domain profile.
-+>SH3 11.812 664 pos. 279 - 341 PS50002|SH3 Src homology 3 (SH3) domain profile.
- EDRRRVRAILPYTKVPDTDEISFLKGDMFIVHNELEDGWMWVTNLRTDEQGLIVEDLVEE
- VGR
-->RAS_GTPASE_ACTIV_2 56.401 3900 pos. 748 - 942 PS50018|RAS_GTPASE_ACTIV_2 Ras GTPase-activating proteins profile.
-+>RAS_GTPASE_ACTIV_2 56.401 3900 pos. 748 - 942 PS50018|RAS_GTPASE_ACTIV_2 Ras GTPase-activating proteins profile.
- DRTLLASILLRIFLHEKLESLLLCTLNDREISMEDEATTLFRATTLASTLMEQYMKATAT
- QFVHHALKDSILKIMESKQSCELSPSKLEKNEDVNTNLTHLLNILSELVEKIFMASEILP
- PTLRYIYGCLQKSVQHKWPTNTTMRTRVVSGFVFLRLICPAILNPRMFNIISDSPSPIAA
- RTLILVAKSVQNLAN
- #----------------------------------------------------------------------#
--# pftools test 4: ./pfscan -by CVPBR322 ecp.prf L=2
-+# pftools test 4: pfscan -by CVPBR322 ecp.prf L=2
- #----------------------------------------------------------------------#
-- 63.920 271 pos. 1 - 41 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
-+ 63.920 271 pos. 1 - 41 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
- #
--# P 1 *********TTGACA*********************TATAAT*** -1
--# S 1 TTCTCATGTTTGACAGCTTATCATC----GATAAGCTTTAATGCG -4321
-+# P 1 *********TTGACA*********************TATAAT*** -1
-+# S 1 TTCTCATGTTTGACAGCTTATCATC----GATAAGCTTTAATGCG -4321
- #
-- 55.617 257 pos. 1589 - 1629 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
-+ 55.617 257 pos. 1589 - 1629 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
- #
--# P 1 *********TTGACA*********************TATAAT*** -1
--# S 1589 CAACATGAATGGTCTTCGGTTTCCG----TGTTTCGTAAAGTCTG -2733
-+# P 1 *********TTGACA*********************TATAAT*** -1
-+# S 1589 CAACATGAATGGTCTTCGGTTTCCG----TGTTTCGTAAAGTCTG -2733
- #
-- 64.513 272 pos. 2931 - 2972 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
-+ 64.513 272 pos. 2931 - 2972 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
- #
--# P 1 *********TTGACA*********************TATAAT*** -1
--# S 2931 ACAGAGTTCTTGAAGTGGTGGCCTA---ACTACGGCTACACTAGA -1390
-+# P 1 *********TTGACA*********************TATAAT*** -1
-+# S 2931 ACAGAGTTCTTGAAGTGGTGGCCTA---ACTACGGCTACACTAGA -1390
- #
-- 56.210 258 pos. 4133 - 4173 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
-+ 56.210 258 pos. 4133 - 4173 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
- #
--# P 1 *********TTGACA*********************TATAAT*** -1
--# S 4133 ACGGAAATGTTGAATACTCATACTC----TTCCTTTTTCAATATT -189
-+# P 1 *********TTGACA*********************TATAAT*** -1
-+# S 4133 ACGGAAATGTTGAATACTCATACTC----TTCCTTTTTCAATATT -189
- #
-- 56.803 259 pos. 4273 - 4312 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
-+ 56.803 259 pos. 4273 - 4312 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
- #
--# P 1 *********TTGACA*********************TATAAT*** -1
--# S 4273 AAGTGCCACCTGACGTCTAAGAAAC-----CATTATTATCATGAC -50
-+# P 1 *********TTGACA*********************TATAAT*** -1
-+# S 4273 AAGTGCCACCTGACGTCTAAGAAAC-----CATTATTATCATGAC -50
- #
-- 60.362 265 pos. 3131 - 3091 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
-+ 60.362 265 pos. 3131 - 3091 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
- #
--# P 1 *********TTGACA*********************TATAAT*** -1
--# S 3131 AGGATCTTCTTGAGATCCTTTTTTT----CTGCGCGTAATCTGCT -1271
-+# P 1 *********TTGACA*********************TATAAT*** -1
-+# S 3131 AGGATCTTCTTGAGATCCTTTTTTT----CTGCGCGTAATCTGCT -1271
- #
-- 58.582 262 pos. 85 - 41 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
-+ 58.582 262 pos. 85 - 41 NS00001|ECOLI_PROM_RP70 E. coli RNA POL sigma-70 promoter.
- #
--# P 1 *********TTGACA*********************TATAAT*** -1
--# S 85 ACACGGTGCCTGACTGCGTTAGCAATTTAACTGTGATAAACTACC -4321
-+# P 1 *********TTGACA*********************TATAAT*** -1
-+# S 85 ACACGGTGCCTGACTGCGTTAGCAATTTAACTGTGATAAACTACC -4321
- #
- #----------------------------------------------------------------------#
--# pftools test 5: ./gtop sh3.gpr F=50 | ./pfsearch -far - sh3.seq
-+# pftools test 5: gtop sh3.gpr F=50 | pfsearch -far - sh3.seq
- # | sort -nr
- #----------------------------------------------------------------------#
- 944 sp|P00523|SRC_CHICK PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC (EC 2.7.1.112) (P60-SRC).
-@@ -187,7 +187,7 @@ RTLILVAKSVQNLAN
- 293 sp|Q08289|MSAB_HUMAN LAMBERT-EATON MYASTHENIC SYNDROME ANTIGEN B (MYSB).
- 279 sp|P20936|GTPA_HUMAN GTPASE-ACTIVATING PROTEIN (GAP) (RAS P21 PROTEIN ACTIVATOR).
- #----------------------------------------------------------------------#
--# pftools test 6: ./htop pfam_sh3.hmm | ./pfsearch -f - sh3.seq
-+# pftools test 6: htop pfam_sh3.hmm | pfsearch -f - sh3.seq
- | sort -nr
- #----------------------------------------------------------------------#
- 19.485 100384 pos. 317 - 373 sp|P43603|YFJ4_YEAST HYPOTHETICAL 40.4 KD PROTEIN IN PES4-HIS2 INTERGENIC REGION.
-@@ -214,8 +214,8 @@ RTLILVAKSVQNLAN
- 11.218 26047 pos. 61 - 126 sp|P04821|CC25_YEAST CELL DIVISION CONTROL PROTEIN 25.
- 10.425 18915 pos. 601 - 658 sp|P15498|VAV_HUMAN VAV ONCOGENE.
- #----------------------------------------------------------------------#
--# pftools test 7: ./pfw sh3.msf N=1000 |
--# ./pfmake -b - blosum45.cmp H=0.6
-+# pftools test 7: pfw sh3.msf N=1000 |
-+# pfmake -b - blosum45.cmp H=0.6
- #----------------------------------------------------------------------#
- ID SEQUENCE_RPOFILE; MATRIX.
- AC ZZ99999;
-@@ -298,10 +298,10 @@ MA /M: SY='I'; M=-7,-12,-22,-14,-10,-8
- MA /M: SY='N'; M=-7,5,-24,6,-2,-22,6,-8,-22,-5,-19,-14,7,-17,-4,-5,2,-5,-17,-27,-15,-4;
- MA /M: SY='S'; M=0,-1,-13,-3,-4,-19,-13,-4,-15,-4,-15,-10,2,-16,-2,-2,7,2,-9,-30,-13,-4;
- MA /I: E1=0; IE=-105; DE=-105;
--CC /GENERATED_BY="./pfmake -b - blosum45.cmp H=0.6";
-+CC /GENERATED_BY="pfmake -b - blosum45.cmp H=0.6";
- //
- #----------------------------------------------------------------------#
--# pftools test 8:./ptoh ecp.prf L=1.15
-+# pftools test 8: ptoh ecp.prf L=1.15
- #----------------------------------------------------------------------#
- # HMM v1.7
- 45 # M -- length of model
-@@ -1231,7 +1231,7 @@ no # Optional consensus structure a
- 0.250000 # Symbol G probability
- 0.250000 # Symbol T probability
- #----------------------------------------------------------------------#
--# pftools test 9: ./pfscale score.lis N=14147368 P=0.0001
-+# pftools test 9: pfscale score.lis N=14147368 P=0.0001
- # Q=0.000001 | sed -n 1,25p
- #----------------------------------------------------------------------#
- # -LogP = 2.0437 + 0.00741886 * raw-score
-@@ -1260,78 +1260,78 @@ no # Optional consensus structure a
- 20 523.00 5.8606 5.9238
- 21 519.00 5.8389 5.8941
- #----------------------------------------------------------------------#
--# pftools test 10: ./pfsearch -y coils.prf MYSA_HUMAN
-+# pftools test 10: pfsearch -y coils.prf MYSA_HUMAN
- #----------------------------------------------------------------------#
-- 82.697 2354 pos. 848 - 1922 P13533|MYSA_HUMAN MYOSIN HEAVY CHAIN, CARDIAC MUSCLE ALPHA ISOFORM.
-+ 82.697 2354 pos. 848 - 1922 P13533|MYSA_HUMAN MYOSIN HEAVY CHAIN, CARDIAC MUSCLE ALPHA ISOFORM.
- #
--# P 5 efgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefga -7
--# S 848 EKEMATMKEEFGRIKETLEKSEARRKELEEKMVSLLQEKNDLQLQVQAEQDNLNDAEERC -1033
-+# P 5 efgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefga -7
-+# S 848 EKEMATMKEEFGRIKETLEKSEARRKELEEKMVSLLQEKNDLQLQVQAEQDNLNDAEERC -1033
- #
--# P 2 bcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcde -3
--# S 908 DQLIKNKIQLEAKVKEMNERLEDEEEMNAELTAKKRKLEDECSELKKDIDDLELTLAKVE -973
-+# P 2 bcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcde -3
-+# S 908 DQLIKNKIQLEAKVKEMNERLEDEEEMNAELTAKKRKLEDECSELKKDIDDLELTLAKVE -973
- #
--# P 6 fgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgab -6
--# S 968 KEKHATENKVKNLTEEMAGLDEIIAKLTKEKKALQEAHQQALDDLQAEEDKVNTLSKSKV -913
-+# P 6 fgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgab -6
-+# S 968 KEKHATENKVKNLTEEMAGLDEIIAKLTKEKKALQEAHQQALDDLQAEEDKVNTLSKSKV -913
- #
--# P 3 cdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdef -2
--# S 1028 KLEQQVDDLEGSLEQEKKVRMDLERAKRKLEGDLKLTQESIMDLENDKLQLEEKLKKKEF -853
-+# P 3 cdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdef -2
-+# S 1028 KLEQQVDDLEGSLEQEKKVRMDLERAKRKLEGDLKLTQESIMDLENDKLQLEEKLKKKEF -853
- #
--# P 7 gabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabc -5
--# S 1088 DINQQNSKIEDEQVLALQLQKKLKENQARIEELEEELEAERTARAKVEKLRSDLSRELEE -793
-+# P 7 gabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabc -5
-+# S 1088 DINQQNSKIEDEQVLALQLQKKLKENQARIEELEEELEAERTARAKVEKLRSDLSRELEE -793
- #
--# P 4 defgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefga-bcdefgabcdef -2
--# S 1148 ISERLEEAGGATSVQIEMNKKREAEFQKMRRDLEEATLQHEATAAALrKKHADSVAELGE -733
-+# P 4 defgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefga-bcdefgabcdef -2
-+# S 1148 ISERLEEAGGATSVQIEMNKKREAEFQKMRRDLEEATLQHEATAAALrKKHADSVAELGE -733
- #
--# P 7 gabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabc -5
--# S 1208 QIDNLQRVKQKLEKEKSEFKLELDDVTSNMEQIIKAKANLEKVSRTLEDQANEYRVKLEE -673
-+# P 7 gabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabc -5
-+# S 1208 QIDNLQRVKQKLEKEKSEFKLELDDVTSNMEQIIKAKANLEKVSRTLEDQANEYRVKLEE -673
- #
--# P 4 defgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefg -1
--# S 1268 AQRSLNDFTTQRAKLQTENGELSRQLEEKEALISQLTRGKLSYTQQMEDLKRQLEEEGKA -613
-+# P 4 defgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefg -1
-+# S 1268 AQRSLNDFTTQRAKLQTENGELSRQLEEKEALISQLTRGKLSYTQQMEDLKRQLEEEGKA -613
- #
--# P 1 abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgab-cdefgabc -5
--# S 1328 KNALAHALQSARHDCDLLREQYEEETEAKAELQRVLSKANSEVAQCRTKYEtDAIQRTEE -553
-+# P 1 abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgab-cdefgabc -5
-+# S 1328 KNALAHALQSARHDCDLLREQYEEETEAKAELQRVLSKANSEVAQCRTKYEtDAIQRTEE -553
- #
--# P 4 defgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefg -1
--# S 1388 LEEAKKKLAQRLQDAEEAVEAVNAKCSSLEKTKHRLQNEIEDLMVDVERSNAAAAALDKK -493
-+# P 4 defgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefg -1
-+# S 1388 LEEAKKKLAQRLQDAEEAVEAVNAKCSSLEKTKHRLQNEIEDLMVDVERSNAAAAALDKK -493
- #
--# P 1 abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcd -4
--# S 1448 QRNFDKILAEWKQKYEESQSELESSQKEARSLSTELFKLKNAYEESLEHLETFKRENKNL -433
-+# P 1 abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcd -4
-+# S 1448 QRNFDKILAEWKQKYEESQSELESSQKEARSLSTELFKLKNAYEESLEHLETFKRENKNL -433
- #
--# P 5 efgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefga -7
--# S 1508 QEEISDLTEQLGEGGKNVHELEKVRKQLEVEKLELQSALEEAEASLEHEEGKILRAQLEF -373
-+# P 5 efgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefga -7
-+# S 1508 QEEISDLTEQLGEGGKNVHELEKVRKQLEVEKLELQSALEEAEASLEHEEGKILRAQLEF -373
- #
--# P 2 bcdefgabc-defgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcd -4
--# S 1568 NQIKAEIERkLAEKDEEMEQAKRNHQRVVDSLQTSLDAETRSRNEVLRVKKKMEGDLNEM -313
-+# P 2 bcdefgabc-defgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcd -4
-+# S 1568 NQIKAEIERkLAEKDEEMEQAKRNHQRVVDSLQTSLDAETRSRNEVLRVKKKMEGDLNEM -313
- #
--# P 5 efgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefga -7
--# S 1628 EIQLSHANRMAAEAQKQVKSLQSLLKDTQIQLDDAVRANDDLKENIAIVERRNNLLQAEL -253
-+# P 5 efgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefga -7
-+# S 1628 EIQLSHANRMAAEAQKQVKSLQSLLKDTQIQLDDAVRANDDLKENIAIVERRNNLLQAEL -253
- #
--# P 2 bcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcde -3
--# S 1688 EELRAVVEQTERSRKLADRELIETSERVQLLHSQNTSLINQKKKMDADLSQLQSEVEEAV -193
-+# P 2 bcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcde -3
-+# S 1688 EELRAVVEQTERSRKLADRELIETSERVQLLHSQNTSLINQKKKMDADLSQLQSEVEEAV -193
- #
--# P 6 fgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdef-ga -7
--# S 1748 QECRNAEEKAKKAITHAAMMAEELKKEQDTSAHLERMKKNMEQTIKDLQHRLDEAEQiAL -133
-+# P 6 fgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdef-ga -7
-+# S 1748 QECRNAEEKAKKAITHAAMMAEELKKEQDTSAHLERMKKNMEQTIKDLQHRLDEAEQiAL -133
- #
--# P 2 bcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcde -3
--# S 1808 KGGKKQLQKLEARVRELEGELEAEQKRNAESVKGMRKSERRIKELTYQTEEDKKNLLRLQ -73
-+# P 2 bcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcde -3
-+# S 1808 KGGKKQLQKLEARVRELEGELEAEQKRNAESVKGMRKSERRIKELTYQTEEDKKNLLRLQ -73
- #
--# P 6 fgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcd -4
--# S 1868 DLVDKLQLKVKAYKRQAEEAEEQANTNLSKFRKVQHELDEAEERADIAESQVNKL -18
-+# P 6 fgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcd -4
-+# S 1868 DLVDKLQLKVKAYKRQAEEAEEQANTNLSKFRKVQHELDEAEERADIAESQVNKL -18
- #
- #----------------------------------------------------------------------#
--# pftools test 11: /bin/rm sh3.fsp
--# ./ptof -r sh3.prf F=-1.2 I=0.6 X=-1.5 B=-0.5 >sh3.fsp
--# ./2ft < R76849.seq | ./pfsearch -fy sh3.fsp - C=5.0
--# /bin/rm sh3.fsp
-+# pftools test 11: rm sh3.fsp
-+# ptof -r sh3.prf F=-1.2 I=0.6 X=-1.5 B=-0.5 >sh3.fsp
-+# 2ft < R76849.seq | pfsearch -fy sh3.fsp - C=5.0
-+# rm sh3.fsp
- #----------------------------------------------------------------------#
-- 10.764 600 pos. 186 - 347 x|gi|851481|gb|R76849|R76849_M yi63d09.r1 Homo sapiens cDNA clone 143921 5' similar to gb:M23379
-+ 10.764 600 pos. 186 - 347 x|gi|851481|gb|R76849|R76849_M yi63d09.r1 Homo sapiens cDNA clone 143921 5' similar to gb:M23379
- #
--# P 28 Y><D><Y><E>----<A><E><D><P><D><E><L><S><F>-<K><K><G><D><I><I -103
--# S 186 YTPPLLYTHTQkkksVYTPPQRDTHTLODMOEKNIOKSVFFSpLLOKKKRGERDIYMCVF -253
-+# P 28 Y><D><Y><E>----<A><E><D><P><D><E><L><S><F>-<K><K><G><D><I><I -103
-+# S 186 YTPPLLYTHTQkkksVYTPPQRDTHTLODMOEKNIOKSVFFSpLLOKKKRGERDIYMCVF -253
- #
--# P 83 ><Y><I><L><E><K><S><D><D><D><W><W><R><G><R><N><X><R><T><G><Q -43
--# S 246 SHILCVFSHIONMOENILOREKRDMWGDMWGDMCVWGGVLYTQKNIFLOKRENTQRDMOE -193
-+# P 83 ><Y><I><L><E><K><S><D><D><D><W><W><R><G><R><N><X><R><T><G><Q -43
-+# S 246 SHILCVFSHIONMOENILOREKRDMWGDMWGDMCVWGGVLYTQKNIFLOKRENTQRDMOE -193
- #
--# P 143 ><E><G><Y><I><P><S><N><Y><V><E><E><X><D><S -1
--# S 306 NTQKRGAPLLYILCVLOEKRDTPLOSVOREKRERGVWGGAPR -151
-+# P 143 ><E><G><Y><I><P><S><N><Y><V><E><E><X><D><S -1
-+# S 306 NTQKRGAPLLYILCVLOEKRDTPLOSVOREKRERGVWGGAPR -151
- #
=====================================
debian/patches/gcc10.patch deleted
=====================================
@@ -1,15 +0,0 @@
-Description: Fix gcc-10 FTBFS with extern attribute
-Author: Nilesh Patra <npatra974 at gmail.com>
-Forwarded: <URL|no|not-needed, useless if you have a Bug field, optional>
-Last-Changed: Nov 24, 2020
---- a/src/C/include/profile.h
-+++ b/src/C/include/profile.h
-@@ -67,7 +67,7 @@
- _XM = 4*EXTRA+MATCH, _XI = 4*EXTRA+INSERTION, _XD = 4*EXTRA+DELETION, _DUMMY = 4*EXTRA+EXTRA,
- /* Overall Size of transtion structure */
- INSERTION_TRANSITIONS_SIZE = 16
--} VectorPosition ;
-+};
- ////////////////////////////// FOR SSE4.1 to WORK //////////////////////////////////////////////
- // WARNING: MATCH and INSERTION should be next to each other (in this ordering)
- // and either in the upper part of xmm or the lower part.
=====================================
debian/patches/getopt_for_pgdump.patch deleted
=====================================
@@ -1,49 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 21 Mar 2017 22:14:51 +0100
-Description: pfdump was crashing if any option (-x) was given.
- To prevent SIGSEGV crashes getopt is introduced by this patch
-
---- a/src/C/utils/io.c
-+++ b/src/C/utils/io.c
-@@ -3,6 +3,7 @@
- #include <inttypes.h>
- #include <stdbool.h>
- #include <mm_malloc.h>
-+#include <getopt.h>
- #include <errno.h>
- #define _GNU_SOURCE
- #include <string.h>
-@@ -1025,11 +1026,29 @@ int main(int argc, char *argv[])
- {
- struct Profile prf;
-
-- if (argc < 2 ) {
-- fputs("Give at least a profile file name\n" , stderr);
-- return 1;
-+ /* getopt_long stores the option index here. */
-+ struct option long_options[] =
-+ {
-+ {"help", no_argument, 0, 'h'},
-+ };
-+ while (1) {
-+ int option_index = 0;
-+ const int c = getopt_long (argc, argv, "h", long_options, &option_index);
-+
-+ /* Detect the end of the options. */
-+ if (c == -1) break;
-+ switch (c) {
-+ case 'h':
-+ default:
-+ fprintf(stderr, "Usage: %s <profile_file>\n", argv[0]);
-+ return 1;
-+ }
-+ }
-+ if (optind == argc) {
-+ fputs("Give at least a profile file name\n", stderr);
-+ return 1;
- }
-- if (ReadProfile(argv[1], &prf) != 0) {
-+ if (ReadProfile(argv[optind], &prf) != 0) {
- FreeProfile(&prf);
- return 1;
- }
=====================================
debian/patches/hardening.patch deleted
=====================================
@@ -1,30 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 21 Mar 2017 22:14:51 +0100
-Description: Propagate hardening options
-
---- a/Makefile
-+++ b/Makefile
-@@ -14,12 +14,13 @@ CC = gcc
- #FFLAGS= -O2 -finit-local-zero -fno-automatic io.o
- FFLAGS= -O2 -fno-automatic io.o
- #PRFLAG= -g -pg
-+PRFLAG=$(LDFLAGS)
-
-
- # For MAC OX X SnowLeopard we need to specify the 32bit architecture for gcc
- #CFLAGS= -m32
- # otherwise keep it empty
--CFLAGS=
-+#CFLAGS=
-
-
- #----------------------------------------------------------------------#
-@@ -99,7 +100,7 @@ pfw : pfw.f sterr.f remsf.f lblnk.f re
- pfscale : pfscale.f sterr.f recmd.f ardim.f psdat.f gsdat.f djdat.f nodat.f codat.f \
- pfdat.f dfdat.f sterr.f cvini.f reprf.f wrprf.f recmd.f NtoR.f lblnk.f ardim.f \
- Xblnk.f
-- $(F77) $(FFLAGS) pfscale.f -o pfscale
-+ $(F77) $(FFLAGS) pfscale.f -o pfscale $(LDFLAGS)
-
- 2ft : 2ft.f lblnk.f ardim.f sterr.f
- $(F77) $(FFLAGS) 2ft.f -o 2ft $(PRFLAG)
=====================================
debian/patches/series
=====================================
@@ -1,9 +1 @@
-#fix_install.patch
-#hardening.patch
-#spelling.patch
-fix_path_in_test_script.patch
-fix_test_output.patch
-build_gtop.patch
-getopt_for_pgdump.patch
spelling.patch
-gcc10.patch
=====================================
debian/patches/spelling.patch
=====================================
@@ -2,53 +2,9 @@ Description: Fix spelling
Author: Andreas Tille <tille at debian.org>
Last-Update: 2017-03-31
---- a/src/C/include/system.h
-+++ b/src/C/include/system.h
-@@ -835,7 +835,7 @@ printSystemInfo(const SystemInfo * const
- const size_t Length = strlen(Template);
- const char * LastCharacter = &Buffer[Length - 2];
-
-- fputs("| System informations |\n"
-+ fputs("| System information |\n"
- "%----------------------------------------------------------------------------%\n", stderr);
-
- #define WRITE(LeftSpace, Title, Value) {\
-@@ -947,4 +947,4 @@ int main (int argc, char * argv[])
- }
-
- #endif
--#endif
-\ No newline at end of file
-+#endif
---- a/src/C/prg/pfsearch.c
-+++ b/src/C/prg/pfsearch.c
-@@ -209,12 +209,12 @@ static void __attribute__((noreturn)) Us
- " --output-method [-o] : printing output method\n"
- " == 0 replicates the pfseach output without\n"
- " options (DEFAULT)\n"
-- " == 1 simple ouput\n"
-+ " == 1 simple output\n"
- " == 2 replicates pfsearch -lxz output\n"
- " == 3 replicates pfscan -lxz output\n"
- " == 4 tsv output (single line tab delimited)\n"
- " --output-length [-W] : maximum number of column for sequence\n"
-- " ouput printing\n"
-+ " output printing\n"
- " Other\n"
- " --verbose [-v] : verbose on stderr\n"
- " --help [-h] : output command help\n",
-@@ -388,7 +388,7 @@ int main (int argc, char *argv[])
- } else if (method == 4) {
- PrintFunction = &PrintTSV;
- } else {
-- fputs("Unrecognized ouput method.\n", stderr);
-+ fputs("Unrecognized output method.\n", stderr);
- exit(1);
- }
- }
--- a/src/C/utils/ReadSequence.c
+++ b/src/C/utils/ReadSequence.c
-@@ -35,13 +35,13 @@ int AnalyzeFASTAStructure(char * const F
+@@ -42,13 +42,13 @@ int AnalyzeFASTAStructure(const char * c
const int FileDescriptor = open(FileName, O_RDONLY);
if ( FileDescriptor == -1) {
@@ -64,36 +20,3 @@ Last-Update: 2017-03-31
perror("The error reads ");
return 1;
}
---- a/man/pfmake.1
-+++ b/man/pfmake.1
-@@ -148,7 +148,7 @@ Default: M=0.333.
- .TP
- S=#
- Score matrix multiplier. On input, the numbers of the score matrix
--are multipled by this factor. Default: S=0.1.
-+are multiplied by this factor. Default: S=0.1.
- .TP
- T=#
- Gap region threshold. This is the minimal fraction of gap characters
---- a/man/pfscan.1
-+++ b/man/pfscan.1
-@@ -11,7 +11,7 @@ pfscan \- scan a protein or DNA sequence
- compares a protein or nucleic acid sequence against a profile library.
- The result is an unsorted list of profile-sequence matches written to
- the standard output.
--A variety of output formats containing different informations can be specified
-+A variety of output formats containing different information can be specified
- via the options
- .I -a, -l, -L, -r, -u, -s, -x, -y
- and
---- a/man/pfsearchV2.1
-+++ b/man/pfsearchV2.1
-@@ -10,7 +10,7 @@ matching a profile
- .B pfsearchV2
- compares a query profile against a DNA or protein sequence library.
- The result is an unsorted list of profile-sequence matches written to the standard output.
--A variety of output formats containing different informations can be specified
-+A variety of output formats containing different information can be specified
- via the options
- .I -a, -l, -L, -r, -u, -s,
- .I -x, -y, -z,
View it on GitLab: https://salsa.debian.org/med-team/pftools/-/compare/e6b456a8c403e2098c077fbd92f883dd743cd710...12d78f5fefc142603742a074b7defff3a5637f1d
--
View it on GitLab: https://salsa.debian.org/med-team/pftools/-/compare/e6b456a8c403e2098c077fbd92f883dd743cd710...12d78f5fefc142603742a074b7defff3a5637f1d
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