Preprocess.ipynb

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    "<a href=\"https://colab.research.google.com/github/UriNeri/ColabScan/blob/main/ColabScan.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
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   "source": [
    "# Preprocess!\n",
    "Creates the HMM collection and posts it somewhere (this repo for now).  \n",
    "Simple Workflow - download all data (various RNA virus resources NeoRdRp, RVMT, RdRp-Scan, PalmDB... more to come?), bundles them, maybe deduplicates, and builds an hmmdb (+ in the future maybe mmseqsdb +blastdb + whatever?). Eventually the last step would be periodical/on-change deposit in a continous Zenodo repo for archivability/reproducibilty and versioning.  \n",
    "See the [README](https://github.com/UriNeri/ColabScan/blob/main/README.md) for more details"
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   "source": [
    "## Enviroment setup\n",
    "First, we need to install the dependencies required. If you are a wizard and know your way around you might want to modify to following block...\n"
   ]
  },
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      "hmmer-3.3.2/documentation/userguide/inclusions/hmmc2_2.out\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/jackhmmer-hbb-uniprot.out7\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/hit-serialize.pdf\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/hmmscan-minifam-sevenless.out2\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/hmmsearch-globins.out2\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/alidisplay-serialize.ai\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/hmmsearch-globins.out3\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/hmmscan-minifam-sevenless.out3\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/hmmbuild-made1.out\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/jackhmmer-hbb-uniprot.out6\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/globins4.sto\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/Makefile.in\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/gen-inclusions.py\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/hmmsearch-fn3-sevenless.out\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/hmmc2.out\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/sevenless_domains.out\n",
      "hmmer-3.3.2/documentation/userguide/inclusions/hmmpgmd-search-stats-serialize.ai\n",
      "hmmer-3.3.2/documentation/man/nhmmscan.man.in\n",
      "hmmer-3.3.2/documentation/man/phmmer.man.in\n",
      "hmmer-3.3.2/documentation/man/makehmmerdb.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmconvert.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmalign.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmpgmd.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmstat.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmc2.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmpgmd_shard.man.in\n",
      "hmmer-3.3.2/documentation/man/alimask.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmpress.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmfetch.man.in\n",
      "hmmer-3.3.2/documentation/man/nhmmer.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmsearch.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmer.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmsim.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmlogo.man.in\n",
      "hmmer-3.3.2/documentation/man/jackhmmer.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmbuild.man.in\n",
      "hmmer-3.3.2/documentation/man/hmmemit.man.in\n",
      "hmmer-3.3.2/documentation/man/Makefile.in\n",
      "hmmer-3.3.2/documentation/man/hmmscan.man.in\n",
      "\n",
      "\n",
      "HMMER configuration:\n",
      "   compiler:             gcc -O3   -pthread \n",
      "   host:                 x86_64-pc-linux-gnu\n",
      "   linker:               \n",
      "   libraries:              \n",
      "   DP implementation:    sse\n",
      "\n",
      "Now do 'make'  to build HMMER, and optionally:\n",
      "       'make check'  to run self tests,\n",
      "       'make install'  to install programs and man pages,\n",
      "       '(cd easel; make install)'  to install Easel tools.\n",
      "\n",
      "     SUBDIR easel\n",
      "     CC easel.o\n",
      "     CC esl_alloc.o\n",
      "     CC esl_alphabet.o\n",
      "     CC esl_arr2.o\n",
      "     CC esl_arr3.o\n",
      "     CC esl_bitfield.o\n",
      "     CC esl_buffer.o\n",
      "     CC esl_cluster.o\n",
      "     CC esl_composition.o\n",
      "     CC esl_cpu.o\n",
      "     CC esl_dirichlet.o\n",
      "     CC esl_distance.o\n",
      "     CC esl_dmatrix.o\n",
      "     CC esl_dsqdata.o\n",
      "     CC esl_exponential.o\n",
      "     CC esl_fileparser.o\n",
      "     CC esl_gamma.o\n",
      "     CC esl_gencode.o\n",
      "     CC esl_getopts.o\n",
      "     CC esl_gev.o\n",
      "     CC esl_graph.o\n",
      "     CC esl_gumbel.o\n",
      "     CC esl_heap.o\n",
      "     CC esl_histogram.o\n",
      "     CC esl_hmm.o\n",
      "     CC esl_huffman.o\n",
      "     CC esl_hyperexp.o\n",
      "     CC esl_json.o\n",
      "     CC esl_keyhash.o\n",
      "     CC esl_matrixops.o\n",
      "     CC esl_mem.o\n",
      "     CC esl_minimizer.o\n",
      "     CC esl_mixdchlet.o\n",
      "     CC esl_mixgev.o\n",
      "     CC esl_mpi.o\n",
      "     CC esl_msa.o\n",
      "     CC esl_msacluster.o\n",
      "     CC esl_msafile.o\n",
      "     CC esl_msafile2.o\n",
      "     CC esl_msafile_a2m.o\n",
      "     CC esl_msafile_afa.o\n",
      "     CC esl_msafile_clustal.o\n",
      "     CC esl_msafile_phylip.o\n",
      "     CC esl_msafile_psiblast.o\n",
      "     CC esl_msafile_selex.o\n",
      "     CC esl_msafile_stockholm.o\n",
      "     CC esl_msashuffle.o\n",
      "     CC esl_msaweight.o\n",
      "     CC esl_normal.o\n",
      "     CC esl_paml.o\n",
      "     CC esl_quicksort.o\n",
      "     CC esl_random.o\n",
      "     CC esl_rand64.o\n",
      "     CC esl_randomseq.o\n",
      "     CC esl_ratematrix.o\n",
      "     CC esl_recorder.o\n",
      "     CC esl_red_black.o\n",
      "     CC esl_regexp.o\n",
      "     CC esl_rootfinder.o\n",
      "     CC esl_scorematrix.o\n",
      "     CC esl_sq.o\n",
      "     CC esl_sqio.o\n",
      "     CC esl_sqio_ascii.o\n",
      "     CC esl_sqio_ncbi.o\n",
      "     CC esl_ssi.o\n",
      "     CC esl_stack.o\n",
      "     CC esl_stats.o\n",
      "     CC esl_stopwatch.o\n",
      "     CC esl_stretchexp.o\n",
      "     CC esl_subcmd.o\n",
      "     CC esl_threads.o\n",
      "     CC esl_tree.o\n",
      "     CC esl_varint.o\n",
      "     CC esl_vectorops.o\n",
      "     CC esl_weibull.o\n",
      "     CC esl_workqueue.o\n",
      "     CC esl_wuss.o\n",
      "     CC esl_sse.o\n",
      "     CC esl_avx.o\n",
      "     CC esl_avx512.o\n",
      "     CC esl_neon.o\n",
      "     CC esl_vmx.o\n",
      "     AR libeasel.a\n",
      "     SUBDIR miniapps\n",
      "     GEN esl-afetch\n",
      "     GEN esl-alimanip\n",
      "     GEN esl-alimap\n",
      "     GEN esl-alimask\n",
      "     GEN esl-alimerge\n",
      "     GEN esl-alipid\n",
      "     GEN esl-alirev\n",
      "     GEN esl-alistat\n",
      "     GEN esl-compalign\n",
      "     GEN esl-compstruct\n",
      "     GEN esl-construct\n",
      "     GEN esl-histplot\n",
      "     GEN esl-mask\n",
      "     GEN esl-mixdchlet\n",
      "     GEN esl-reformat\n",
      "     GEN esl-selectn\n",
      "     GEN esl-seqrange\n",
      "     GEN esl-seqstat\n",
      "     GEN esl-sfetch\n",
      "     GEN esl-shuffle\n",
      "     GEN esl-ssdraw\n",
      "     GEN esl-translate\n",
      "     GEN esl-weight\n",
      "     CC cmd_alistat.o\n",
      "     CC cmd_downsample.o\n",
      "     CC cmd_filter.o\n",
      "     CC cmd_index.o\n",
      "     GEN easel\n",
      "     SUBDIR libdivsufsort\n",
      "     CC divsufsort.o\n",
      "     AR libdivsufsort.a\n",
      "     SUBDIR src\n",
      "     CC alimask.o\n",
      "     CC build.o\n",
      "     CC cachedb.o\n",
      "     CC cachedb_shard.o\n",
      "     CC emit.o\n",
      "     CC errors.o\n",
      "     CC evalues.o\n",
      "     CC eweight.o\n",
      "     CC generic_decoding.o\n",
      "     CC generic_fwdback.o\n",
      "     CC generic_fwdback_chk.o\n",
      "     CC generic_fwdback_banded.o\n",
      "     CC generic_null2.o\n",
      "     CC generic_msv.o\n",
      "     CC generic_optacc.o\n",
      "     CC generic_stotrace.o\n",
      "     CC generic_viterbi.o\n",
      "     CC generic_vtrace.o\n",
      "     CC h2_io.o\n",
      "     CC heatmap.o\n",
      "     CC hmmlogo.o\n",
      "     CC hmmdmstr.o\n",
      "     CC hmmdmstr_shard.o\n",
      "     CC hmmd_search_status.o\n",
      "     CC hmmdwrkr.o\n",
      "     CC hmmdwrkr_shard.o\n",
      "     CC hmmdutils.o\n",
      "     CC hmmer.o\n",
      "     CC logsum.o\n",
      "     CC modelconfig.o\n",
      "     CC modelstats.o\n",
      "     CC mpisupport.o\n",
      "     CC seqmodel.o\n",
      "     CC tracealign.o\n",
      "     CC p7_alidisplay.o\n",
      "     CC p7_bg.o\n",
      "     CC p7_builder.o\n",
      "     CC p7_domain.o\n",
      "     CC p7_domaindef.o\n",
      "     CC p7_gbands.o\n",
      "     CC p7_gmx.o\n",
      "     CC p7_gmxb.o\n",
      "     CC p7_gmxchk.o\n",
      "     CC p7_hit.o\n",
      "     CC p7_hmm.o\n",
      "     CC p7_hmmcache.o\n",
      "     CC p7_hmmd_search_stats.o\n",
      "     CC p7_hmmfile.o\n",
      "     CC p7_hmmwindow.o\n",
      "     CC p7_pipeline.o\n",
      "     CC p7_prior.o\n",
      "     CC p7_profile.o\n",
      "     CC p7_spensemble.o\n",
      "     CC p7_tophits.o\n",
      "     CC p7_trace.o\n",
      "     CC p7_scoredata.o\n",
      "     CC hmmpgmd2msa.o\n",
      "     CC fm_alphabet.o\n",
      "     CC fm_general.o\n",
      "     CC fm_sse.o\n",
      "     CC fm_ssv.o\n",
      "     AR libhmmer-src.stamp\n",
      "     SUBDIR impl_sse\n",
      "     CC decoding.o\n",
      "     CC fwdback.o\n",
      "     CC io.o\n",
      "     CC ssvfilter.o\n",
      "     CC msvfilter.o\n",
      "     CC null2.o\n",
      "     CC optacc.o\n",
      "     CC stotrace.o\n",
      "     CC vitfilter.o\n",
      "     CC p7_omx.o\n",
      "     CC p7_oprofile.o\n",
      "     CC mpi.o\n",
      "     AR libhmmer-impl.stamp\n",
      "     GEN alimask\n",
      "     CC hmmalign.o\n",
      "     GEN hmmalign\n",
      "     CC hmmbuild.o\n",
      "     GEN hmmbuild\n",
      "     CC hmmconvert.o\n",
      "     GEN hmmconvert\n",
      "     CC hmmemit.o\n",
      "     GEN hmmemit\n",
      "     CC hmmfetch.o\n",
      "     GEN hmmfetch\n",
      "     GEN hmmlogo\n",
      "     CC hmmpgmd.o\n",
      "     GEN hmmpgmd\n",
      "     CC hmmpgmd_shard.o\n",
      "     GEN hmmpgmd_shard\n",
      "     CC hmmpress.o\n",
      "     GEN hmmpress\n",
      "     CC hmmscan.o\n",
      "     GEN hmmscan\n",
      "     CC hmmsearch.o\n",
      "     GEN hmmsearch\n",
      "     CC hmmsim.o\n",
      "     GEN hmmsim\n",
      "     CC hmmstat.o\n",
      "     GEN hmmstat\n",
      "     CC jackhmmer.o\n",
      "     GEN jackhmmer\n",
      "     CC phmmer.o\n",
      "     GEN phmmer\n",
      "     CC nhmmer.o\n",
      "     GEN nhmmer\n",
      "     CC nhmmscan.o\n",
      "     GEN nhmmscan\n",
      "     CC makehmmerdb.o\n",
      "     GEN makehmmerdb\n",
      "     CC hmmc2.o\n",
      "     GEN hmmc2\n",
      "     CC hmmerfm-exactmatch.o\n",
      "     GEN hmmerfm-exactmatch\n",
      "     SUBDIR profmark\n",
      "     CC create-profmark.o\n",
      "     GEN create-profmark\n",
      "     CC rocplot.o\n",
      "     GEN rocplot\n",
      "     SUBDIR easel\n",
      "     SUBDIR miniapps\n",
      "     SUBDIR libdivsufsort\n",
      "     SUBDIR src\n",
      "     SUBDIR impl_sse\n",
      "     SUBDIR profmark\n",
      "/usr/bin/install -c -d /usr/local/bin\n",
      "/usr/bin/install -c -d /usr/local/share/man/man1\n",
      "make -C src install\n",
      "make[1]: Entering directory '/home/neri/work/ColabScan/bin/hmmer-3.3.2/src'\n",
      "for file in alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer nhmmer nhmmscan makehmmerdb; do \\\n",
      "   /usr/bin/install -c -m 0755 $file /usr/local/bin/ ;\\\n",
      "done\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/usr/bin/install: cannot create regular file '/usr/local/bin/alimask': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmalign': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmbuild': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmconvert': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmemit': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmfetch': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmlogo': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmpgmd': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmpgmd_shard': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmpress': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmscan': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmsearch': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmsim': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/hmmstat': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/jackhmmer': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/phmmer': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/nhmmer': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/nhmmscan': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/makehmmerdb': Permission denied\n",
      "make[1]: *** [Makefile:343: install] Error 1\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "make[1]: Leaving directory '/home/neri/work/ColabScan/bin/hmmer-3.3.2/src'\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "make: *** [Makefile:135: install] Error 2\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "checking for a BSD-compatible install... /usr/bin/install -c\n",
      "checking whether build environment is sane... yes\n",
      "checking for a race-free mkdir -p... /usr/bin/mkdir -p\n",
      "checking for gawk... gawk\n",
      "checking whether make sets $(MAKE)... yes\n",
      "checking whether make supports nested variables... yes\n",
      "checking whether ln -s works... yes\n",
      "checking that generated files are newer than configure... done\n",
      "configure: creating ./config.status\n",
      "config.status: creating Makefile\n",
      "config.status: creating src/Makefile\n",
      "config.status: creating config.h\n",
      "Making all in src\n",
      "Making install in src\n",
      "make[1]: Entering directory '/home/neri/work/ColabScan/bin/parallel-20230622/src'\n",
      "make[2]: Entering directory '/home/neri/work/ColabScan/bin/parallel-20230622/src'\n",
      " /usr/bin/mkdir -p '/usr/local/bin'\n",
      " /usr/bin/install -c parallel sql niceload parcat parset parsort env_parallel env_parallel.ash env_parallel.bash env_parallel.csh env_parallel.dash env_parallel.fish env_parallel.ksh env_parallel.mksh env_parallel.pdksh env_parallel.sh env_parallel.tcsh env_parallel.zsh '/usr/local/bin'\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/usr/bin/install: cannot create regular file '/usr/local/bin/parallel': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/sql': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/niceload': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/parcat': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/parset': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/parsort': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/env_parallel': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/env_parallel.ash': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/env_parallel.bash': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/env_parallel.csh': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/env_parallel.dash': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/env_parallel.fish': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/env_parallel.ksh': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/env_parallel.mksh': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/env_parallel.pdksh': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/env_parallel.sh': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/env_parallel.tcsh': Permission denied\n",
      "/usr/bin/install: cannot create regular file '/usr/local/bin/env_parallel.zsh': Permission denied\n",
      "make[2]: *** [Makefile:321: install-binSCRIPTS] Error 1\n",
      "make[1]: *** [Makefile:513: install-am] Error 2\n",
      "make: *** [Makefile:353: install-recursive] Error 1\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "make[2]: Leaving directory '/home/neri/work/ColabScan/bin/parallel-20230622/src'\n",
      "make[1]: Leaving directory '/home/neri/work/ColabScan/bin/parallel-20230622/src'\n",
      "Requirement already satisfied: itables in /home/neri/work/miniconda3/lib/python3.10/site-packages (1.5.3)\n",
      "Requirement already satisfied: numpy in /home/neri/work/miniconda3/lib/python3.10/site-packages (from itables) (1.24.3)\n",
      "Requirement already satisfied: pandas in /home/neri/work/miniconda3/lib/python3.10/site-packages (from itables) (2.0.2)\n",
      "Requirement already satisfied: IPython in /home/neri/work/miniconda3/lib/python3.10/site-packages (from itables) (8.14.0)\n",
      "Requirement already satisfied: decorator in /home/neri/work/miniconda3/lib/python3.10/site-packages (from IPython->itables) (5.1.1)\n",
      "Requirement already satisfied: pickleshare in /home/neri/work/miniconda3/lib/python3.10/site-packages (from IPython->itables) (0.7.5)\n",
      "Requirement already satisfied: jedi>=0.16 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from IPython->itables) (0.18.2)\n",
      "Requirement already satisfied: stack-data in /home/neri/work/miniconda3/lib/python3.10/site-packages (from IPython->itables) (0.6.2)\n",
      "Requirement already satisfied: matplotlib-inline in /home/neri/work/miniconda3/lib/python3.10/site-packages (from IPython->itables) (0.1.6)\n",
      "Requirement already satisfied: pexpect>4.3 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from IPython->itables) (4.8.0)\n",
      "Requirement already satisfied: prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30 in /home/neri/.local/lib/python3.10/site-packages (from IPython->itables) (3.0.38)\n",
      "Requirement already satisfied: pygments>=2.4.0 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from IPython->itables) (2.15.0)\n",
      "Requirement already satisfied: backcall in /home/neri/work/miniconda3/lib/python3.10/site-packages (from IPython->itables) (0.2.0)\n",
      "Requirement already satisfied: traitlets>=5 in /home/neri/.local/lib/python3.10/site-packages (from IPython->itables) (5.8.1)\n",
      "Requirement already satisfied: pytz>=2020.1 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from pandas->itables) (2023.3)\n",
      "Requirement already satisfied: python-dateutil>=2.8.2 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from pandas->itables) (2.8.2)\n",
      "Requirement already satisfied: tzdata>=2022.1 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from pandas->itables) (2023.3)\n",
      "Requirement already satisfied: parso<0.9.0,>=0.8.0 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from jedi>=0.16->IPython->itables) (0.8.3)\n",
      "Requirement already satisfied: ptyprocess>=0.5 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from pexpect>4.3->IPython->itables) (0.7.0)\n",
      "Requirement already satisfied: wcwidth in /home/neri/.local/lib/python3.10/site-packages (from prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30->IPython->itables) (0.2.6)\n",
      "Requirement already satisfied: six>=1.5 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas->itables) (1.16.0)\n",
      "Requirement already satisfied: pure-eval in /home/neri/work/miniconda3/lib/python3.10/site-packages (from stack-data->IPython->itables) (0.2.2)\n",
      "Requirement already satisfied: executing>=1.2.0 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from stack-data->IPython->itables) (1.2.0)\n",
      "Requirement already satisfied: asttokens>=2.1.0 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from stack-data->IPython->itables) (2.2.1)\n",
      "Requirement already satisfied: pandas in /home/neri/work/miniconda3/lib/python3.10/site-packages (2.0.2)\n",
      "Requirement already satisfied: pytz>=2020.1 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from pandas) (2023.3)\n",
      "Requirement already satisfied: tzdata>=2022.1 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from pandas) (2023.3)\n",
      "Requirement already satisfied: numpy>=1.21.0 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from pandas) (1.24.3)\n",
      "Requirement already satisfied: python-dateutil>=2.8.2 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from pandas) (2.8.2)\n",
      "Requirement already satisfied: six>=1.5 in /home/neri/work/miniconda3/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas) (1.16.0)\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "mkdir bin\n",
    "cd bin \n",
    "wget https://github.com/shenwei356/seqkit/releases/download/v2.4.0/seqkit_linux_amd64.tar.gz --quiet\n",
    "tar -zxvf  seqkit_linux_amd64.tar.gz\n",
    "\n",
    "wget http://eddylab.org/software/hmmer/hmmer.tar.gz --quiet\n",
    "tar -zxvf hmmer.tar.gz\n",
    "cd hmmer-3.3.2\n",
    "./configure --silent\n",
    "make --silent\n",
    "make install\n",
    "\n",
    "cd ..\n",
    "wget https://ftpmirror.gnu.org/parallel/parallel-latest.tar.bz2 --quiet\n",
    "tar -xf parallel-latest.tar.bz2\n",
    "cd parallel-20230622/\n",
    "./configure\n",
    "make --silent\n",
    "make install\n",
    "\n",
    "cd ..\n",
    "\n",
    "pip install itables\n",
    "pip install pandas\n",
    "pip install multiprocessing\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Binary workaround \n",
    "Becuase for the life of me it seems variables are lost between blocks except for the python codeblocks/kernal, we'll add the above installed binaries directly from Python.  \n",
    "If it was up to me, this was a single bash script, but notebook helps people..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    },
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/neri/work/miniconda3/bin:/home/neri/work/miniconda3/condabin:/home/neri/bin:/home/neri/Documents/mmseqs/bin:/home/neri/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/var/lib/flatpak/exports/bin:/usr/lib/jvm/default/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/home/neri/stl/prefix:/home/neri/work/ColabScan/bin/:/home/neri/work/ColabScan/bin/:/home/neri/work/ColabScan/bin/hmmer-3.3.2/src/:/home/neri/work/ColabScan/bin/parallel-20230622/src/:/home/neri/work/ColabScan/bin/:/home/neri/work/ColabScan/bin/hmmer-3.3.2/src/:/home/neri/work/ColabScan/bin/parallel-20230622/src/\n"
     ]
    }
   ],
   "source": [
    "import os as os\n",
    "\n",
    "os.environ['PATH'] = os.environ['PATH']+\":\"+os.getcwd()+\"/bin/\"\n",
    "os.environ['PATH'] = os.environ['PATH']+\":\"+os.getcwd()+\"/bin/hmmer-3.3.2/src/\"\n",
    "os.environ['PATH'] = os.environ['PATH']+\":\"+os.getcwd()+\"/bin/parallel-20230622/src/\"\n",
    "print(os.environ['PATH'])\n",
    "os.environ['USE_parallel'] = \"FALSE\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Multithreading (optional - not yet implemented!)\n",
    "It is possible to speed things up by parallelizing some tasks. This only applies to running the notebook locally. If you want to go ahead with this, run the following code block, which will download [GNU parallel](https://www.gnu.org/software/parallel/) and set an enviromental variables `THREADS` which would use all available cores minus one (you can manually change this if you want).\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "from multiprocessing import cpu_count\n",
    "import os as os\n",
    "os.environ['THREADS'] = str(cpu_count() - 1)\n",
    "os.environ['USE_parallel'] = \"TRUE\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "# %%bash\n",
    "# THREADS=$(grep -c ^processor /proc/cpuinfo)\n",
    "# THREADS=$((THREADS -1))\n",
    "# echo $THREADS"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "Qwjxkg0uwbVg"
   },
   "source": [
    "## Data fetching\n",
    "Next we're gonna fetch several public resources (RdRp-scan, NeoRdRp, RVMT, and hopefully more in the future). If possible we'll download the MSA files and create the pHMMs from scratch, using the same version of hmmer.\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "collapsed": true,
    "id": "td5dYDSswX2-",
    "jupyter": {
     "outputs_hidden": true
    },
    "outputId": "708b8f6b-fbce-415d-80df-0a4f7404ae16",
    "tags": []
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mkdir: cannot create directory ‘DBs’: File exists\n",
      "Cloning into 'RdRp-scan'...\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Archive:  TSA_Olendraite.zip\n",
      "  inflating: Zhaovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Zetaarterivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Yuyuevirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Zybavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Yanvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Wumivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Wubeivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Umbravirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Varicosavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Zeavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Waikavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Vesivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Vitivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Yingvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Wuhivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Wastrivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Weivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Vesiculovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Tritimovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Torradovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Torovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Trichomonasvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Torchivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Tymovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Victorivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Tupavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Trichovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Totivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Tombusvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Teschovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Thogotovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Tenuivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Velarivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Thottimvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Triatovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Tobamovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sripuvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Tremovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Socyvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Striwavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sogarnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sprivivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sopolycivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sunshinevirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Thetaarterivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Tobravirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Tapwovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Tiruvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sclerotimonavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Shanbavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Shangavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sinaivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sapelovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Senecavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Scleroulivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Salovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sapovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sequivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Tepovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Salivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Rymovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Rubivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Rotavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sobemovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Shaspivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Recovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Robigovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sakobuvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Rosavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Salemvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Roymovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Respirovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Tibrovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sicinivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Prunevirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Reptarenavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sigmavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Seadornavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Rafivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Quadrivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Pregotovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sclerodarnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Quaranjavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Platypuvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Pomovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Salisharnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Poacevirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Potyvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Phytoreovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Potexvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Potamipivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Pidchovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Phlebovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Phasivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Passerivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Pacuvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Sadwavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Picobirnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Peropuvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Pestivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Pelarspovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Pegivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Rabovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orthorubulavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Pararubulavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orthotospovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orthophasmavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Oryzavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Parechovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Posavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Ourmiavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orthohepevirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orthonairovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Piscihepevirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Polerovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orthopneumovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orthobornavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Pecluvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orthohantavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Ophiovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Perhabdovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orthobunyavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Nyavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Okavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Paraavulavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Narmovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Nucleorhabdovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Mycoreovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Oleavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Nyfulvavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Panicovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orbivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Omegatetravirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Mosavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Oscivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Mobuvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orthoreovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Mycoflexivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Mivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Novirhabdovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orthoavulavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Orinovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Oncotshavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Mitovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Metaavulavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Nepovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Mischivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Norovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Marafivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Pasivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Marburgvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Megabirnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Magoulivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Machlomovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Lyssavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Narnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Nebovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Lolavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Nacovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Morbillivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Minovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Mobatvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Leishmaniavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Levivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Lagovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Macluravirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Negevirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Maculavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Mamastrovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Luteovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Metapneumovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Megrivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Marnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Ledantevirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Mandarivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Ipomovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Kunsagivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Invictavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Iflavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Higrevirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Isavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Hypovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Idaeovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Hunnivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Herbevirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Hepatovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Gammapartitivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Harkavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Hudovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Hudivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Gammacoronavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Husavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Kabutovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Livupivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Locarnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Mammarenavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Limnipivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Jeilongvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Jonvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Inshuvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Kobuvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Kappaarterivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Hubavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Giardiavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Hapavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Gammacarmovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Gammainfluenzavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Gallantivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Ferlavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Entomobirnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Epsilonarterivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Hepacivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Goukovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Erbovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Dianthovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Labyrnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Goravirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Hartmanivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Deltacoronavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Cypovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Lincruvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Ilarvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Fisavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Gallivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Fesavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Divavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Dinovernavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Enterovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Flavivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Henipavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Fabavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Emaravirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Dinornavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Cystovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Fijivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Ephemerovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Deltapartitivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Deltaflexivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Cryspovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Cucumovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Curiovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Cosavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Chordovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Horwuvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Deltaarterivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Cytorhabdovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Enamovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Crustavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Cripavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Chengtivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Chipolycivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Coltivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Comovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Hordeivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Feravirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Botybirnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Caligrhavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Bromovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Foveavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Botoulivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Furovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Ebolavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Deltainfluenzavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Dicipivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Cuevavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Capillovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Cilevirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Cheravirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Brambyvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Bostovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Dichorhavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Betanecrovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Betatetravirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Crohivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Betacoronavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Betaendornavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Crinivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Carbovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Betapartitivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Bopivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Betaarterivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Coguvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Closterovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Cardiovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Centovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Bacillarnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Betainfluenzavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Bafinivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Citrivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Beidivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Bevemovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Carlavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Betachrysovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Betacarmovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Benyvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Bymovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Betanodavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Berhavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Arlivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Botrexvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Aureusvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Bavovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Avibirnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Anulavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Aquaparamyxovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Aquamavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Ampivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Avihepatovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Aquabirnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Blunervirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphapermutotetravirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Aphthovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Aquareovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Ampelovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Aparavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Anphevirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Blosnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Avisivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphaendornavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Amalgavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Almendravirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphacoronavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Barnavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphaarterivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Aalivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alfamovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Avastrovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Banyangvirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Allolevivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Allexivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphachrysovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Avenavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphapartitivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphanemrhavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphainfluenzavirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphamesonivirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphanecrovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphacarmovirus_consensusadded.c090.fasta.sto  \n",
      "  inflating: Alphanodavirus_consensusadded.c090.fasta.sto  \n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "mkdir DBs\n",
    "cd DBs\n",
    "\n",
    "# NeoRdRp\n",
    "wget https://github.com/shoichisakaguchi/NeoRdRp/raw/main/NeoRdRp-HMM.v1.1.hmm.gz  --quiet\n",
    "gzip -d NeoRdRp-HMM.v1.1.hmm.gz\n",
    "sed  -e '/^NAME/s/$/_NeoRdRp/' NeoRdRp-HMM.v1.1.hmm -i # add NeoRdRp suffix to each profile\n",
    "\n",
    "# RdRp-scan\n",
    "git clone --recursive https://github.com/JustineCharon/RdRp-scan\n",
    "cd RdRp-scan\n",
    "mkdir RdRp-scan_HMMs\n",
    "cd Profile_db_and_alignments\n",
    "for alignm_file in ./ALL_NCBI_Palmdb_RdRp.*.fasta.CLUSTALO\n",
    "do\n",
    "ali_name=$(basename $alignm_file .fasta.CLUSTALO)\n",
    "ali_name=$(echo $ali_name | cut -d \".\" -f2)\n",
    "hmmbuild  -n \"$ali_name\"_RdRp-scan  -o /dev/null ../RdRp-scan_HMMs/\"$ali_name\".hmm $alignm_file\n",
    "done\n",
    "\n",
    "for alignm_file in ./ALL_FINAL_RdRp_cores_0.3.*.fasta.CLUSTALO\n",
    "do\n",
    "ali_name=$(basename $alignm_file .fasta.CLUSTALO)\n",
    "ali_name=$(echo $ali_name | cut -d \".\" -f3)\n",
    "hmmbuild  -n \"$ali_name\"_RdRp-scan  -o /dev/null ../RdRp-scan_HMMs/\"$ali_name\".hmm $alignm_file\n",
    "# parallel -j\"$THREADS\" hmmbuild --informat a2m -n {/.} -o /dev/null ../HMMfiles/{/.}\".hmm\" {} ::: ./*.msa.Cons.msa.afa\n",
    "\n",
    "done\n",
    "cd ../RdRp-scan_HMMs/\n",
    "cat ./*hmm  > ../RdRp-scan.hmm\n",
    "cd ..\n",
    "cd ..\n",
    "\n",
    "\n",
    "\n",
    "# RVMT\n",
    "### wget https://zenodo.org/record/7368133/files/RVMT_Zenodo_V4.zip?download=1\n",
    "# *too big, download would take 4 hours, going to improvise:\n",
    "wget https://portal.nersc.gov/dna/microbial/prokpubs/Riboviria/RiboV1.4/Alignments/zip.ali.220515.tgz  --quiet\n",
    "tar -zxf zip.ali.220515.tgz\n",
    "mkdir RVMT_HMMs\n",
    "\n",
    "for ali_folder in ./ali.*\n",
    "do\n",
    "cd $ali_folder\n",
    "for alignm_file in ./*.FASTA\n",
    "do\n",
    "ali_name=$(basename $alignm_file .FASTA)\n",
    "hmmbuild  -n \"$ali_name\"_RVMT  -o /dev/null ../RVMT_HMMs/\"$ali_name\".hmm $alignm_file\n",
    "done\n",
    "cd ..\n",
    "done\n",
    "cd RVMT_HMMs\n",
    "cat ./*hmm  > ../RVMT.hmm\n",
    "cd ..\n",
    "\n",
    "\n",
    "# TSA_Olendraite\n",
    "## used gdrive/manual to fetch from Google Drive: https://drive.google.com/drive/folders/12rfwCDNROm-kwPRjlVOsSCzp-Gs7-wQq\n",
    "## Will include the zip of ^ for prosperity...\n",
    "mkdir TSA_Olendraite\n",
    "cp TSA_Olendraite.zip TSA_Olendraite/TSA_Olendraite.zip\n",
    "cd TSA_Olendraite\n",
    "unzip TSA_Olendraite.zip\n",
    "mkdir TSA_Olendraite_HMMs\n",
    "for alignm_file in ./*.sto\n",
    "do\n",
    "ali_name=$(basename $alignm_file _consensusadded.c090.fasta.sto)\n",
    "hmmbuild  -n \"$ali_name\"_TSA_Olendraite  -o /dev/null ./TSA_Olendraite_HMMs/\"$ali_name\".hmm $alignm_file\n",
    "done\n",
    "cd TSA_Olendraite_HMMs\n",
    "cat ./*hmm  > ../TSA_Olendraite.hmm\n",
    "cd .."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Cleanup\n",
    "Next we'll concatenate th HMM sets by the hmmer version used to create them.  \n",
    "We'll also remove some intermideary files and what not...\n",
    "Finally we'll write a \"watermark\" - text file with the date and version of the script we used (going by commit?)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mv: cannot stat './RdRp-scan/RdRp-scan.hmm': No such file or directory\n",
      "mv: cannot stat 'TSA_Olendraite/TSA_Olendraite.hmm': No such file or directory\n",
      "rm: cannot remove 'zip.ali.*': No such file or directory\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "cd DBs\n",
    "mv ./RdRp-scan/RdRp-scan.hmm RdRp-scan.hmm\n",
    "mv TSA_Olendraite/TSA_Olendraite.hmm TSA_Olendraite.hmm\n",
    "rm ./RdRp-scan/ -rf\n",
    "\n",
    "rm ali* -rf\n",
    "rm TSA_Olendraite -rf\n",
    "rm zip.ali.*\n",
    "\n",
    "rm RVMT_HMMs -rf\n",
    "\n",
    "cat RdRp-scan.hmm RVMT.hmm TSA_Olendraite.hmm > Colab_RdRp_hmmer_3.2.2.hmm\n",
    "# hmmpress Colab_RdRp_hmmer_3.2.2.hmm\n",
    "bzip2 -z Colab_RdRp_hmmer_3.2.2.hmm\n",
    "bzip2 -z NeoRdRp-HMM.v1.1.hmm\n",
    "bzip2 -z TSA_Olendraite.hmm\n",
    "bzip2 -z RVMT.hmm\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "colab": {
   "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": "3.10.8"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}