diff --git a/benchmarks/cmsearch-rmark/infernal2glbf.pl b/benchmarks/cmsearch-rmark/infernal2glbf.pl index 676de623..ef10fdd6 100644 --- a/benchmarks/cmsearch-rmark/infernal2glbf.pl +++ b/benchmarks/cmsearch-rmark/infernal2glbf.pl @@ -40,96 +40,113 @@ &infernal::ParseINFERNAL($output); # First determine if infernal was run with or without E-values -if($infernal::nhit > 0) +$at_least_one_hit = 0; +for($c = 0; $c < $infernal::ncm; $c++) { - if (exists($infernal::hitevalue[0])) + if($infernal::nhit[$c] > 0) { - $has_evalues = 1; - } - else - { - $has_evalues = 0; + $at_least_one_hit = 1; + if (exists($infernal::hitevalue[$c][0])) + { + $has_evalues = 1; + } + else + { + $has_evalues = 0; + } + last; } } - -if(($infernal::nhit > 0) && ($use_evalues && (!$has_evalues))) +if(!($at_least_one_hit)) +{ + die("No hits found. Exiting.\n"); +} +if($use_evalues && (!$has_evalues)) { - die("ERROR in infernal2glbf.pl, trying to use E-values but none reported.\n"); + die("ERROR, trying to use E-values but none reported.\n"); } # if we're not sorting the scores, print them out in the order cmsearch reported them if(!($sort_scores)) { - for ($i = 0; $i < $infernal::nhit; $i++) + for ($c = 0; $c < $infernal::ncm; $c++) { - if ((($use_bitscores) && $infernal::hitbitscore[$i] > $b_cutoff) || - (($use_evalues) && $infernal::hitevalue[$i] < $e_cutoff)) + for ($i = 0; $i < $infernal::nhit[$c]; $i++) { - #printf("%-24s %-6f\n", $infernal::targname[$i], $infernal::seqbitscore{$infernal::targname[$i]}); - if($infernal::hitsqfrom[$i] > $infernal::hitsqto[$i]) + if ((($use_bitscores) && $infernal::hitbitscore[$c][$i] > $b_cutoff) || + (($use_evalues) && $infernal::hitevalue[$c][$i] < $e_cutoff)) { - #hit to reverse strand of query - $orient = 1; - } - else - { - $orient = 0; + #printf("%-24s %-6f\n", $infernal::targname[$i], $infernal::seqbitscore{$infernal::targname[$i]}); + if($infernal::hitsqfrom[$c][$i] > $infernal::hitsqto[$c][$i]) + { + #hit to reverse strand of query + $orient = 1; + } + else + { + $orient = 0; + } + if($use_evalues) + { + printf("%-24s %-6f %d %d %d\n", $infernal::targname_byhit[$c][$i], $infernal::hitevalue[$c][$i], $infernal::hitsqfrom[$c][$i], $infernal::hitsqto[$c][$i], $orient); + } + else + { + printf("%-24s %-6f %d %d %d\n", $infernal::targname_byhit[$c][$i], $infernal::hitbitscore[$c][$i], $infernal::hitsqfrom[$c][$i], $infernal::hitsqto[$c][$i], $orient); + } } + } + } +} +else # sort scores +{ + for ($c = 0; $c < $infernal::ncm; $c++) + { + for ($i = 0; $i < $infernal::nhit; $i++) + { + $key = "$c:$i"; if($use_evalues) { - printf("%-24s %-6f %d %d %d\n", $infernal::targname_byhit[$i], $infernal::hitevalue[$i], $infernal::hitsqfrom[$i], $infernal::hitsqto[$i], $orient); + $sc_H{$key} = $infernal::hitevalue[$c][$i]; } else { - printf("%-24s %-6f %d %d %d\n", $infernal::targname_byhit[$i], $infernal::hitbitscore[$i], $infernal::hitsqfrom[$i], $infernal::hitsqto[$i], $orient); + $sc_H{$key} = $infernal::hitbitscore[$c][$i]; } } - } -} -else # sort scores -{ - for ($i = 0; $i < $infernal::nhit; $i++) - { if($use_evalues) { - $sc_H{$i} = $infernal::hitevalue[$i]; + @sorted_i_A = sort { $sc_H{$a} <=> $sc_H{$b} } (keys (%sc_H)); } else { - $sc_H{$i} = $infernal::hitbitscore[$i]; + @sorted_i_A = sort { $sc_H{$b} <=> $sc_H{$a} } (keys (%sc_H)); } - } - if($use_evalues) - { - @sorted_i_A = sort { $sc_H{$a} <=> $sc_H{$b} } (keys (%sc_H)); - } - else - { - @sorted_i_A = sort { $sc_H{$b} <=> $sc_H{$a} } (keys (%sc_H)); - } - for ($j = 0; $j < scalar(@sorted_i_A); $j++) - { - $i = $sorted_i_A[$j]; - if ((($use_bitscores) && $infernal::hitbitscore[$i] > $b_cutoff) || - (($use_evalues) && $infernal::hitevalue[$i] < $e_cutoff)) + for ($j = 0; $j < scalar(@sorted_i_A); $j++) { - #printf("%-24s %-6f\n", $infernal::targname[$i], $infernal::seqbitscore{$infernal::targname[$i]}); - if($infernal::hitsqfrom[$i] > $infernal::hitsqto[$i]) - { - #hit to reverse strand of query - $orient = 1; - } - else - { - $orient = 0; - } - if($use_evalues) - { - printf("%-24s %-6f %d %d %d\n", $infernal::targname_byhit[$i], $infernal::hitevalue[$i], $infernal::hitsqfrom[$i], $infernal::hitsqto[$i], $orient); - } - else + $key = $sorted_i_A[$j]; + ($c, $i) = split(":", $key); + if ((($use_bitscores) && $infernal::hitbitscore[$c][$i] > $b_cutoff) || + (($use_evalues) && $infernal::hitevalue[$c][$i] < $e_cutoff)) { - printf("%-24s %-6f %d %d %d\n", $infernal::targname_byhit[$i], $infernal::hitbitscore[$i], $infernal::hitsqfrom[$i], $infernal::hitsqto[$i], $orient); + #printf("%-24s %-6f\n", $infernal::targname[$c][$i], $infernal::seqbitscore{$infernal::targname[$c][$i]}); + if($infernal::hitsqfrom[$c][$i] > $infernal::hitsqto[$c][$i]) + { + #hit to reverse strand of query + $orient = 1; + } + else + { + $orient = 0; + } + if($use_evalues) + { + printf("%-24s %-6f %d %d %d\n", $infernal::targname_byhit[$c][$i], $infernal::hitevalue[$c][$i], $infernal::hitsqfrom[$c][$i], $infernal::hitsqto[$c][$i], $orient); + } + else + { + printf("%-24s %-6f %d %d %d\n", $infernal::targname_byhit[$c][$i], $infernal::hitbitscore[$c][$i], $infernal::hitsqfrom[$c][$i], $infernal::hitsqto[$c][$i], $orient); + } } } } diff --git a/configure.ac b/configure.ac index a4f9723d..bae0f360 100644 --- a/configure.ac +++ b/configure.ac @@ -58,12 +58,43 @@ AC_DEFINE_UNQUOTED(PACKAGE_LICENSE, "$PACKAGE_LICENSE") if ((! test -d binaries) && test -d src); then AC_MSG_NOTICE([This is a full source distribution - using full config]) +cwd=`pwd` +AC_SUBST(TOPDIR,$cwd) +# EPN, Thu Apr 5 07:58:07 2007 +# First, check for --with-mpi= to build MPI cmsearch and cmalign progs. +# if enabled, set compiler as , if no "=" provided, set compiler as mpicc +# currently PROGS are not affected, though eventually we may want +# to create 'mpicmsearch' and 'mpicmalign' +usempi=0 +AC_ARG_WITH(mpi, +[ --with-mpi enable MPI for search and alignment], +[case $with_mpi in + yes) AC_MSG_NOTICE([configured cmalign and cmsearch for MPI]) + mpi="mpicc" + usempi=1 + AC_DEFINE(USE_MPI) + ;; + no) mpi="" + ;; + *) mpi=$with_mpi + usempi=1 + ;; + esac]) +AC_SUBST(USEMPI,$usempi) + +# if $mpi == "", use default C compiler, set CFLAGS by default +if test -z "$mpi"; then + AC_PROG_CC +# if $mpi != "", use compiler $mpi, manually set CFLAGS +else + AC_PROG_CC($mpi) + CFLAGS="-g -O2" +fi # Checks for programs. -# Sets output variables CC, CFLAGS, and RANLIB. +# Sets output variables RANLIB. # AR might be hidden away on Solaris; provide some hints in the PATH. # -AC_PROG_CC AC_PROG_CXX AC_PROG_RANLIB AC_PATH_PROG([AR], [ar], [:], [$PATH:/usr/ccs/bin:/usr/xpg4/bin]) @@ -250,20 +281,6 @@ AC_ARG_WITH(rigfilters, esac]) # -# --with-mpi MPI support for cmalign and cmsearch -AC_ARG_WITH(mpi, -[ --with-mpi enable MPI for search and alignment], -[case $with_mpi in - yes) AC_MSG_NOTICE([configured cmalign and cmsearch for MPI]) - AC_PROG_CC(mpicc) - ;; - no) ;; - *) echo "Ignoring unknown argument to --with-mpi: $with_mpi" - ;; - esac]) - - -# # end of optionally configured features ################################################################ diff --git a/matrices/RIBOSUM100-25.mat b/matrices/RIBOSUM100-25.mat index a0274213..d119c711 100644 --- a/matrices/RIBOSUM100-25.mat +++ b/matrices/RIBOSUM100-25.mat @@ -1,30 +1,33 @@ RIBOSUM100-25 - A C G U -A 1.97 -C -1.34 1.00 -G -0.92 -1.70 0.85 -U -1.01 -0.61 -1.11 1.38 + A C G U + 0.258308 0.219504 0.297310 0.224878 + + A C G U +A 1.971671 +C -1.343217 1.001064 +G -0.921788 -1.699044 0.854147 +U -1.005464 -0.613591 -1.111982 1.382532 H: 0.5617 E: -0.0957 - AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU -AA -2.60 -AC -8.47 -1.85 -AG -8.82 -9.59 -1.33 -AU -5.08 -1.65 -6.07 4.25 -CA -10.06 -10.55 -10.65 -5.77 -6.21 -CC -13.44 -8.85 -15.14 -2.37 -11.69 -3.46 -CG -3.87 -5.44 -2.57 2.03 -3.24 -5.07 5.22 -CU -12.11 -10.68 -9.36 -4.18 -8.33 -6.86 -4.39 -2.56 -GA -6.63 -7.17 -9.39 -3.79 -7.76 -12.90 -6.03 -7.14 -1.62 -GC -5.22 -2.70 -6.29 2.88 -5.40 -3.75 2.80 -2.20 -2.57 5.49 -GG -9.69 -10.38 -4.22 -4.93 -11.48 -12.06 -4.71 -9.14 -9.91 -4.77 -2.31 -GU -6.50 -4.92 -7.13 0.75 -6.20 -7.10 0.25 -4.41 -6.19 1.42 -5.53 3.32 -UA -2.49 -5.59 -2.82 1.88 -2.91 -6.47 2.93 -4.33 -4.87 1.89 -6.32 0.06 4.72 -UC -12.26 -8.88 -8.01 -4.54 -8.03 -8.95 -4.35 -4.67 -6.98 -4.16 -10.57 -4.61 -3.53 -4.14 -UG -3.55 -7.17 -5.83 -0.39 -6.21 -8.30 1.19 -6.47 -7.67 0.33 -4.34 -1.26 1.04 -4.20 3.19 -UU -8.87 -8.39 -9.76 -2.46 -8.85 -6.64 -3.01 -5.43 -10.15 -3.03 -5.02 -2.58 -1.58 -5.90 -3.64 -0.72 + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -2.604645 +AC -8.470563 -1.853570 +AG -8.822189 -9.594620 -1.327118 +AU -5.075545 -1.654552 -6.067763 4.252767 +CA -10.056671 -10.552723 -10.646974 -5.774248 -6.205123 +CC -13.442368 -8.854252 -15.136720 -2.374419 -11.693921 -3.456602 +CG -3.871417 -5.438003 -2.572185 2.030624 -3.240493 -5.067212 5.222069 +CU -12.105264 -10.682421 -9.357424 -4.179064 -8.325364 -6.862516 -4.386954 -2.559931 +GA -6.625421 -7.170250 -9.390651 -3.792122 -7.764439 -12.895778 -6.029141 -7.141504 -1.623429 +GC -5.219950 -2.695725 -6.290820 2.876080 -5.395295 -3.754027 2.801056 -2.204690 -2.569771 5.489061 +GG -9.691680 -10.383497 -4.223349 -4.930131 -11.479506 -12.063889 -4.707853 -9.136017 -9.906732 -4.774241 -2.305253 +GU -6.496390 -4.924699 -7.125769 0.745252 -6.201344 -7.102632 0.251253 -4.410597 -6.189448 1.424712 -5.534224 3.320225 +UA -2.485010 -5.590836 -2.822798 1.878540 -2.907659 -6.465319 2.926758 -4.327115 -4.869013 1.889057 -6.320650 0.064069 4.723641 +UC -12.263343 -8.877730 -8.011171 -4.540962 -8.030163 -8.946997 -4.345131 -4.669281 -6.980707 -4.161804 -10.568347 -4.611892 -3.529918 -4.138184 +UG -3.546296 -7.166265 -5.829573 -0.392702 -6.206307 -8.303615 1.189462 -6.470759 -7.672941 0.327564 -4.341610 -1.261343 1.043982 -4.199517 3.189382 +UU -8.867475 -8.385429 -9.762040 -2.456123 -8.850458 -6.641057 -3.008435 -5.429174 -10.145796 -3.034762 -5.019912 -2.575165 -1.581614 -5.904415 -3.644739 -0.715714 H: 3.4639 E: -2.6040 diff --git a/matrices/RIBOSUM100-30.mat b/matrices/RIBOSUM100-30.mat index e69ffa1f..4fa89f42 100644 --- a/matrices/RIBOSUM100-30.mat +++ b/matrices/RIBOSUM100-30.mat @@ -1,30 +1,33 @@ RIBOSUM100-30 - A C G U -A 1.97 -C -1.34 1.00 -G -0.92 -1.70 0.85 -U -1.01 -0.61 -1.11 1.38 + A C G U + 0.258284 0.219532 0.297342 0.224842 + + A C G U +A 1.972360 +C -1.344047 1.001351 +G -0.922482 -1.699386 0.854425 +U -1.006582 -0.614272 -1.113000 1.383155 H: 0.5622 E: -0.0959 - AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU -AA -2.60 -AC -8.47 -1.85 -AG -8.82 -9.59 -1.33 -AU -5.07 -1.65 -6.07 4.25 -CA -10.06 -10.55 -10.65 -5.78 -6.20 -CC -13.44 -8.85 -15.14 -2.37 -11.69 -3.46 -CG -3.87 -5.44 -2.57 2.03 -3.24 -5.07 5.22 -CU -12.10 -10.68 -9.36 -4.18 -8.33 -6.86 -4.39 -2.56 -GA -6.62 -7.17 -9.39 -3.79 -7.76 -12.90 -6.03 -7.14 -1.62 -GC -5.22 -2.70 -6.29 2.88 -5.40 -3.75 2.80 -2.20 -2.57 5.49 -GG -9.69 -10.38 -4.22 -4.93 -11.48 -12.06 -4.71 -9.14 -9.91 -4.77 -2.31 -GU -6.50 -4.92 -7.13 0.75 -6.20 -7.10 0.25 -4.41 -6.19 1.42 -5.53 3.32 -UA -2.49 -5.60 -2.82 1.88 -2.91 -6.47 2.93 -4.33 -4.87 1.89 -6.32 0.06 4.72 -UC -12.26 -8.88 -8.01 -4.54 -8.03 -8.95 -4.35 -4.67 -6.98 -4.16 -10.57 -4.61 -3.53 -4.14 -UG -3.55 -7.17 -5.83 -0.39 -6.21 -8.30 1.19 -6.47 -7.67 0.33 -4.34 -1.26 1.04 -4.20 3.19 -UU -8.87 -8.38 -9.76 -2.46 -8.85 -6.64 -3.01 -5.43 -10.15 -3.03 -5.02 -2.57 -1.58 -5.90 -3.64 -0.71 + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -2.603894 +AC -8.470122 -1.853437 +AG -8.821726 -9.594466 -1.326941 +AU -5.074954 -1.654023 -6.067754 4.253602 +CA -10.056229 -10.552590 -10.646820 -5.775143 -6.204990 +CC -13.442235 -8.854428 -15.136875 -2.374198 -11.694097 -3.457087 +CG -3.871265 -5.438174 -2.572318 2.030071 -3.240654 -5.067683 5.221619 +CU -12.104720 -10.682187 -9.357168 -4.178441 -8.325129 -6.862591 -4.387006 -2.559595 +GA -6.624957 -7.170095 -9.390474 -3.791566 -7.764284 -12.895932 -6.029273 -7.141247 -1.623253 +GC -5.220724 -2.695882 -6.291214 2.875845 -5.395536 -3.754496 2.800486 -2.204757 -2.569904 5.488602 +GG -9.691504 -10.383629 -4.223460 -4.929956 -11.479638 -12.064330 -4.708279 -9.136048 -9.906843 -4.774661 -2.305651 +GU -6.495910 -4.924468 -7.125567 0.745141 -6.201176 -7.102715 0.250943 -4.410244 -6.189170 1.424606 -5.534233 3.320576 +UA -2.485164 -5.596511 -2.824172 1.878742 -2.907259 -6.465591 2.926251 -4.326510 -4.868630 1.888583 -6.320774 0.063396 4.724416 +UC -12.262800 -8.877496 -8.010915 -4.540369 -8.029929 -8.947071 -4.345193 -4.668945 -6.980451 -4.161876 -10.568378 -4.611534 -3.529380 -4.137848 +UG -3.545733 -7.166062 -5.829295 -0.393684 -6.206051 -8.303667 1.189222 -6.470420 -7.672718 0.327374 -4.341619 -1.261042 1.044086 -4.199159 3.189760 +UU -8.866521 -8.384784 -9.761374 -2.455107 -8.849813 -6.640721 -3.008077 -5.428428 -10.145129 -3.034405 -5.019533 -2.574439 -1.580581 -5.903669 -3.643971 -0.714557 H: 3.4640 E: -2.6041 diff --git a/matrices/RIBOSUM100-35.mat b/matrices/RIBOSUM100-35.mat index 96ae2e28..203161c2 100644 --- a/matrices/RIBOSUM100-35.mat +++ b/matrices/RIBOSUM100-35.mat @@ -1,30 +1,33 @@ RIBOSUM100-35 - A C G U -A 1.97 -C -1.35 1.00 -G -0.92 -1.70 0.85 -U -1.01 -0.62 -1.11 1.38 + A C G U + 0.258251 0.219570 0.297390 0.224789 + + A C G U +A 1.973243 +C -1.345056 1.001678 +G -0.923217 -1.699819 0.854726 +U -1.008059 -0.615004 -1.114157 1.383881 H: 0.5628 E: -0.0961 - AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU -AA -2.60 -AC -8.47 -1.85 -AG -8.82 -9.59 -1.33 -AU -5.07 -1.65 -6.07 4.25 -CA -10.06 -10.55 -10.65 -5.78 -6.20 -CC -13.45 -8.85 -15.14 -2.37 -11.69 -3.46 -CG -3.87 -5.44 -2.57 2.03 -3.24 -5.07 5.22 -CU -12.10 -10.68 -9.36 -4.18 -8.32 -6.86 -4.39 -2.56 -GA -6.62 -7.17 -9.39 -3.79 -7.76 -12.90 -6.03 -7.14 -1.62 -GC -5.22 -2.70 -6.29 2.88 -5.40 -3.76 2.80 -2.20 -2.57 5.49 -GG -9.69 -10.38 -4.22 -4.93 -11.48 -12.06 -4.71 -9.14 -9.91 -4.78 -2.31 -GU -6.50 -4.92 -7.13 0.75 -6.20 -7.10 0.25 -4.41 -6.19 1.42 -5.53 3.32 -UA -2.49 -5.60 -2.83 1.88 -2.91 -6.47 2.93 -4.33 -4.87 1.89 -6.32 0.06 4.73 -UC -12.26 -8.88 -8.01 -4.54 -8.03 -8.95 -4.35 -4.67 -6.98 -4.16 -10.57 -4.61 -3.53 -4.14 -UG -3.54 -7.17 -5.83 -0.39 -6.21 -8.30 1.19 -6.47 -7.67 0.33 -4.34 -1.26 1.04 -4.20 3.19 -UU -8.87 -8.38 -9.76 -2.45 -8.85 -6.64 -3.01 -5.43 -10.14 -3.03 -5.02 -2.57 -1.58 -5.90 -3.64 -0.71 + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -2.602836 +AC -8.469565 -1.853251 +AG -8.821086 -9.594263 -1.326721 +AU -5.074235 -1.653292 -6.067736 4.254784 +CA -10.055606 -10.552404 -10.646617 -5.777001 -6.204804 +CC -13.451740 -8.854678 -15.137108 -2.373916 -11.694347 -3.457774 +CG -3.871153 -5.438665 -2.572538 2.029397 -3.240895 -5.068367 5.220945 +CU -12.103943 -10.681846 -9.356810 -4.177615 -8.324788 -6.862686 -4.387101 -2.559100 +GA -6.624318 -7.169892 -9.390254 -3.790805 -7.764081 -12.896165 -6.029490 -7.140890 -1.623033 +GC -5.224986 -2.696159 -6.291856 2.875561 -5.397047 -3.755178 2.799648 -2.204872 -2.570120 5.487917 +GG -9.691479 -10.383846 -4.223659 -4.929646 -11.479854 -12.064983 -4.708946 -9.136109 -9.907042 -4.775327 -2.306269 +GU -6.496019 -4.924115 -7.125249 0.745190 -6.201035 -7.102942 0.250418 -4.409740 -6.188825 1.424391 -5.534278 3.321054 +UA -2.485541 -5.603296 -2.825868 1.878789 -2.906682 -6.466914 2.925681 -4.325743 -4.867918 1.887915 -6.320834 0.062652 4.725481 +UC -12.262023 -8.877155 -8.010557 -4.539510 -8.029588 -8.947167 -4.345284 -4.668449 -6.980093 -4.161989 -10.568440 -4.611037 -3.528521 -4.137353 +UG -3.544942 -7.165704 -5.828944 -0.394783 -6.205693 -8.303746 1.188952 -6.469926 -7.672468 0.327214 -4.341664 -1.260632 1.044421 -4.198705 3.190287 +UU -8.865153 -8.383852 -9.760424 -2.453624 -8.848881 -6.640225 -3.007572 -5.427341 -10.144180 -3.033892 -5.019003 -2.573382 -1.579161 -5.902582 -3.642957 -0.712879 H: 3.4641 E: -2.6042 diff --git a/matrices/RIBOSUM100-40.mat b/matrices/RIBOSUM100-40.mat index 47c316ed..ba45c137 100644 --- a/matrices/RIBOSUM100-40.mat +++ b/matrices/RIBOSUM100-40.mat @@ -1,30 +1,33 @@ RIBOSUM100-40 - 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A C G U -A 2.51 -C -5.56 1.70 -G -5.07 -5.91 1.39 -U -5.06 -3.99 -5.52 2.05 + A C G U + 0.256593 0.218634 0.293799 0.230975 + + A C G U +A 2.512232 +C -5.564475 1.699756 +G -5.066604 -5.911098 1.394526 +U -5.060932 -3.988181 -5.522276 2.045924 H: 1.8665 E: -1.4737 - AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU -AA -0.89 -AC -8.89 -0.26 -AG -8.50 -10.71 -0.33 -AU -6.76 -5.05 -7.64 5.29 -CA -999.00 -11.41 -13.54 -9.14 -1.46 -CC -999.00 -8.94 -999.00 -10.52 -9.83 -1.20 -CG -12.65 -11.94 -6.91 -3.45 -4.89 -6.23 5.88 -CU -13.62 -999.00 -999.00 -6.53 -10.23 -7.68 -6.17 -0.66 -GA -8.24 -999.00 -9.67 -13.62 -10.42 -14.51 -9.46 -13.59 -0.54 -GC -9.24 -5.21 -10.30 -1.44 -10.45 -5.72 -3.12 -8.28 -6.86 6.00 -GG -11.24 -11.17 -9.29 -9.06 -10.05 -12.80 -6.49 -15.37 -9.24 -6.07 -1.49 -GU -11.28 -9.05 -11.29 -1.94 -13.10 -10.27 -4.78 -7.09 -7.43 -1.55 -7.79 3.97 -UA -7.33 -10.49 -9.51 -3.31 -4.95 -8.83 -1.40 -9.53 -8.45 -3.87 -16.97 -5.34 5.51 -UC -999.00 -7.79 -11.88 -8.42 -11.46 -9.24 -10.27 -9.28 -999.00 -6.05 -999.00 -10.93 -6.59 -1.07 -UG -9.83 -11.97 -8.80 -5.48 -8.66 -12.47 -1.26 -9.81 -10.61 -4.77 -8.00 -6.35 -1.97 -7.24 4.00 -UU -999.00 -12.30 -12.12 -5.59 -11.75 -999.00 -8.28 -7.83 -999.00 -8.09 -16.09 -7.08 -5.67 -6.05 -6.96 0.58 + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -0.889170 +AC -8.892653 -0.257793 +AG -8.501385 -10.711335 -0.330886 +AU -6.763221 -5.046739 -7.641741 5.288135 +CA -999.000000 -11.412078 -13.540924 -9.144031 -1.462121 +CC -999.000000 -8.939330 -999.000000 -10.523369 -9.827476 -1.201276 +CG -12.653784 -11.937514 -6.910055 -3.449706 -4.892668 -6.233577 5.880812 +CU -13.620582 -999.000000 -999.000000 -6.529142 -10.226387 -7.678200 -6.174925 -0.658202 +GA -8.239196 -999.000000 -9.669759 -13.620631 -10.423354 -14.514318 -9.455281 -13.593539 -0.540741 +GC -9.240083 -5.206258 -10.302109 -1.436769 -10.445411 -5.716880 -3.119711 -8.283714 -6.859892 6.003788 +GG -11.237484 -11.166786 -9.294972 -9.061736 -10.053919 -12.802776 -6.490472 -15.373851 -9.244899 -6.068602 -1.494985 +GU -11.276444 -9.046222 -11.291932 -1.940563 -13.101686 -10.269675 -4.777164 -7.087585 -7.428595 -1.548385 -7.790152 3.967277 +UA -7.330413 -10.491299 -9.512132 -3.305226 -4.953849 -8.831197 -1.402468 -9.528791 -8.446450 -3.865559 -16.970943 -5.339284 5.510212 +UC -999.000000 -7.791484 -11.879293 -8.421178 -11.461968 -9.238466 -10.272698 -9.282161 -999.000000 -6.049876 -999.000000 -10.928268 -6.589518 -1.068690 +UG -9.834767 -11.974629 -8.801008 -5.476239 -8.663530 -12.470495 -1.261145 -9.814605 -10.612079 -4.772666 -8.002710 -6.352017 -1.971203 -7.243733 4.000777 +UU -999.000000 -12.295433 -12.122563 -5.589483 -11.754593 -999.000000 -8.277627 -7.830848 -999.000000 -8.089051 -16.090502 -7.084722 -5.665304 -6.050974 -6.955989 0.577555 H: 5.1321 E: -46.4133 diff --git a/matrices/RIBOSUM95.mat b/matrices/RIBOSUM95.mat index 5b8a61f8..94fa8952 100644 --- a/matrices/RIBOSUM95.mat +++ b/matrices/RIBOSUM95.mat @@ -1,30 +1,33 @@ RIBOSUM95 - A C G U -A 1.96 -C -1.33 0.99 -G -0.91 -1.69 0.85 -U -0.97 -0.62 -1.10 1.37 + A C G U + 0.259590 0.218935 0.296865 0.224609 + + A C G U +A 1.957050 +C -1.327709 0.993553 +G -0.912937 -1.688811 0.851274 +U -0.967605 -0.616901 -1.100374 1.371214 H: 0.5525 E: -0.0920 - AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU -AA -2.84 -AC -8.54 -2.06 -AG -9.17 -9.34 -1.33 -AU -4.96 -1.63 -5.89 4.22 -CA -9.97 -10.36 -10.35 -5.61 -6.19 -CC -13.47 -8.79 -14.75 -2.48 -11.36 -3.69 -CG -3.83 -5.35 -2.56 2.06 -3.14 -5.02 5.22 -CU -11.94 -10.61 -9.50 -4.13 -8.34 -6.95 -4.33 -2.68 -GA -6.95 -7.67 -9.63 -3.86 -7.99 -12.70 -5.85 -7.60 -1.65 -GC -5.18 -2.70 -6.11 2.89 -5.34 -3.70 2.82 -2.20 -2.61 5.50 -GG -9.66 -10.14 -4.36 -4.81 -11.46 -11.71 -4.66 -9.31 -9.51 -4.64 -2.19 -GU -6.42 -4.68 -7.08 0.74 -6.09 -6.99 0.26 -4.45 -6.24 1.43 -5.52 3.31 -UA -2.49 -5.39 -2.84 1.90 -2.90 -6.31 2.96 -4.32 -4.74 1.94 -6.22 0.09 4.71 -UC -11.83 -8.91 -7.96 -4.30 -7.83 -8.56 -4.27 -4.58 -7.14 -4.06 -10.72 -4.57 -3.55 -3.99 -UG -3.65 -7.12 -5.78 -0.37 -6.10 -8.23 1.22 -6.41 -7.63 0.32 -4.28 -1.33 1.05 -4.24 3.18 -UU -8.89 -8.30 -9.54 -2.40 -8.87 -6.51 -3.04 -5.40 -9.79 -2.94 -5.03 -2.63 -1.59 -6.03 -3.68 -0.74 + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -2.836339 +AC -8.542075 -2.063198 +AG -9.171443 -9.338787 -1.333369 +AU -4.960081 -1.625652 -5.886511 4.218933 +CA -9.972106 -10.361264 -10.348975 -5.608631 -6.185568 +CC -13.465209 -8.794781 -14.748599 -2.479611 -11.362358 -3.691113 +CG -3.825019 -5.346431 -2.561524 2.055697 -3.135092 -5.019910 5.216376 +CU -11.940979 -10.614086 -9.498182 -4.127227 -8.338771 -6.954490 -4.329356 -2.679123 +GA -6.945877 -7.670429 -9.634198 -3.861365 -7.986957 -12.695520 -5.852565 -7.602646 -1.652584 +GC -5.177890 -2.701291 -6.114440 2.889332 -5.339947 -3.700908 2.819353 -2.196868 -2.605374 5.501172 +GG -9.663110 -10.140342 -4.364132 -4.805366 -11.459665 -11.708041 -4.659171 -9.314241 -9.514881 -4.641712 -2.189426 +GU -6.415936 -4.682229 -7.083086 0.741036 -6.093825 -6.988342 0.257087 -4.454374 -6.238974 1.425776 -5.524756 3.305492 +UA -2.489150 -5.392276 -2.840219 1.902883 -2.900026 -6.309171 2.956730 -4.320234 -4.742708 1.937261 -6.221954 0.092109 4.710644 +UC -11.834851 -8.906122 -7.963261 -4.301568 -7.830062 -8.563464 -4.273898 -4.579988 -7.141185 -4.064262 -10.719490 -4.570908 -3.547309 -3.991383 +UG -3.648875 -7.122901 -5.782214 -0.374404 -6.101134 -8.231842 1.222936 -6.405424 -7.631738 0.315068 -4.283793 -1.330153 1.045372 -4.243835 3.179516 +UU -8.891744 -8.300177 -9.535487 -2.399937 -8.874837 -6.512299 -3.041975 -5.400998 -9.790375 -2.944840 -5.028789 -2.627723 -1.586224 -6.027980 -3.684502 -0.741342 H: 3.4585 E: -2.5897 diff --git a/scripts/cmsearch_pp.pl b/scripts/cmsearch_pp.pl index e4086d27..bb84f08a 100644 --- a/scripts/cmsearch_pp.pl +++ b/scripts/cmsearch_pp.pl @@ -19,6 +19,8 @@ # -E : use E values [default], sets max E-val to keep as [df = 10] # -B : use bit scores, sets min score to keep as # -A : sort all hits across CMs [default: sort hits for each CM] +# -Q : print top hits per query +# -T : print top hits per target require "sre.pl"; use constant FASTA_LINE_LENGTH => 50; @@ -33,13 +35,17 @@ $sort_all_scores = 0; $do_extract = 0; $do_overlap = 0; +$do_top_query = 0; +$do_top_target = 0; -getopts('E:B:X:AR:'); +getopts('E:B:X:AR:Q:T:'); if (defined $opt_X) { $do_extract = 1; $db_file = $opt_X; } if (defined $opt_E) { $e_cutoff = $opt_E; } if (defined $opt_B) { $b_cutoff = $opt_B; $use_evalues = 0; $use_bitscores = 1; } if (defined $opt_A) { $sort_all_scores = 1; } if (defined $opt_R) { $remove_overlaps = 1; $overlap_fraction = $opt_R; } +if (defined $opt_Q) { $do_top_query = 1; $ntop_query = $opt_Q; } +if (defined $opt_T) { $do_top_target = 1; $ntop_target= $opt_T; } $usage = "Usage: perl cmsearch_pp.pl\n\t\n\t\n"; $options_usage = "\nOptions:\n\t"; @@ -47,7 +53,10 @@ $options_usage .= "-E : use E values [default], sets max E-val to keep as [df= 10]\n\t"; $options_usage .= "-B : use bit scores, sets min score to keep as \n\t"; $options_usage .= "-A : sort all hits across CMs [default: sort hits for each CM]\n\t"; -$options_usage .= "-R : remove overlapping hits of fraction (0: no overlap allowed)\n"; +$options_usage .= "-R : remove overlapping hits of fraction (0: no overlap allowed)\n\t"; +$options_usage .= "-Q : print top hits per query\n\t"; +$options_usage .= "-T : print top hits per target\n\n"; +# -T : print top hits per target if(scalar(@ARGV) == 2) { @@ -88,18 +97,24 @@ # First determine if infernal was run with or without E-values -if($infernal::nhit[0] > 0) +$at_least_one_hit = 0; +for($c = 0; $c < $infernal::ncm; $c++) { - if (exists($infernal::hitevalue[0][0])) + if($infernal::nhit[$c] > 0) { - $has_evalues = 1; - } - else - { - $has_evalues = 0; + $at_least_one_hit = 1; + if (exists($infernal::hitevalue[$c][0])) + { + $has_evalues = 1; + } + else + { + $has_evalues = 0; + } + last; } } -else +if(!($at_least_one_hit)) { die("No hits found in $cmsearch_output. Exiting.\n"); } @@ -174,7 +189,7 @@ ($c, $i) = split(":", $sorted_ci_A[$x]); if ((($use_bitscores) && $infernal::hitbitscore[$c][$i] > $b_cutoff) || - (($use_evalues) && $infernal::hitevalue[$c][$i] < $e_cutoff)) + (($use_evalues) && $infernal::hitevalue[$c][$i] < $e_cutoff)) { $gc_content = $infernal::hitgccontent[$c][$i]; #printf("%-24s %-6f\n", $infernal::targname[$i], $infernal::seqbitscore{$infernal::targname[$i]}); @@ -208,10 +223,14 @@ { $out_lines_A[$x] = sprintf("%-24s %-24s %7.2f %9d %9d %d (GC=%2d)\n", $cm, $targname, $sc, $start, $end, $orient, $gc_content); $cm .= "|"; + if($do_top_query) { $cm_for_out_lines_A[$x] = $cm; } + if($do_top_target){ $target_for_out_lines_A[$x] = $targname;} } else { $out_lines_A[$x] = sprintf("%-24s %7.2f %9d %9d %d (GC=%2d)\n", $targname, $sc, $start, $end, $orient, $gc_content); + if($do_top_query) { $cm_for_out_lines_A[$x] = "ONLYONE";} + if($do_top_target){ $target_for_out_lines_A[$x] = $targname; } } if($do_extract) { @@ -283,7 +302,22 @@ $prev_c = $c; if($print_lines_A[$x]) { - printf $out_lines_A[$x]; + $print_flag = 1; + if($do_top_query) + { + if(($printed_per_cm_H{$cm_for_out_lines_A[$x]}++) >= $ntop_query) + { + $print_flag = 0; + } + } + if($do_top_target) + { + if(($printed_per_target_H{$target_for_out_lines_A[$x]}++) >= $ntop_target) + { + $print_flag = 0; + } + } + if($print_flag) { printf $out_lines_A[$x]; } } } diff --git a/src/Makefile.in b/src/Makefile.in index 7123fe42..e3e45b7f 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -17,8 +17,9 @@ CFLAGS = @CFLAGS@ # DEFS contains stuff that autoconf decides on. # LIBS contains system libraries that the configure script decides we need. # -DEFS = @DEFS@ -DMATRIX_DIR=\"$(DATADIR)/infernal/matrices\" -#MDEFS = @MDEFS@ @DEFS@ -DMATRIX_DIR=\"$(DATADIR)/infernal/matrices\" +# EPN 04.05.07 -DMATRIX_DIR is set as 'matrices' subdir within directory +# that 'configure' was run in, probably not the best way to do this +DEFS = @DEFS@ -DMATRIX_DIR=\"@TOPDIR@/matrices\" -DUSE_MPI=@USEMPI@ LIBS = @LIBS@ ## archiving command, and ranlib command if you need one.