methods/RNAfold_with_constraints.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "TDPiVD2lK5sU"
      },
      "source": [
        "# Standard packages"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 1,
      "metadata": {
        "id": "RDB7DJGMoEYK"
      },
      "outputs": [],
      "source": [
        "import os\n",
        "import numpy as np\n",
        "import pandas as pd\n",
        "import time"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "I6bOkFD6K-8K"
      },
      "source": [
        "# Specific installs"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 2,
      "metadata": {
        "id": "xwSM-JQ5yKF4"
      },
      "outputs": [],
      "source": [
        "method_name = \"RNAfold\""
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 3,
      "metadata": {
        "id": "A0n2MN2-F8l9"
      },
      "outputs": [],
      "source": [
        "!wget -q https://www.tbi.univie.ac.at/RNA/download/sourcecode/1_6_x/ViennaRNA-1.6.1.tar.gz\n",
        "!tar xfz ViennaRNA-1.6.1.tar.gz"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 4,
      "metadata": {
        "id": "Pzn9H4-8zhP2",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "825602d9-fc71-4c32-db96-b920704206d7"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "/content/ViennaRNA-1.6.1\n",
            "checking for a BSD-compatible install... /usr/bin/install -c\n",
            "checking whether build environment is sane... yes\n",
            "checking for gawk... no\n",
            "checking for mawk... mawk\n",
            "checking whether make sets $(MAKE)... yes\n",
            "checking if malloc debugging is wanted... no\n",
            "checking build system type... x86_64-unknown-linux-gnu\n",
            "checking host system type... x86_64-unknown-linux-gnu\n",
            "checking for gcc... gcc\n",
            "checking for C compiler default output file name... a.out\n",
            "checking whether the C compiler works... yes\n",
            "checking whether we are cross compiling... no\n",
            "checking for suffix of executables... \n",
            "checking for suffix of object files... o\n",
            "checking whether we are using the GNU C compiler... yes\n",
            "checking whether gcc accepts -g... yes\n",
            "checking for gcc option to accept ANSI C... none needed\n",
            "checking for style of include used by make... GNU\n",
            "checking dependency style of gcc... gcc3\n",
            "checking whether gcc accepts -fpic... yes\n",
            "checking for a BSD-compatible install... /usr/bin/install -c\n",
            "checking for ranlib... ranlib\n",
            "checking for perl... /usr/bin/perl\n",
            "checking how to run the C preprocessor... gcc -E\n",
            "checking for egrep... grep -E\n",
            "checking for ANSI C header files... yes\n",
            "checking for sys/types.h... yes\n",
            "checking for sys/stat.h... yes\n",
            "checking for stdlib.h... yes\n",
            "checking for string.h... yes\n",
            "checking for memory.h... yes\n",
            "checking for strings.h... yes\n",
            "checking for inttypes.h... yes\n",
            "checking for stdint.h... yes\n",
            "checking for unistd.h... yes\n",
            "checking malloc.h usability... yes\n",
            "checking malloc.h presence... yes\n",
            "checking for malloc.h... yes\n",
            "checking for strings.h... (cached) yes\n",
            "checking for unistd.h... (cached) yes\n",
            "checking for an ANSI C-conforming const... yes\n",
            "checking for size_t... yes\n",
            "checking for inline... inline\n",
            "checking for strdup... yes\n",
            "checking for strstr... yes\n",
            "checking for strchr... yes\n",
            "checking for erand48... yes\n",
            "configure: creating ./config.status\n",
            "config.status: creating Makefile\n",
            "config.status: creating ViennaRNA.spec\n",
            "config.status: creating Utils/Makefile\n",
            "config.status: creating Progs/Makefile\n",
            "config.status: creating lib/Makefile\n",
            "config.status: creating man/Makefile\n",
            "config.status: creating Cluster/Makefile\n",
            "config.status: creating H/Makefile\n",
            "config.status: creating Perl/Makefile\n",
            "config.status: creating man/RNAheat.1\n",
            "config.status: creating man/RNAsubopt.1\n",
            "config.status: creating man/RNAdistance.1\n",
            "config.status: creating man/RNAinverse.1\n",
            "config.status: creating man/RNAeval.1\n",
            "config.status: creating man/RNAfold.1\n",
            "config.status: creating man/RNApdist.1\n",
            "config.status: creating man/RNAplot.1\n",
            "config.status: creating man/RNALfold.1\n",
            "config.status: creating man/RNAalifold.1\n",
            "config.status: creating man/RNAduplex.1\n",
            "config.status: creating man/RNAcofold.1\n",
            "config.status: creating man/RNAplfold.1\n",
            "config.status: creating config.h\n",
            "config.status: executing depfiles commands\n",
            "configure: configuring in RNAforester\n",
            "configure: running /bin/bash './configure' --prefix=/usr/local  --cache-file=/dev/null --srcdir=.\n",
            "checking for a BSD-compatible install... /usr/bin/install -c\n",
            "checking whether build environment is sane... yes\n",
            "checking for gawk... no\n",
            "checking for mawk... mawk\n",
            "checking whether make sets $(MAKE)... yes\n",
            "checking for g++... g++\n",
            "checking for C++ compiler default output file name... a.out\n",
            "checking whether the C++ compiler works... yes\n",
            "checking whether we are cross compiling... no\n",
            "checking for suffix of executables... \n",
            "checking for suffix of object files... o\n",
            "checking whether we are using the GNU C++ compiler... yes\n",
            "checking whether g++ accepts -g... yes\n",
            "checking for style of include used by make... GNU\n",
            "checking dependency style of g++... gcc3\n",
            "checking for gcc... gcc\n",
            "checking whether we are using the GNU C compiler... yes\n",
            "checking whether gcc accepts -g... yes\n",
            "checking for gcc option to accept ANSI C... none needed\n",
            "checking dependency style of gcc... gcc3\n",
            "using (to be built) libRNA.a in ../lib\n",
            "checking for gdImageLine in -lgd... no\n",
            "checking how to run the C++ preprocessor... g++ -E\n",
            "checking for egrep... grep -E\n",
            "checking for ANSI C header files... no\n",
            "checking for sys/types.h... yes\n",
            "checking for sys/stat.h... yes\n",
            "checking for stdlib.h... yes\n",
            "checking for string.h... yes\n",
            "checking for memory.h... yes\n",
            "checking for strings.h... yes\n",
            "checking for inttypes.h... yes\n",
            "checking for stdint.h... yes\n",
            "checking for unistd.h... yes\n",
            "checking g2.h usability... yes\n",
            "checking g2.h presence... yes\n",
            "checking for g2.h... yes\n",
            "checking for an ANSI C-conforming const... yes\n",
            "checking for inline... inline\n",
            "checking for size_t... yes\n",
            "configure: creating ./config.status\n",
            "config.status: creating Makefile\n",
            "config.status: creating src/Makefile\n",
            "config.status: creating man/Makefile\n",
            "config.status: creating config.h\n",
            "config.status: executing depfiles commands\n",
            "configure: configuring in g2-0.70\n",
            "configure: running /bin/bash './configure' --prefix=/usr/local  '--prefix=/usr/local' '--cache-file=/dev/null' '--srcdir=.' --cache-file=/dev/null --srcdir=.\n",
            "checking build system type... x86_64-unknown-linux-gnu\n",
            "checking host system type... x86_64-unknown-linux-gnu\n",
            "checking for gcc... gcc\n",
            "checking for C compiler default output file name... a.out\n",
            "checking whether the C compiler works... yes\n",
            "checking whether we are cross compiling... no\n",
            "checking for suffix of executables... \n",
            "checking for suffix of object files... o\n",
            "checking whether we are using the GNU C compiler... yes\n",
            "checking whether gcc accepts -g... yes\n",
            "checking for gcc option to accept ANSI C... none needed\n",
            "checking how to run the C preprocessor... gcc -E\n",
            "checking for g++... g++\n",
            "checking whether we are using the GNU C++ compiler... yes\n",
            "checking whether g++ accepts -g... yes\n",
            "checking for ranlib... ranlib\n",
            "checking for a BSD-compatible install... /usr/bin/install -c\n",
            "checking for find... find\n",
            "checking for makedepend... :\n",
            "checking for dlopen in -ldl... yes\n",
            "checking for X... libraries , headers \n",
            "checking for gethostbyname... yes\n",
            "checking for connect... yes\n",
            "checking for remove... yes\n",
            "checking for shmat... yes\n",
            "checking for IceConnectionNumber in -lICE... yes\n",
            "checking for main in -lm... yes\n",
            "checking for main in -lX11... yes\n",
            "checking for main in -lgd... no\n",
            "checking for egrep... grep -E\n",
            "checking for ANSI C header files... yes\n",
            "checking for sys/types.h... yes\n",
            "checking for sys/stat.h... yes\n",
            "checking for stdlib.h... yes\n",
            "checking for string.h... yes\n",
            "checking for memory.h... yes\n",
            "checking for strings.h... yes\n",
            "checking for inttypes.h... yes\n",
            "checking for stdint.h... yes\n",
            "checking for unistd.h... yes\n",
            "checking limits.h usability... yes\n",
            "checking limits.h presence... yes\n",
            "checking for limits.h... yes\n",
            "\n",
            "configure: creating ./config.status\n",
            "config.status: creating Makefile\n",
            "config.status: creating demo/Makefile\n",
            "config.status: creating g2_perl/Makefile.PL\n",
            "\n",
            "Supported devices:\n",
            "    PostScript\n",
            "    FIG\n",
            "    X11\n",
            "\n",
            "Unsupported devices:\n",
            "    Win32\n",
            "    GD\n",
            "\n",
            "Run 'make depend' to create dependencies.\n",
            "\n",
            "configure: configuring in Kinfold\n",
            "configure: running /bin/bash './configure' --prefix=/usr/local  --cache-file=/dev/null --srcdir=.\n",
            "checking for a BSD-compatible install... /usr/bin/install -c\n",
            "checking whether build environment is sane... yes\n",
            "checking for gawk... no\n",
            "checking for mawk... mawk\n",
            "checking whether make sets $(MAKE)... yes\n",
            "checking if malloc debugging is wanted... no\n",
            "checking for gcc... gcc\n",
            "checking for C compiler default output file name... a.out\n",
            "checking whether the C compiler works... yes\n",
            "checking whether we are cross compiling... no\n",
            "checking for suffix of executables... \n",
            "checking for suffix of object files... o\n",
            "checking whether we are using the GNU C compiler... yes\n",
            "checking whether gcc accepts -g... yes\n",
            "checking for gcc option to accept ANSI C... none needed\n",
            "checking for style of include used by make... GNU\n",
            "checking dependency style of gcc... gcc3\n",
            "checking whether make sets $(MAKE)... (cached) yes\n",
            "checking build system type... x86_64-unknown-linux-gnu\n",
            "checking host system type... x86_64-unknown-linux-gnu\n",
            "checking for ViennaRNA package...  headers in \"../H\" and library... \"../lib\"\n",
            "checking for exp in -lm... yes\n",
            "checking how to run the C preprocessor... gcc -E\n",
            "checking for egrep... grep -E\n",
            "checking for ANSI C header files... no\n",
            "checking for sys/types.h... yes\n",
            "checking for sys/stat.h... yes\n",
            "checking for stdlib.h... yes\n",
            "checking for string.h... yes\n",
            "checking for memory.h... yes\n",
            "checking for strings.h... yes\n",
            "checking for inttypes.h... yes\n",
            "checking for stdint.h... yes\n",
            "checking for unistd.h... yes\n",
            "checking limits.h usability... yes\n",
            "checking limits.h presence... yes\n",
            "checking for limits.h... yes\n",
            "checking sys/time.h usability... yes\n",
            "checking sys/time.h presence... yes\n",
            "checking for sys/time.h... yes\n",
            "checking for unistd.h... (cached) yes\n",
            "checking fold.h usability... yes\n",
            "checking fold.h presence... yes\n",
            "checking for fold.h... yes\n",
            "checking for an ANSI C-conforming const... yes\n",
            "checking for strdup... no\n",
            "configure: creating ./config.status\n",
            "config.status: creating Makefile\n",
            "config.status: creating Example/Makefile\n",
            "config.status: creating config.h\n",
            "config.status: executing depfiles commands\n",
            "configure:\n",
            "Configure successful with the following options:\n",
            "\n",
            "  Perl Extension:      yes\n",
            "  Analyse{Dists,Seqs}: no\n",
            "  Kinfold:             yes\n",
            "  RNAforester:         yes\n",
            "\n",
            "Files will be installed in the following directories:\n",
            "\n",
            "  Executables:  /usr/local/bin\n",
            "  Libraries:      /usr/local/lib\n",
            "  Header files: /usr/local/include\n",
            "  Extra Data:   /usr/local/share\n",
            "  Man pages:    /usr/local/man\n",
            "\n",
            "make  all-recursive\n",
            "make[1]: Entering directory '/content/ViennaRNA-1.6.1'\n",
            "Making all in lib\n",
            "make[2]: Entering directory '/content/ViennaRNA-1.6.1/lib'\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-dist_vars.o -MD -MP -MF \".deps/libRNA_a-dist_vars.Tpo\" -c -o libRNA_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c; \\\n",
            "then mv -f \".deps/libRNA_a-dist_vars.Tpo\" \".deps/libRNA_a-dist_vars.Po\"; else rm -f \".deps/libRNA_a-dist_vars.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-fold_vars.o -MD -MP -MF \".deps/libRNA_a-fold_vars.Tpo\" -c -o libRNA_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c; \\\n",
            "then mv -f \".deps/libRNA_a-fold_vars.Tpo\" \".deps/libRNA_a-fold_vars.Po\"; else rm -f \".deps/libRNA_a-fold_vars.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-part_func.o -MD -MP -MF \".deps/libRNA_a-part_func.Tpo\" -c -o libRNA_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c; \\\n",
            "then mv -f \".deps/libRNA_a-part_func.Tpo\" \".deps/libRNA_a-part_func.Po\"; else rm -f \".deps/libRNA_a-part_func.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-read_epars.o -MD -MP -MF \".deps/libRNA_a-read_epars.Tpo\" -c -o libRNA_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c; \\\n",
            "then mv -f \".deps/libRNA_a-read_epars.Tpo\" \".deps/libRNA_a-read_epars.Po\"; else rm -f \".deps/libRNA_a-read_epars.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-treedist.o -MD -MP -MF \".deps/libRNA_a-treedist.Tpo\" -c -o libRNA_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c; \\\n",
            "then mv -f \".deps/libRNA_a-treedist.Tpo\" \".deps/libRNA_a-treedist.Po\"; else rm -f \".deps/libRNA_a-treedist.Tpo\"; exit 1; fi\n",
            "\u001b[01m\u001b[Ktreedist.c:\u001b[m\u001b[K In function ‘\u001b[01m\u001b[Kprint_postorder_list\u001b[m\u001b[K’:\n",
            "\u001b[01m\u001b[Ktreedist.c:437:13:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[Ktype defaults to ‘\u001b[01m\u001b[Kint\u001b[m\u001b[K’ in declaration of ‘\u001b[01m\u001b[Ki\u001b[m\u001b[K’ [\u001b[01;35m\u001b[K-Wimplicit-int\u001b[m\u001b[K]\n",
            "    register \u001b[01;35m\u001b[Ki\u001b[m\u001b[K;\n",
            "             \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-energy_par.o -MD -MP -MF \".deps/libRNA_a-energy_par.Tpo\" -c -o libRNA_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c; \\\n",
            "then mv -f \".deps/libRNA_a-energy_par.Tpo\" \".deps/libRNA_a-energy_par.Po\"; else rm -f \".deps/libRNA_a-energy_par.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-inverse.o -MD -MP -MF \".deps/libRNA_a-inverse.Tpo\" -c -o libRNA_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c; \\\n",
            "then mv -f \".deps/libRNA_a-inverse.Tpo\" \".deps/libRNA_a-inverse.Po\"; else rm -f \".deps/libRNA_a-inverse.Tpo\"; exit 1; fi\n",
            "\u001b[01m\u001b[Kinverse.c:\u001b[m\u001b[K In function ‘\u001b[01m\u001b[Kpf_cost\u001b[m\u001b[K’:\n",
            "\u001b[01m\u001b[Kinverse.c:483:16:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[Kpassing argument 1 of ‘\u001b[01m\u001b[Kpf_fold\u001b[m\u001b[K’ discards ‘\u001b[01m\u001b[Kconst\u001b[m\u001b[K’ qualifier from pointer target type [\u001b[01;35m\u001b[K-Wdiscarded-qualifiers\u001b[m\u001b[K]\n",
            "    f = pf_fold(\u001b[01;35m\u001b[Kstring\u001b[m\u001b[K, structure);\n",
            "                \u001b[01;35m\u001b[K^~~~~~\u001b[m\u001b[K\n",
            "In file included from \u001b[01m\u001b[Kinverse.c:19:0\u001b[m\u001b[K:\n",
            "\u001b[01m\u001b[K../H/part_func.h:2:15:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kexpected ‘\u001b[01m\u001b[Kchar *\u001b[m\u001b[K’ but argument is of type ‘\u001b[01m\u001b[Kconst char *\u001b[m\u001b[K’\n",
            " extern float  \u001b[01;36m\u001b[Kpf_fold\u001b[m\u001b[K(char *sequence, char *structure);\n",
            "               \u001b[01;36m\u001b[K^~~~~~~\u001b[m\u001b[K\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-ProfileDist.o -MD -MP -MF \".deps/libRNA_a-ProfileDist.Tpo\" -c -o libRNA_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c; \\\n",
            "then mv -f \".deps/libRNA_a-ProfileDist.Tpo\" \".deps/libRNA_a-ProfileDist.Po\"; else rm -f \".deps/libRNA_a-ProfileDist.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-RNAstruct.o -MD -MP -MF \".deps/libRNA_a-RNAstruct.Tpo\" -c -o libRNA_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c; \\\n",
            "then mv -f \".deps/libRNA_a-RNAstruct.Tpo\" \".deps/libRNA_a-RNAstruct.Po\"; else rm -f \".deps/libRNA_a-RNAstruct.Tpo\"; exit 1; fi\n",
            "\u001b[01m\u001b[KRNAstruct.c:\u001b[m\u001b[K In function ‘\u001b[01m\u001b[Kb2HIT\u001b[m\u001b[K’:\n",
            "\u001b[01m\u001b[KRNAstruct.c:99:21:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[K%d\u001b[m\u001b[K’ directive writing between 1 and 10 bytes into a region of size 8 [\u001b[01;35m\u001b[K-Wformat-overflow=\u001b[m\u001b[K]\n",
            "      sprintf(tt, \"(U\u001b[01;35m\u001b[K%d\u001b[m\u001b[K)\" , u);\n",
            "                     \u001b[01;35m\u001b[K^~\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[KRNAstruct.c:99:18:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kdirective argument in the range [0, 2147483647]\n",
            "      sprintf(tt, \u001b[01;36m\u001b[K\"(U%d)\"\u001b[m\u001b[K , u);\n",
            "                  \u001b[01;36m\u001b[K^~~~~~~\u001b[m\u001b[K\n",
            "In file included from \u001b[01m\u001b[K/usr/include/stdio.h:862:0\u001b[m\u001b[K,\n",
            "                 from \u001b[01m\u001b[KRNAstruct.c:9\u001b[m\u001b[K:\n",
            "\u001b[01m\u001b[K/usr/include/x86_64-linux-gnu/bits/stdio2.h:33:10:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[K‘\u001b[01m\u001b[K__builtin___sprintf_chk\u001b[m\u001b[K’ output between 5 and 14 bytes into a destination of size 10\n",
            "   return \u001b[01;36m\u001b[K__builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,\u001b[m\u001b[K\n",
            "          \u001b[01;36m\u001b[K^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\u001b[m\u001b[K\n",
            " \u001b[01;36m\u001b[K      __bos (__s), __fmt, __va_arg_pack ())\u001b[m\u001b[K;\n",
            "       \u001b[01;36m\u001b[K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[KRNAstruct.c:108:21:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[K%d\u001b[m\u001b[K’ directive writing between 1 and 10 bytes into a region of size 8 [\u001b[01;35m\u001b[K-Wformat-overflow=\u001b[m\u001b[K]\n",
            "      sprintf(tt, \"(U\u001b[01;35m\u001b[K%d\u001b[m\u001b[K)\" , u);\n",
            "                     \u001b[01;35m\u001b[K^~\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[KRNAstruct.c:108:18:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kdirective argument in the range [0, 2147483647]\n",
            "      sprintf(tt, \u001b[01;36m\u001b[K\"(U%d)\"\u001b[m\u001b[K , u);\n",
            "                  \u001b[01;36m\u001b[K^~~~~~~\u001b[m\u001b[K\n",
            "In file included from \u001b[01m\u001b[K/usr/include/stdio.h:862:0\u001b[m\u001b[K,\n",
            "                 from \u001b[01m\u001b[KRNAstruct.c:9\u001b[m\u001b[K:\n",
            "\u001b[01m\u001b[K/usr/include/x86_64-linux-gnu/bits/stdio2.h:33:10:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[K‘\u001b[01m\u001b[K__builtin___sprintf_chk\u001b[m\u001b[K’ output between 5 and 14 bytes into a destination of size 10\n",
            "   return \u001b[01;36m\u001b[K__builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,\u001b[m\u001b[K\n",
            "          \u001b[01;36m\u001b[K^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\u001b[m\u001b[K\n",
            " \u001b[01;36m\u001b[K      __bos (__s), __fmt, __va_arg_pack ())\u001b[m\u001b[K;\n",
            "       \u001b[01;36m\u001b[K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[KRNAstruct.c:117:21:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[K%d\u001b[m\u001b[K’ directive writing between 1 and 10 bytes into a region of size 8 [\u001b[01;35m\u001b[K-Wformat-overflow=\u001b[m\u001b[K]\n",
            "      sprintf(tt, \"(U\u001b[01;35m\u001b[K%d\u001b[m\u001b[K)\" , u);\n",
            "                     \u001b[01;35m\u001b[K^~\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[KRNAstruct.c:117:18:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kdirective argument in the range [0, 2147483647]\n",
            "      sprintf(tt, \u001b[01;36m\u001b[K\"(U%d)\"\u001b[m\u001b[K , u);\n",
            "                  \u001b[01;36m\u001b[K^~~~~~~\u001b[m\u001b[K\n",
            "In file included from \u001b[01m\u001b[K/usr/include/stdio.h:862:0\u001b[m\u001b[K,\n",
            "                 from \u001b[01m\u001b[KRNAstruct.c:9\u001b[m\u001b[K:\n",
            "\u001b[01m\u001b[K/usr/include/x86_64-linux-gnu/bits/stdio2.h:33:10:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[K‘\u001b[01m\u001b[K__builtin___sprintf_chk\u001b[m\u001b[K’ output between 5 and 14 bytes into a destination of size 10\n",
            "   return \u001b[01;36m\u001b[K__builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,\u001b[m\u001b[K\n",
            "          \u001b[01;36m\u001b[K^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\u001b[m\u001b[K\n",
            " \u001b[01;36m\u001b[K      __bos (__s), __fmt, __va_arg_pack ())\u001b[m\u001b[K;\n",
            "       \u001b[01;36m\u001b[K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[KRNAstruct.c:122:16:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[K%d\u001b[m\u001b[K’ directive writing between 1 and 10 bytes into a region of size 9 [\u001b[01;35m\u001b[K-Wformat-overflow=\u001b[m\u001b[K]\n",
            "   sprintf(tt,\"P\u001b[01;35m\u001b[K%d\u001b[m\u001b[K)\", p+1);\n",
            "                \u001b[01;35m\u001b[K^~\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[KRNAstruct.c:122:14:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kdirective argument in the range [1, 2147483647]\n",
            "   sprintf(tt,\u001b[01;36m\u001b[K\"P%d)\"\u001b[m\u001b[K, p+1);\n",
            "              \u001b[01;36m\u001b[K^~~~~~\u001b[m\u001b[K\n",
            "In file included from \u001b[01m\u001b[K/usr/include/stdio.h:862:0\u001b[m\u001b[K,\n",
            "                 from \u001b[01m\u001b[KRNAstruct.c:9\u001b[m\u001b[K:\n",
            "\u001b[01m\u001b[K/usr/include/x86_64-linux-gnu/bits/stdio2.h:33:10:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[K‘\u001b[01m\u001b[K__builtin___sprintf_chk\u001b[m\u001b[K’ output between 4 and 13 bytes into a destination of size 10\n",
            "   return \u001b[01;36m\u001b[K__builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,\u001b[m\u001b[K\n",
            "          \u001b[01;36m\u001b[K^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\u001b[m\u001b[K\n",
            " \u001b[01;36m\u001b[K      __bos (__s), __fmt, __va_arg_pack ())\u001b[m\u001b[K;\n",
            "       \u001b[01;36m\u001b[K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[KRNAstruct.c:131:22:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[K%d\u001b[m\u001b[K’ directive writing between 1 and 10 bytes into a region of size 8 [\u001b[01;35m\u001b[K-Wformat-overflow=\u001b[m\u001b[K]\n",
            "       sprintf(tt, \"(U\u001b[01;35m\u001b[K%d\u001b[m\u001b[K)\" , u);\n",
            "                      \u001b[01;35m\u001b[K^~\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[KRNAstruct.c:131:19:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kdirective argument in the range [0, 2147483647]\n",
            "       sprintf(tt, \u001b[01;36m\u001b[K\"(U%d)\"\u001b[m\u001b[K , u);\n",
            "                   \u001b[01;36m\u001b[K^~~~~~~\u001b[m\u001b[K\n",
            "In file included from \u001b[01m\u001b[K/usr/include/stdio.h:862:0\u001b[m\u001b[K,\n",
            "                 from \u001b[01m\u001b[KRNAstruct.c:9\u001b[m\u001b[K:\n",
            "\u001b[01m\u001b[K/usr/include/x86_64-linux-gnu/bits/stdio2.h:33:10:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[K‘\u001b[01m\u001b[K__builtin___sprintf_chk\u001b[m\u001b[K’ output between 5 and 14 bytes into a destination of size 10\n",
            "   return \u001b[01;36m\u001b[K__builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,\u001b[m\u001b[K\n",
            "          \u001b[01;36m\u001b[K^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\u001b[m\u001b[K\n",
            " \u001b[01;36m\u001b[K      __bos (__s), __fmt, __va_arg_pack ())\u001b[m\u001b[K;\n",
            "       \u001b[01;36m\u001b[K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\u001b[m\u001b[K\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-utils.o -MD -MP -MF \".deps/libRNA_a-utils.Tpo\" -c -o libRNA_a-utils.o `test -f 'utils.c' || echo './'`utils.c; \\\n",
            "then mv -f \".deps/libRNA_a-utils.Tpo\" \".deps/libRNA_a-utils.Po\"; else rm -f \".deps/libRNA_a-utils.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-fold.o -MD -MP -MF \".deps/libRNA_a-fold.Tpo\" -c -o libRNA_a-fold.o `test -f 'fold.c' || echo './'`fold.c; \\\n",
            "then mv -f \".deps/libRNA_a-fold.Tpo\" \".deps/libRNA_a-fold.Po\"; else rm -f \".deps/libRNA_a-fold.Tpo\"; exit 1; fi\n",
            "\u001b[01m\u001b[Kfold.c:912:2:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "  \u001b[01;35m\u001b[KP\u001b[m\u001b[K->mismatchI[type_2][sq1][sp1];\n",
            "  \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:911:17:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "       energy += \u001b[01;35m\u001b[KP\u001b[m\u001b[K->mismatchI[type][si1][sj1]+\n",
            "                 \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:909:41:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "       energy += MIN2(MAX_NINIO, (nl-ns)*\u001b[01;35m\u001b[KP\u001b[m\u001b[K->F_ninio[2]);\n",
            "                                         \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:67:45:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kin definition of macro ‘\u001b[01m\u001b[KMIN2\u001b[m\u001b[K’\n",
            " #define MIN2(A, B)      ((A) < (B) ? (A) : (\u001b[01;36m\u001b[KB\u001b[m\u001b[K))\n",
            "                                             \u001b[01;36m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:909:41:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "       energy += MIN2(MAX_NINIO, (nl-ns)*\u001b[01;35m\u001b[KP\u001b[m\u001b[K->F_ninio[2]);\n",
            "                                         \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:67:33:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kin definition of macro ‘\u001b[01m\u001b[KMIN2\u001b[m\u001b[K’\n",
            " #define MIN2(A, B)      ((A) < (\u001b[01;36m\u001b[KB\u001b[m\u001b[K) ? (A) : (B))\n",
            "                                 \u001b[01;36m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:907:30:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "  (P->internal_loop[30]+(int)(\u001b[01;35m\u001b[KP\u001b[m\u001b[K->lxc*log((n1+n2)/30.)));\n",
            "                              \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:907:3:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "  (\u001b[01;35m\u001b[KP\u001b[m\u001b[K->internal_loop[30]+(int)(P->lxc*log((n1+n2)/30.)));\n",
            "   \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:906:34:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "       energy = (n1+n2<=MAXLOOP)?(\u001b[01;35m\u001b[KP\u001b[m\u001b[K->internal_loop[n1+n2]):\n",
            "                                  \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:904:14:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "       return \u001b[01;35m\u001b[KP\u001b[m\u001b[K->int22[type][type_2][si1][sp1][sq1][sj1];\n",
            "              \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:899:13:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "    energy = \u001b[01;35m\u001b[KP\u001b[m\u001b[K->int21[type_2][type][sq1][si1][sp1];\n",
            "             \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:897:13:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "    energy = \u001b[01;35m\u001b[KP\u001b[m\u001b[K->int21[type][type_2][si1][sq1][sj1];\n",
            "             \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:894:9:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "  return \u001b[01;35m\u001b[KP\u001b[m\u001b[K->int11[type][type_2][si1][sj1];\n",
            "         \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:887:31:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "       if (type_2>2) energy += \u001b[01;35m\u001b[KP\u001b[m\u001b[K->TerminalAU;\n",
            "                               \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:886:29:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "       if (type>2) energy += \u001b[01;35m\u001b[KP\u001b[m\u001b[K->TerminalAU;\n",
            "                             \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:884:26:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "     if (nl==1) energy += \u001b[01;35m\u001b[KP\u001b[m\u001b[K->stack[type][type_2];\n",
            "                          \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:883:27:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "       (P->bulge[30]+(int)(\u001b[01;35m\u001b[KP\u001b[m\u001b[K->lxc*log(nl/30.)));\n",
            "                           \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:883:8:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "       (\u001b[01;35m\u001b[KP\u001b[m\u001b[K->bulge[30]+(int)(P->lxc*log(nl/30.)));\n",
            "        \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:882:28:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "     energy = (nl<=MAXLOOP)?\u001b[01;35m\u001b[KP\u001b[m\u001b[K->bulge[nl]:\n",
            "                            \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:879:12:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KLoopEnergy\u001b[m\u001b[K’ which is not static\n",
            "     return \u001b[01;35m\u001b[KP\u001b[m\u001b[K->stack[type][type_2];    /* stack */\n",
            "            \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:821:15:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KHairpinE\u001b[m\u001b[K’ which is not static\n",
            "     energy += \u001b[01;35m\u001b[KP\u001b[m\u001b[K->mismatchH[type][si1][sj1];\n",
            "               \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:818:17:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KHairpinE\u001b[m\u001b[K’ which is not static\n",
            "       energy += \u001b[01;35m\u001b[KP\u001b[m\u001b[K->TerminalAU; /* penalty for closing AU GU pair */\n",
            "                 \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:815:36:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KHairpinE\u001b[m\u001b[K’ which is not static\n",
            "       energy += P->Triloop_E[(ts - \u001b[01;35m\u001b[KP\u001b[m\u001b[K->Triloops)/6];\n",
            "                                    \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:815:17:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KHairpinE\u001b[m\u001b[K’ which is not static\n",
            "       energy += \u001b[01;35m\u001b[KP\u001b[m\u001b[K->Triloop_E[(ts - P->Triloops)/6];\n",
            "                 \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:814:20:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KHairpinE\u001b[m\u001b[K’ which is not static\n",
            "     if ((ts=strstr(\u001b[01;35m\u001b[KP\u001b[m\u001b[K->Triloops, tl)))\n",
            "                    \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:809:34:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KHairpinE\u001b[m\u001b[K’ which is not static\n",
            "  energy += P->TETRA_ENERGY[(ts - \u001b[01;35m\u001b[KP\u001b[m\u001b[K->Tetraloops)/7];\n",
            "                                  \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:809:12:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KHairpinE\u001b[m\u001b[K’ which is not static\n",
            "  energy += \u001b[01;35m\u001b[KP\u001b[m\u001b[K->TETRA_ENERGY[(ts - P->Tetraloops)/7];\n",
            "            \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:808:22:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KHairpinE\u001b[m\u001b[K’ which is not static\n",
            "       if ((ts=strstr(\u001b[01;35m\u001b[KP\u001b[m\u001b[K->Tetraloops, tl)))\n",
            "                      \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:803:26:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KHairpinE\u001b[m\u001b[K’ which is not static\n",
            "     P->hairpin[30]+(int)(\u001b[01;35m\u001b[KP\u001b[m\u001b[K->lxc*log((size)/30.));\n",
            "                          \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:803:5:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KHairpinE\u001b[m\u001b[K’ which is not static\n",
            "     \u001b[01;35m\u001b[KP\u001b[m\u001b[K->hairpin[30]+(int)(P->lxc*log((size)/30.));\n",
            "     \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kfold.c:802:27:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K‘\u001b[01m\u001b[KP\u001b[m\u001b[K’ is static but used in inline function ‘\u001b[01m\u001b[KHairpinE\u001b[m\u001b[K’ which is not static\n",
            "   energy = (size <= 30) ? \u001b[01;35m\u001b[KP\u001b[m\u001b[K->hairpin[size] :\n",
            "                           \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-naview.o -MD -MP -MF \".deps/libRNA_a-naview.Tpo\" -c -o libRNA_a-naview.o `test -f 'naview.c' || echo './'`naview.c; \\\n",
            "then mv -f \".deps/libRNA_a-naview.Tpo\" \".deps/libRNA_a-naview.Po\"; else rm -f \".deps/libRNA_a-naview.Tpo\"; exit 1; fi\n",
            "\u001b[01m\u001b[Knaview.c:\u001b[m\u001b[K In function ‘\u001b[01m\u001b[Kdump_loops\u001b[m\u001b[K’:\n",
            "\u001b[01m\u001b[Knaview.c:334:28:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[Kformat ‘\u001b[01m\u001b[K%d\u001b[m\u001b[K’ expects argument of type ‘\u001b[01m\u001b[Kint\u001b[m\u001b[K’, but argument 2 has type ‘\u001b[01m\u001b[Klong int\u001b[m\u001b[K’ [\u001b[01;35m\u001b[K-Wformat=\u001b[m\u001b[K]\n",
            "   printf(\"\\nRoot loop is #\u001b[01;35m\u001b[K%d\u001b[m\u001b[K\\n\",\u001b[32m\u001b[K(root-loops)+1\u001b[m\u001b[K);\n",
            "                           \u001b[01;35m\u001b[K~^\u001b[m\u001b[K    \u001b[32m\u001b[K~~~~~~~~~~~~~~\u001b[m\u001b[K\n",
            "                           \u001b[32m\u001b[K%ld\u001b[m\u001b[K\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-PS_dot.o -MD -MP -MF \".deps/libRNA_a-PS_dot.Tpo\" -c -o libRNA_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c; \\\n",
            "then mv -f \".deps/libRNA_a-PS_dot.Tpo\" \".deps/libRNA_a-PS_dot.Po\"; else rm -f \".deps/libRNA_a-PS_dot.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-stringdist.o -MD -MP -MF \".deps/libRNA_a-stringdist.Tpo\" -c -o libRNA_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c; \\\n",
            "then mv -f \".deps/libRNA_a-stringdist.Tpo\" \".deps/libRNA_a-stringdist.Po\"; else rm -f \".deps/libRNA_a-stringdist.Tpo\"; exit 1; fi\n",
            "\u001b[01m\u001b[Kstringdist.c:24:0:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K\"INFINITY\" redefined\n",
            " #define INFINITY       10000\n",
            " \n",
            "In file included from \u001b[01m\u001b[Kstringdist.c:12:0\u001b[m\u001b[K:\n",
            "\u001b[01m\u001b[K/usr/include/math.h:91:0:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kthis is the location of the previous definition\n",
            " #  define INFINITY (__builtin_inff ())\n",
            " \n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-params.o -MD -MP -MF \".deps/libRNA_a-params.Tpo\" -c -o libRNA_a-params.o `test -f 'params.c' || echo './'`params.c; \\\n",
            "then mv -f \".deps/libRNA_a-params.Tpo\" \".deps/libRNA_a-params.Po\"; else rm -f \".deps/libRNA_a-params.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-subopt.o -MD -MP -MF \".deps/libRNA_a-subopt.Tpo\" -c -o libRNA_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c; \\\n",
            "then mv -f \".deps/libRNA_a-subopt.Tpo\" \".deps/libRNA_a-subopt.Po\"; else rm -f \".deps/libRNA_a-subopt.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-list.o -MD -MP -MF \".deps/libRNA_a-list.Tpo\" -c -o libRNA_a-list.o `test -f 'list.c' || echo './'`list.c; \\\n",
            "then mv -f \".deps/libRNA_a-list.Tpo\" \".deps/libRNA_a-list.Po\"; else rm -f \".deps/libRNA_a-list.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-Lfold.o -MD -MP -MF \".deps/libRNA_a-Lfold.Tpo\" -c -o libRNA_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c; \\\n",
            "then mv -f \".deps/libRNA_a-Lfold.Tpo\" \".deps/libRNA_a-Lfold.Po\"; else rm -f \".deps/libRNA_a-Lfold.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-cofold.o -MD -MP -MF \".deps/libRNA_a-cofold.Tpo\" -c -o libRNA_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c; \\\n",
            "then mv -f \".deps/libRNA_a-cofold.Tpo\" \".deps/libRNA_a-cofold.Po\"; else rm -f \".deps/libRNA_a-cofold.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-part_func_co.o -MD -MP -MF \".deps/libRNA_a-part_func_co.Tpo\" -c -o libRNA_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c; \\\n",
            "then mv -f \".deps/libRNA_a-part_func_co.Tpo\" \".deps/libRNA_a-part_func_co.Po\"; else rm -f \".deps/libRNA_a-part_func_co.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-ProfileAln.o -MD -MP -MF \".deps/libRNA_a-ProfileAln.Tpo\" -c -o libRNA_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c; \\\n",
            "then mv -f \".deps/libRNA_a-ProfileAln.Tpo\" \".deps/libRNA_a-ProfileAln.Po\"; else rm -f \".deps/libRNA_a-ProfileAln.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-duplex.o -MD -MP -MF \".deps/libRNA_a-duplex.Tpo\" -c -o libRNA_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c; \\\n",
            "then mv -f \".deps/libRNA_a-duplex.Tpo\" \".deps/libRNA_a-duplex.Po\"; else rm -f \".deps/libRNA_a-duplex.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-alifold.o -MD -MP -MF \".deps/libRNA_a-alifold.Tpo\" -c -o libRNA_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c; \\\n",
            "then mv -f \".deps/libRNA_a-alifold.Tpo\" \".deps/libRNA_a-alifold.Po\"; else rm -f \".deps/libRNA_a-alifold.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-alipfold.o -MD -MP -MF \".deps/libRNA_a-alipfold.Tpo\" -c -o libRNA_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c; \\\n",
            "then mv -f \".deps/libRNA_a-alipfold.Tpo\" \".deps/libRNA_a-alipfold.Po\"; else rm -f \".deps/libRNA_a-alipfold.Tpo\"; exit 1; fi\n",
            "\u001b[01m\u001b[Kalipfold.c:\u001b[m\u001b[K In function ‘\u001b[01m\u001b[Kalipf_fold\u001b[m\u001b[K’:\n",
            "\u001b[01m\u001b[Kalipfold.c:98:40:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[Kpassing argument 2 of ‘\u001b[01m\u001b[Kmake_pscores\u001b[m\u001b[K’ from incompatible pointer type [\u001b[01;35m\u001b[K-Wincompatible-pointer-types\u001b[m\u001b[K]\n",
            "   make_pscores((const short *const*)S, \u001b[01;35m\u001b[Ksequences\u001b[m\u001b[K, n_seq, structure);\n",
            "                                        \u001b[01;35m\u001b[K^~~~~~~~~\u001b[m\u001b[K\n",
            "\u001b[01m\u001b[Kalipfold.c:42:14:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kexpected ‘\u001b[01m\u001b[Kconst char * const*\u001b[m\u001b[K’ but argument is of type ‘\u001b[01m\u001b[Kchar **\u001b[m\u001b[K’\n",
            " PRIVATE void \u001b[01;36m\u001b[Kmake_pscores\u001b[m\u001b[K(const short *const *S, const char *const* AS,\n",
            "              \u001b[01;36m\u001b[K^~~~~~~~~~~~\u001b[m\u001b[K\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-aln_util.o -MD -MP -MF \".deps/libRNA_a-aln_util.Tpo\" -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c; \\\n",
            "then mv -f \".deps/libRNA_a-aln_util.Tpo\" \".deps/libRNA_a-aln_util.Po\"; else rm -f \".deps/libRNA_a-aln_util.Tpo\"; exit 1; fi\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -fpic -g -O2 -MT libRNA_a-LPfold.o -MD -MP -MF \".deps/libRNA_a-LPfold.Tpo\" -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c; \\\n",
            "then mv -f \".deps/libRNA_a-LPfold.Tpo\" \".deps/libRNA_a-LPfold.Po\"; else rm -f \".deps/libRNA_a-LPfold.Tpo\"; exit 1; fi\n",
            "rm -f libRNA.a\n",
            "ar cru libRNA.a libRNA_a-dist_vars.o libRNA_a-fold_vars.o libRNA_a-part_func.o libRNA_a-read_epars.o libRNA_a-treedist.o libRNA_a-energy_par.o libRNA_a-inverse.o libRNA_a-ProfileDist.o libRNA_a-RNAstruct.o libRNA_a-utils.o libRNA_a-fold.o libRNA_a-naview.o libRNA_a-PS_dot.o libRNA_a-stringdist.o libRNA_a-params.o libRNA_a-subopt.o libRNA_a-list.o libRNA_a-Lfold.o libRNA_a-cofold.o libRNA_a-part_func_co.o libRNA_a-ProfileAln.o libRNA_a-duplex.o libRNA_a-alifold.o libRNA_a-alipfold.o libRNA_a-aln_util.o libRNA_a-LPfold.o \n",
            "ar: `u' modifier ignored since `D' is the default (see `U')\n",
            "ranlib libRNA.a\n",
            "make[2]: Leaving directory '/content/ViennaRNA-1.6.1/lib'\n",
            "Making all in Progs\n",
            "make[2]: Entering directory '/content/ViennaRNA-1.6.1/Progs'\n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -g -O2 -MT RNAfold.o -MD -MP -MF \".deps/RNAfold.Tpo\" -c -o RNAfold.o RNAfold.c; \\\n",
            "then mv -f \".deps/RNAfold.Tpo\" \".deps/RNAfold.Po\"; else rm -f \".deps/RNAfold.Tpo\"; exit 1; fi\n",
            "gcc  -g -O2   -o RNAfold  RNAfold.o ../lib/libRNA.a -lm \n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -g -O2 -MT RNAeval.o -MD -MP -MF \".deps/RNAeval.Tpo\" -c -o RNAeval.o RNAeval.c; \\\n",
            "then mv -f \".deps/RNAeval.Tpo\" \".deps/RNAeval.Po\"; else rm -f \".deps/RNAeval.Tpo\"; exit 1; fi\n",
            "gcc  -g -O2   -o RNAeval  RNAeval.o ../lib/libRNA.a -lm \n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -g -O2 -MT RNAheat.o -MD -MP -MF \".deps/RNAheat.Tpo\" -c -o RNAheat.o RNAheat.c; \\\n",
            "then mv -f \".deps/RNAheat.Tpo\" \".deps/RNAheat.Po\"; else rm -f \".deps/RNAheat.Tpo\"; exit 1; fi\n",
            "gcc  -g -O2   -o RNAheat  RNAheat.o ../lib/libRNA.a -lm \n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -g -O2 -MT RNApdist.o -MD -MP -MF \".deps/RNApdist.Tpo\" -c -o RNApdist.o RNApdist.c; \\\n",
            "then mv -f \".deps/RNApdist.Tpo\" \".deps/RNApdist.Po\"; else rm -f \".deps/RNApdist.Tpo\"; exit 1; fi\n",
            "gcc  -g -O2   -o RNApdist  RNApdist.o ../lib/libRNA.a -lm \n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -g -O2 -MT RNAdistance.o -MD -MP -MF \".deps/RNAdistance.Tpo\" -c -o RNAdistance.o RNAdistance.c; \\\n",
            "then mv -f \".deps/RNAdistance.Tpo\" \".deps/RNAdistance.Po\"; else rm -f \".deps/RNAdistance.Tpo\"; exit 1; fi\n",
            "gcc  -g -O2   -o RNAdistance  RNAdistance.o ../lib/libRNA.a -lm \n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -g -O2 -MT RNAinverse.o -MD -MP -MF \".deps/RNAinverse.Tpo\" -c -o RNAinverse.o RNAinverse.c; \\\n",
            "then mv -f \".deps/RNAinverse.Tpo\" \".deps/RNAinverse.Po\"; else rm -f \".deps/RNAinverse.Tpo\"; exit 1; fi\n",
            "\u001b[01m\u001b[KRNAinverse.c:31:0:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[K\"INFINITY\" redefined\n",
            " #define  INFINITY        100000\n",
            " \n",
            "In file included from \u001b[01m\u001b[KRNAinverse.c:9:0\u001b[m\u001b[K:\n",
            "\u001b[01m\u001b[K/usr/include/math.h:91:0:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kthis is the location of the previous definition\n",
            " #  define INFINITY (__builtin_inff ())\n",
            " \n",
            "gcc  -g -O2   -o RNAinverse  RNAinverse.o ../lib/libRNA.a -lm \n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -g -O2 -MT RNAplot.o -MD -MP -MF \".deps/RNAplot.Tpo\" -c -o RNAplot.o RNAplot.c; \\\n",
            "then mv -f \".deps/RNAplot.Tpo\" \".deps/RNAplot.Po\"; else rm -f \".deps/RNAplot.Tpo\"; exit 1; fi\n",
            "gcc  -g -O2   -o RNAplot  RNAplot.o ../lib/libRNA.a -lm \n",
            "if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../H    -g -O2 -MT RNAsubopt.o -MD -MP -MF \".deps/RNAsubopt.Tpo\" -c -o RNAsubopt.o RNAsubopt.c; \\\n",
            "then mv -f \".deps/RNAsubopt.Tpo\" \".deps/RNAsubopt.Po\"; else rm -f \".deps/RNAsubopt.Tpo\"; exit 1; fi\n",
            "gcc  -g -O2   -o RNAsubopt  RNAsubopt.o ../lib/libRNA.a -lm \n",
            "../lib/libRNA.a(libRNA_a-subopt.o): In function `repeat':\n",
            "/content/ViennaRNA-1.6.1/lib/subopt.c:855: undefined reference to `LoopEnergy'\n",
            "/content/ViennaRNA-1.6.1/lib/subopt.c:828: undefined reference to `LoopEnergy'\n",
            "/content/ViennaRNA-1.6.1/lib/subopt.c:914: undefined reference to `HairpinE'\n",
            "collect2: error: ld returned 1 exit status\n",
            "Makefile:320: recipe for target 'RNAsubopt' failed\n",
            "make[2]: *** [RNAsubopt] Error 1\n",
            "make[2]: Leaving directory '/content/ViennaRNA-1.6.1/Progs'\n",
            "Makefile:270: recipe for target 'all-recursive' failed\n",
            "make[1]: *** [all-recursive] Error 1\n",
            "make[1]: Leaving directory '/content/ViennaRNA-1.6.1'\n",
            "Makefile:189: recipe for target 'all' failed\n",
            "make: *** [all] Error 2\n",
            "/content\n"
          ]
        }
      ],
      "source": [
        "install_path = \"/content/ViennaRNA-1.6.1/Progs/\"\n",
        "\n",
        "%cd /content/ViennaRNA-1.6.1\n",
        "!./configure \n",
        "!make all\n",
        "# (exit with 2 but RNAfold is compiled OK)\n",
        "%cd /content"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "bCdjGI0grQpm"
      },
      "source": [
        "# S. cerevisiae (sce) 18 long non-coding RNA dataset\n",
        "Data source: https://genie.weizmann.ac.il/pubs/PARS10/data/sce_genes_folded.tab.gz"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 5,
      "metadata": {
        "id": "Fmvg_3l4_TBH"
      },
      "outputs": [],
      "source": [
        "gh_path = \"https://raw.githubusercontent.com/sinc-lab/lncRNA-folding/master/data/\"\n",
        "sce = pd.read_csv(gh_path + \"sce_genes_folded.tab\", delimiter='\\t', \n",
        "                  header=None, index_col=0, \n",
        "                  names=(\"Gene ID\", \"sequence\", \"PARS-assisted folding\"))"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 6,
      "metadata": {
        "id": "eeup_dp2AHrN"
      },
      "outputs": [],
      "source": [
        "# Sequences to process\n",
        "yeast18lnc = [\"snR81\", \"snR34\", \"snR43\", \"snR44\",  \"snR31\",  \"snR10\",\n",
        "              \"snR63\", \"snR11\", \"snR82\", \"snR17b\", \"snR17a\", \"snR37\",\n",
        "              \"SCR1\",  \"SRG1\",  \"snR19\", \"snR30\",  \"LSR1\",   \"TLC1\"]"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# Scores for constraints\n",
        "pars = pd.read_csv(gh_path + \"sce_PARS_score.tab\", sep='\\t').set_index('gene')"
      ],
      "metadata": {
        "id": "gBOWD7UxIca-"
      },
      "execution_count": 7,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Vz9-OyOlshXJ"
      },
      "source": [
        "# Compute structures"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "def run_folding(fasta_name):\n",
        "\n",
        "    # Compute structure\n",
        "    command_line = [install_path + \"RNAfold \",  \n",
        "                    \"-T 37 \",\n",
        "                    \"-C \",  \n",
        "                    \"< tmp.fasta > rnafold_tmp.fasta\"]\n",
        "    !{\"\".join(command_line)}\n",
        "    \n",
        "    \n",
        "    return \"rnafold_tmp.fasta\""
      ],
      "metadata": {
        "id": "KbhRjJo-I7g2"
      },
      "execution_count": 8,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!/content/ViennaRNA-1.6.1/Progs/RNAfold -h"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "Ylw3JHalEwgL",
        "outputId": "744e1385-6e6c-4ea3-b924-7e468a63f8db"
      },
      "execution_count": 9,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "\n",
            "usage:\n",
            "RNAfold [-p[0]] [-C] [-T temp] [-4] [-d[2|3]] [-noGU] [-noCloseGU]\n",
            "        [-noLP] [-e e_set] [-P paramfile] [-nsp pairs] [-S scale]\n",
            "        [-noconv] [-circ] \n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# Convert scores to contraints with RNAfold 1.6 format\n",
        "# https://genie.weizmann.ac.il/pubs/PARS10/pars10_notes.html\n",
        "def get_constraints(pars, lnc):\n",
        "    scores = np.array(pars.loc[lnc, 'score'].split(';'), dtype=float)\n",
        "    cons = [\".\"]*len(scores)\n",
        "    for i,s in enumerate(scores):\n",
        "        if s>5: cons[i] = \"|\"\n",
        "        elif s<-5: cons[i] = \"x\"\n",
        "    cons_str = \"\".join(cons)\n",
        "    return cons_str\n",
        "    \n",
        "# Get prediction in a string to compare with PARS assited references\n",
        "def get_pred(file_name, slen):\n",
        "    str_out = \"\"\n",
        "    with open(file_name,'r') as fasta:\n",
        "        for i, line in enumerate(fasta):\n",
        "            if i==2: str_out = line[:slen]\n",
        "    return str_out"
      ],
      "metadata": {
        "id": "-cqhvb7aIZxe"
      },
      "execution_count": 10,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "out_fasta_name = method_name + \"_yeast18\"\n",
        "if os.path.exists(out_fasta_name + \".fasta\"): os.remove(out_fasta_name + \".fasta\")\n",
        "\n",
        "lnc_ids = yeast18lnc\n",
        "print(\"   \\t lnc \\t len \\t time \\t =ref(Kertesz2010)?\")\n",
        "for i, lnc in enumerate(lnc_ids): \n",
        "\n",
        "    start_time = time.time()\n",
        "    seq = sce.loc[lnc][\"sequence\"]\n",
        "    print(f\"{i+1}/{len(lnc_ids)}\\t{lnc} \\t {len(seq)}\", end='\\t')\n",
        "\n",
        "    cons = get_constraints(pars, lnc)\n",
        "    #print(\"Con: \\n\", cons)\n",
        "\n",
        "    # Write a one-sequence fasta\n",
        "    with open(\"tmp.fasta\", \"w\") as ofile: \n",
        "        ofile.write(f\">{lnc}\\n{seq}\\n{cons}\\n\")\n",
        "\n",
        "    dot_file_name = run_folding(\"tmp.fasta\")\n",
        "\n",
        "    # Concatenate outputs\n",
        "    os.system(\"cat \" + dot_file_name + \" >> \" + out_fasta_name + \".fasta\") \n",
        "\n",
        "    print(f\"{time.time() - start_time: .1f} s\", end='\\t')\n",
        "\n",
        "    str_ref = sce.loc[lnc][\"PARS-assisted folding\"]\n",
        "    str_pre = get_pred(dot_file_name, len(seq))\n",
        "    if not (str_ref==str_pre):  \n",
        "        print(\"Ref: \\n\" + str_ref)\n",
        "        print(\"Pre: \\n\" + str_pre)\n",
        "    else:\n",
        "        print(\"  OK\")"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "xhPTIWvUI5NM",
        "outputId": "bb44eac3-1da8-4376-b91e-ae1dbb203b43"
      },
      "execution_count": 11,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "   \t lnc \t len \t time \t =ref(Kertesz2010)?\n",
            "1/18\tsnR81 \t 201\t 0.1 s\t  OK\n",
            "2/18\tsnR34 \t 203\t 0.1 s\t  OK\n",
            "3/18\tsnR43 \t 209\t 0.1 s\t  OK\n",
            "4/18\tsnR44 \t 211\t 0.1 s\t  OK\n",
            "5/18\tsnR31 \t 225\t 0.1 s\t  OK\n",
            "6/18\tsnR10 \t 245\t 0.1 s\t  OK\n",
            "7/18\tsnR63 \t 255\t 0.1 s\t  OK\n",
            "8/18\tsnR11 \t 258\t 0.2 s\t  OK\n",
            "9/18\tsnR82 \t 268\t 0.1 s\t  OK\n",
            "10/18\tsnR17b \t 332\t 0.2 s\t  OK\n",
            "11/18\tsnR17a \t 333\t 0.2 s\t  OK\n",
            "12/18\tsnR37 \t 386\t 0.2 s\t  OK\n",
            "13/18\tSCR1 \t 522\t 0.3 s\t  OK\n",
            "14/18\tSRG1 \t 551\t 0.3 s\t  OK\n",
            "15/18\tsnR19 \t 568\t 0.4 s\t  OK\n",
            "16/18\tsnR30 \t 606\t 0.4 s\t  OK\n",
            "17/18\tLSR1 \t 1175\t 1.8 s\t  OK\n",
            "18/18\tTLC1 \t 1301\t 2.1 s\t  OK\n"
          ]
        }
      ]
    }
  ],
  "metadata": {
    "colab": {
      "collapsed_sections": [],
      "name": "RNAfold_Constraints.ipynb",
      "provenance": []
    },
    "kernelspec": {
      "display_name": "Python 3 (ipykernel)",
      "language": "python",
      "name": "python3"
    },
    "language_info": {
      "codemirror_mode": {
        "name": "ipython",
        "version": 3
      },
      "file_extension": ".py",
      "mimetype": "text/x-python",
      "name": "python",
      "nbconvert_exporter": "python",
      "pygments_lexer": "ipython3",
      "version": "3.9.10"
    }
  },
  "nbformat": 4,
  "nbformat_minor": 0
}