reply_to_biostars_9500386

reply_to_biostars_9500386.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Reply to biostars https://www.biostars.org/p/9500386/\n",
    "\n",
    "reply to https://www.biostars.org/p/9500386/"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Biopython already present in launches from this repo."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
      "                                 Dload  Upload   Total   Spent    Left  Speed\n",
      "100   886  100   886    0     0   4789      0 --:--:-- --:--:-- --:--:--  4789\n"
     ]
    }
   ],
   "source": [
    "# Get example sequences\n",
    "!mv ../data/S288C_YMR054W_STV1_protein.fsa .\n",
    "!curl -o S288C_YOR270C_VPH1_protein.fsa https://gist.githubusercontent.com/fomightez/f46b0624f1d8e3abb6ff908fc447e63b/raw/7ef7cfdaa2c9f9974f22fd60be3cfe7d1935cd86/ux_S288C_YOR270C_VPH1_protein.fsa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# contcatenate into FASTA files into one multi-entry FASTA\n",
    "!cat S288C_YMR054W_STV1_protein.fsa <(echo) S288C_YOR270C_VPH1_protein.fsa > seqs.fasta\n",
    "# adding space between them is based on https://stackoverflow.com/a/23549826/8508004 ; contrast with\n",
    "#!cat S288C_YMR054W_STV1_protein.fsa S288C_YOR270C_VPH1_protein.fsa > seqs.fasta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Collecting package metadata (current_repodata.json): done\n",
      "Solving environment: done\n",
      "\n",
      "\n",
      "==> WARNING: A newer version of conda exists. <==\n",
      "  current version: 4.9.2\n",
      "  latest version: 4.11.0\n",
      "\n",
      "Please update conda by running\n",
      "\n",
      "    $ conda update -n base conda\n",
      "\n",
      "\n",
      "\n",
      "## Package Plan ##\n",
      "\n",
      "  environment location: /srv/conda/envs/notebook\n",
      "\n",
      "  added / updated specs:\n",
      "    - clustalo\n",
      "\n",
      "\n",
      "The following packages will be downloaded:\n",
      "\n",
      "    package                    |            build\n",
      "    ---------------------------|-----------------\n",
      "    argtable2-2.13             |    h14c3975_1001         2.7 MB  conda-forge\n",
      "    ca-certificates-2021.10.8  |       ha878542_0         139 KB  conda-forge\n",
      "    certifi-2021.10.8          |   py37h89c1867_1         145 KB  conda-forge\n",
      "    clustalo-1.2.4             |       h1b792b2_4         313 KB  bioconda\n",
      "    ------------------------------------------------------------\n",
      "                                           Total:         3.3 MB\n",
      "\n",
      "The following NEW packages will be INSTALLED:\n",
      "\n",
      "  argtable2          conda-forge/linux-64::argtable2-2.13-h14c3975_1001\n",
      "  clustalo           bioconda/linux-64::clustalo-1.2.4-h1b792b2_4\n",
      "\n",
      "The following packages will be UPDATED:\n",
      "\n",
      "  ca-certificates                      2021.5.30-ha878542_0 --> 2021.10.8-ha878542_0\n",
      "  certifi                          2021.5.30-py37h89c1867_0 --> 2021.10.8-py37h89c1867_1\n",
      "\n",
      "\n",
      "\n",
      "Downloading and Extracting Packages\n",
      "certifi-2021.10.8    | 145 KB    | ##################################### | 100% \n",
      "argtable2-2.13       | 2.7 MB    | ##################################### | 100% \n",
      "ca-certificates-2021 | 139 KB    | ##################################### | 100% \n",
      "clustalo-1.2.4       | 313 KB    | ##################################### | 100% \n",
      "Preparing transaction: done\n",
      "Verifying transaction: done\n",
      "Executing transaction: done\n",
      "\n",
      "Note: you may need to restart the kernel to use updated packages.\n"
     ]
    }
   ],
   "source": [
    "# install clustalo\n",
    "%conda install -c bioconda clustalo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio import SeqIO\n",
    "from Bio.Align.Applications import ClustalOmegaCommandline\n",
    "clustalomega_cline = ClustalOmegaCommandline(infile=\"seqs.fasta\", outfile=\"new_alignment.aln\", verbose=True, outfmt= \"clu\",\n",
    "auto=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "clustalo -i seqs.fasta -o new_alignment.aln --outfmt clu --auto -v\n"
     ]
    }
   ],
   "source": [
    "print(clustalomega_cline)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Using 8 threads\n",
      "Read 2 sequences (type: Protein) from seqs.fasta\n",
      "not more sequences (2) than cluster-size (100), turn off mBed\n",
      "Setting options automatically based on input sequence characteristics (might overwrite some of your options).\n",
      "Auto settings: Enabling mBed.\n",
      "Auto settings: Setting iteration to 1.\n",
      "Progressive alignment progress done. CPU time: 0.11u 0.02s 00:00:00.13 Elapsed: 00:00:00\n",
      "Iteration step 1 out of 1\n",
      "Computing new guide tree (iteration step 1)\n",
      "Computing HMM from alignment\n",
      "Progressive alignment progress done. CPU time: 0.40u 0.03s 00:00:00.43 Elapsed: 00:00:00\n",
      "Alignment written to new_alignment.aln\n"
     ]
    }
   ],
   "source": [
    "!clustalo -i seqs.fasta -o new_alignment.aln --outfmt clu --auto -v"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CLUSTAL O(1.2.4) multiple sequence alignment\r\n",
      "\r\n",
      "\r\n",
      "STV1      -MNQEEAIFRSADMTYVQLYIPLEVIREVTFLLGKMSVFMVMDLNKDLTAFQRGYVNQLR\r\n",
      "VPH1      MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIR\r\n",
      "            ::********:*: **:*** *: *: :: **::.:. . ***..: **** :**::*\r\n",
      "\r\n",
      "STV1      RFDEVERMVGFLNEVVEKHAAETWKYILHIDDEGNDIAQPDMADLINTMEPLSLENVNDM\r\n",
      "VPH1      RLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGS----------GELYVPPSGSVIDDY\r\n",
      "          *:*:***   :: .:::**  : ::   .   :*.           :   * * . ::* \r\n",
      "\r\n",
      "STV1      VKEITDCESRARQLDESLDSLRSKLNDLLEQRQVIFECSKFIEVNPGIAGRATNPEIEQE\r\n",
      "VPH1      VRNASYLEERLIQMEDATDQIEVQKNDLEQYRFILQSGDE--------------------\r\n",
      "          *:: :  *.*  *:::: *.:. : *** : * :: . .:                    \r\n",
      "\r\n",
      "STV1      ERDVDEFRMTPDDISETLSDAFSFDDETPQDRGALGNDLTRNQSVEDLSFLEQGYQHRYM\r\n",
      "VPH1      ------FFLKGDN-----TDSTSYMDEDMIDAN--GENIAA-----------AIGASVNY\r\n",
      "                * :. *:     :*: *: **   * .  *::::                    \r\n",
      "\r\n",
      "STV1      ITGSIRRTKVDILNRILWRLLRGNLIFQNFPIEEPLLEGK--EKVEKDCFIIFTHGETLL\r\n",
      "VPH1      VTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFSHGDLII\r\n",
      "          :** * * **  *::****:*****:*:.. **:*: : *  *  .*:.**:*:**: ::\r\n",
      "\r\n",
      "STV1      KKVKRVIDSLNGKIVSLNT---RSSELVDTLNRQIDDLQRILDTTEQTLHTELLVIHDQL\r\n",
      "VPH1      KRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELYAIAKEL\r\n",
      "          *::::: :**:.:: .:::     *: : .:*:::.**  :*.**. **.:** .* .:*\r\n",
      "\r\n",
      "STV1      PVWSAMTKREKYVYTTLNK--FQQESQGLIAEGWVPSTELIHLQDSLKDYIETLGSEYST\r\n",
      "VPH1      DSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARLGIDVPS\r\n",
      "            *   ..*** ::  ***  :: : : ******:*  **  **  * : *  ** :  :\r\n",
      "\r\n",
      "STV1      VFNVILTNKLPPTYHRTNKFTQAFQSIVDAYGIATYKEINAGLATVVTFPFMFAIMFGDM\r\n",
      "VPH1      IIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFAIMFGDM\r\n",
      "          :::*: **: ***:******* .**** *.**** *:****** *:**************\r\n",
      "\r\n",
      "STV1      GHGFILFLMALFLVLNERKFGAMHRDEIFDMAFTGRYVLLLMGAFSVYTGLLYNDIFSKS\r\n",
      "VPH1      GHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYNDIFSKT\r\n",
      "          ****:: * ** *****:*:. *:*.***********::****.**:***:********:\r\n",
      "\r\n",
      "STV1      MTIFKSGWQWPSTFRKGESIEAKKTGVYPFGLDFAWHGTDNGLLFSNSYKMKLSILMGYA\r\n",
      "VPH1      MTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLSILMGFI\r\n",
      "          ********:**. ::***** *...*.**:***:*****:*.****************: \r\n",
      "\r\n",
      "STV1      HMTYSFMFSYINYRAKNSKVDIIGNFIPGLVFMQSIFGYLSWAIVYKWSKDWIKDDKPAP\r\n",
      "VPH1      HMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVKDGKPAP\r\n",
      "          *****::**  *:   ** :**********:***.****** .*****: **:**.****\r\n",
      "\r\n",
      "STV1      GLLNMLINMFLAPGTIDDQLYSGQAKLQVVLLLAALVCVPWLLLYKPLTLRRLNKNGGGG\r\n",
      "VPH1      GLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTHKKKSHE\r\n",
      "          ***********:******:**  ***:**.*** ****:***** *** ::  :*: .  \r\n",
      "\r\n",
      "STV1      RPHGYQSVGNIEHEEQIAQQRHSAEGFQGMIISDVASVADSINESVGGGEQGPFNFGDVM\r\n",
      "VPH1      PLPSTEA-------------DASSEDLEAQQLISAMDADDAEEEEVGSGSHG-EDFGDIM\r\n",
      "             . ::               *:*.::.  : .. .. *: :*.**.*.:*  :***:*\r\n",
      "\r\n",
      "STV1      IHQVIHTIEFCLNCISHTASYLRLWALSLAHAQLSSVLWDMTISNAFSSKNSGSPLAVMK\r\n",
      "VPH1      IHQVIHTIEFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGF---VGVFM\r\n",
      "          **************:************************ ***. **. :.    :.*: \r\n",
      "\r\n",
      "STV1      VVFLFAMWFVLTVCILVFMEGTSAMLHALRLHWVEAMSKFFEGEGYAYEPFSFRAIIE*-\r\n",
      "VPH1      TVALFAMWFALTCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEV\r\n",
      "          .* ******.** .:**:*********:*******:***** ***  ****:*.      \r\n",
      "\r\n",
      "STV1      ------------\r\n",
      "VPH1      AVASASSSASS*\r\n",
      "                      \r\n"
     ]
    }
   ],
   "source": [
    "!cat new_alignment.aln"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.79\r\n"
     ]
    }
   ],
   "source": [
    "# show Biopython version present\n",
    "!python -c \"import Bio; print(Bio.__version__)\""
   ]
  }
 ],
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