tutorials/03_Automatic_Annotation_Of_Problematic_Sequences.ipynb

{"cells":[{"cell_type":"markdown","metadata":{"id":"dW2UGT4s32-x"},"source":["# **How to: automatically annotate problematic sequences with Poly package and the friendzymes toolkit**\n","\n","Have you designed your sequence? Now it is time to identify small forbidden parts that can be a problem to you, not only when sequencing (e.g. hairpins, repetitive regions), but also when cloning (e.g. restriction binding sites). The outcome of this tutorial is the automatic annotation of these problems. It will give you a genbank file with these annotations attached, that you can drop into your favorite viewer, such as Benchling or Snapgene. In case you have problems with your CDS, you don't have to solve them by hand. Use the next tutorial.\n","\n","*Important:* \n","- If you are going to evaluate a CDS sequence here and found a problem, you don't have to solve them by hand. Use the next tutorial (Fix_CDS.ipynb).\n","\n","- If it is a non-coding part of your sequence, such as promoters, RBS, etc., we recommend that you manually change the codons to synonymous codons, because these sequences generally must be kept the same to remain with their biological performances. In other words, you often will not be able to simply change the codons, but have to find other ways on a case-by-case basis. Good luck.\n","\n","---\n","\n","Authors: [**@GiovannaMaklouf**](https://twitter.com/giomaklouf), [**@IsaacG**](https://twitter.com/IsaacGuerreiro9)\n","\n","\n"]},{"cell_type":"markdown","metadata":{"id":"PZJDiu_W3_FT"},"source":["# Configurations for this tutorial\n","\n"]},{"cell_type":"markdown","metadata":{"id":"Xqjf_sf0Am-X"},"source":["\n","First let's run some important settings so you can run this tutorial successfully. \n"]},{"cell_type":"markdown","metadata":{"id":"96PZqanZBAle"},"source":["Colab notebooks use python kernels to run each cell. However, because ***Poly*** is written in **Go language (golang)**, we need to install and configure some things in colab to make feasible run something in go lang here.\n","\n","### **1. In order to start the golang environment, run the line below:**"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"executionInfo":{"elapsed":75700,"status":"ok","timestamp":1634426307157,"user":{"displayName":"Isaac Guerreiro","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14Gibo59sdYK-mXxvtGYnmJyGAQyFx3Ml-_Cizj1www=s64","userId":"12892194237443422762"},"user_tz":180},"id":"caT1iMfshw62","outputId":"ad4aa963-e504-4d7a-85de-4495fc4189c7","vscode":{"languageId":"python"}},"outputs":[{"name":"stdout","output_type":"stream","text":["\r0% [Working]\r            \rGet:1 http://security.ubuntu.com/ubuntu bionic-security InRelease [88.7 kB]\n","\r0% [Connecting to archive.ubuntu.com (91.189.88.142)] [1 InRelease 0 B/88.7 kB \r0% [Waiting for headers] [Connecting to cloud.r-project.org] [Waiting for heade\r                                                                               \rIgn:2 https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64  InRelease\n","\r0% [Waiting for headers] [Connecting to cloud.r-project.org] [Waiting for heade\r0% [1 InRelease gpgv 88.7 kB] [Waiting for headers] [Connecting to cloud.r-proj\r                                                                               \rHit:3 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic InRelease\n","\r0% [1 InRelease gpgv 88.7 kB] [Waiting for headers] [Connected to cloud.r-proje\r                                                                               \rHit:4 http://archive.ubuntu.com/ubuntu bionic InRelease\n","\r0% [1 InRelease gpgv 88.7 kB] [Connected to cloud.r-project.org (65.8.185.60)] \r                                                                               \rIgn:5 https://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1804/x86_64  InRelease\n","\r0% [1 InRelease gpgv 88.7 kB] [Waiting for headers] [Connected to cloud.r-proje\r                                                                               \rHit:6 https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64  Release\n","\r0% [1 InRelease gpgv 88.7 kB] [Waiting for headers] [Connected to cloud.r-proje\r                                                                               \rHit:7 https://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1804/x86_64  Release\n","\r0% [1 InRelease gpgv 88.7 kB] [Waiting for headers] [Connected to cloud.r-proje\r                                                                               \rGet:8 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/ InRelease [3,626 B]\n","Get:9 http://archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB]\n","Hit:10 http://ppa.launchpad.net/cran/libgit2/ubuntu bionic InRelease\n","Get:11 http://security.ubuntu.com/ubuntu bionic-security/restricted amd64 Packages [607 kB]\n","Get:12 http://security.ubuntu.com/ubuntu bionic-security/main amd64 Packages [2,367 kB]\n","Hit:13 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu bionic InRelease\n","Get:14 http://archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB]\n","Get:15 http://security.ubuntu.com/ubuntu bionic-security/universe amd64 Packages [1,431 kB]\n","Hit:16 http://ppa.launchpad.net/graphics-drivers/ppa/ubuntu bionic InRelease\n","Get:17 http://ppa.launchpad.net/longsleep/golang-backports/ubuntu bionic InRelease [15.4 kB]\n","Get:20 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 Packages [2,803 kB]\n","Get:21 http://archive.ubuntu.com/ubuntu bionic-updates/restricted amd64 Packages [640 kB]\n","Get:22 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 Packages [2,210 kB]\n","Get:23 http://ppa.launchpad.net/longsleep/golang-backports/ubuntu bionic/main amd64 Packages [6,639 B]\n","Fetched 10.3 MB in 3s (3,282 kB/s)\n","Reading package lists... 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Done\n","Building dependency tree       \n","Reading state information... Done\n","38 packages can be upgraded. Run 'apt list --upgradable' to see them.\n","Reading package lists... Done\n","Building dependency tree       \n","Reading state information... Done\n","The following additional packages will be installed:\n","  golang-1.17-go golang-1.17-src golang-src\n","Suggested packages:\n","  bzr | brz mercurial subversion\n","The following NEW packages will be installed:\n","  golang-1.17-go golang-1.17-src golang-go golang-src\n","0 upgraded, 4 newly installed, 0 to remove and 38 not upgraded.\n","Need to get 71.8 MB of archives.\n","After this operation, 423 MB of additional disk space will be used.\n","Get:1 http://ppa.launchpad.net/longsleep/golang-backports/ubuntu bionic/main amd64 golang-1.17-src all 1.17.2-1longsleep1+focal [15.2 MB]\n","Get:2 http://ppa.launchpad.net/longsleep/golang-backports/ubuntu bionic/main amd64 golang-1.17-go amd64 1.17.2-1longsleep1+focal [56.6 MB]\n","Get:3 http://ppa.launchpad.net/longsleep/golang-backports/ubuntu bionic/main amd64 golang-src amd64 2:1.17~1longsleep1 [5,056 B]\n","Get:4 http://ppa.launchpad.net/longsleep/golang-backports/ubuntu bionic/main amd64 golang-go amd64 2:1.17~1longsleep1 [24.1 kB]\n","Fetched 71.8 MB in 4s (16.4 MB/s)\n","Selecting previously unselected package golang-1.17-src.\n","(Reading database ... 155047 files and directories currently installed.)\n","Preparing to unpack .../golang-1.17-src_1.17.2-1longsleep1+focal_all.deb ...\n","Unpacking golang-1.17-src (1.17.2-1longsleep1+focal) ...\n","Selecting previously unselected package golang-1.17-go.\n","Preparing to unpack .../golang-1.17-go_1.17.2-1longsleep1+focal_amd64.deb ...\n","Unpacking golang-1.17-go (1.17.2-1longsleep1+focal) ...\n","Selecting previously unselected package golang-src:amd64.\n","Preparing to unpack .../golang-src_2%3a1.17~1longsleep1_amd64.deb ...\n","Unpacking golang-src:amd64 (2:1.17~1longsleep1) ...\n","Selecting previously unselected package golang-go.\n","Preparing to unpack .../golang-go_2%3a1.17~1longsleep1_amd64.deb ...\n","Unpacking golang-go (2:1.17~1longsleep1) ...\n","Setting up golang-1.17-src (1.17.2-1longsleep1+focal) ...\n","Setting up golang-src:amd64 (2:1.17~1longsleep1) ...\n","Setting up golang-1.17-go (1.17.2-1longsleep1+focal) ...\n","Setting up golang-go (2:1.17~1longsleep1) ...\n","Processing triggers for man-db (2.8.3-2ubuntu0.1) ...\n","env: GOPATH=/root/go\n","go: downloading github.com/gopherdata/gophernotes v0.7.3\n","go: downloading github.com/cosmos72/gomacro v0.0.0-20210624153544-b4935e406a41\n","go: downloading github.com/go-zeromq/zmq4 v0.13.0\n","go: downloading github.com/gofrs/uuid v4.0.0+incompatible\n","go: downloading golang.org/x/xerrors v0.0.0-20200804184101-5ec99f83aff1\n","go: downloading github.com/gofrs/uuid v4.1.0+incompatible\n","go: downloading github.com/peterh/liner v1.2.1\n","go: downloading github.com/go-zeromq/goczmq/v4 v4.2.2\n","go: downloading golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9\n","go: downloading golang.org/x/sync v0.0.0-20210220032951-036812b2e83c\n","go: downloading golang.org/x/tools v0.1.0\n","go: downloading github.com/go-zeromq/goczmq v4.1.0+incompatible\n","go: downloading github.com/mattn/go-runewidth v0.0.12\n","go: downloading github.com/mattn/go-runewidth v0.0.13\n","go: downloading golang.org/x/tools v0.1.7\n","go: downloading github.com/rivo/uniseg v0.1.0\n","go: downloading github.com/rivo/uniseg v0.2.0\n","go: downloading golang.org/x/sys v0.0.0-20210119212857-b64e53b001e4\n","go: downloading golang.org/x/sys v0.0.0-20211015200801-69063c4bb744\n","go: downloading golang.org/x/mod v0.3.0\n","go: downloading golang.org/x/mod v0.5.1\n","go get: installing executables with 'go get' in module mode is deprecated.\n","\tUse 'go install pkg@version' instead.\n","\tFor more information, see https://golang.org/doc/go-get-install-deprecation\n","\tor run 'go help get' or 'go help install'.\n","\u001b[K\u001b[?25hnpx: installed 1 in 1.817s\n","\u001b[36m> cloned \u001b[1mgopherdata/gophernotes\u001b[22m#\u001b[1mHEAD\u001b[22m to /usr/local/share/jupyter/kernels/gophernotes\u001b[39m\n"]}],"source":["# this process may take a few minutes\n","!add-apt-repository ppa:longsleep/golang-backports -y\n","!apt update\n","!apt install golang-go\n","%env GOPATH=/root/go\n","!go get -u github.com/gopherdata/gophernotes\n","!cp ~/go/bin/gophernotes /usr/bin/\n","!npx degit gopherdata/gophernotes/kernel \\\n","     /usr/local/share/jupyter/kernels/gophernotes"]},{"cell_type":"markdown","metadata":{"id":"cZwRFE9UAGIs"},"source":["### **2. Download important data to run this tutorial**"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"wHmBJ418_5tX","vscode":{"languageId":"python"}},"outputs":[],"source":["!rm -rf $GOPATH/pkg/mod/github.com/!open-!science-!global\n","!rm -rf $GOPATH/pkg/mod/cache/download/github.com/!open-!science-!global\n","!go get -u github.com/Open-Science-Global/poly@e3e1c61"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"executionInfo":{"elapsed":435,"status":"ok","timestamp":1634426318359,"user":{"displayName":"Isaac Guerreiro","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14Gibo59sdYK-mXxvtGYnmJyGAQyFx3Ml-_Cizj1www=s64","userId":"12892194237443422762"},"user_tz":180},"id":"uaxY1xbR-U0F","outputId":"65ab7655-4899-4883-b661-1ce2b85c57db","vscode":{"languageId":"python"}},"outputs":[{"name":"stdout","output_type":"stream","text":["--2021-10-16 23:18:36--  https://raw.githubusercontent.com/Open-Science-Global/friendzymes-toolkit/main/data/ecoli-k12-cdss.fasta\n","Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.108.133, ...\n","Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.\n","HTTP request sent, awaiting response... 200 OK\n","Length: 5054174 (4.8M) [text/plain]\n","Saving to: ‘ecoli-k12-cdss.fasta’\n","\n","ecoli-k12-cdss.fast 100%[===================>]   4.82M  --.-KB/s    in 0.08s   \n","\n","2021-10-16 23:18:37 (62.6 MB/s) - ‘ecoli-k12-cdss.fasta’ saved [5054174/5054174]\n","\n"]}],"source":["!wget https://raw.githubusercontent.com/Open-Science-Global/friendzymes-cookbook/main/data/anno-problematic-seqs/5_bsubori_pbs72_repa.gb"]},{"cell_type":"markdown","metadata":{"id":"3STJpf80Bl9Z"},"source":["### **3. Connect Colab Notebook to your GDrive (not required)**"]},{"cell_type":"markdown","metadata":{"id":"ftGzhtH5AOZM"},"source":["The previous code will download the files temporarily. If you want to download them to a folder on your drive and save it for later analysis or if you are already using this notebook to run your own files, you should connect your Google Drive to Colab and you will be able to access, read and save files permanently. \n","So, if you prefer, you can do this with the code line below:\n","\n"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":527},"executionInfo":{"elapsed":839877,"status":"error","timestamp":1634427158235,"user":{"displayName":"Isaac Guerreiro","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14Gibo59sdYK-mXxvtGYnmJyGAQyFx3Ml-_Cizj1www=s64","userId":"12892194237443422762"},"user_tz":180},"id":"sh661uGn_8R1","outputId":"9d874164-d5ca-4b63-ac83-aa544d2d0fdd","vscode":{"languageId":"python"}},"outputs":[{"ename":"KeyboardInterrupt","evalue":"ignored","output_type":"error","traceback":["\u001b[0;31m---------------------------------------------------------------------------\u001b[0m","\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)","\u001b[0;32m/usr/local/lib/python3.7/dist-packages/ipykernel/kernelbase.py\u001b[0m in \u001b[0;36m_input_request\u001b[0;34m(self, prompt, ident, parent, password)\u001b[0m\n\u001b[1;32m    728\u001b[0m             \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 729\u001b[0;31m                 \u001b[0mident\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreply\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msession\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrecv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstdin_socket\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    730\u001b[0m             \u001b[0;32mexcept\u001b[0m \u001b[0mException\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n","\u001b[0;32m/usr/local/lib/python3.7/dist-packages/jupyter_client/session.py\u001b[0m in \u001b[0;36mrecv\u001b[0;34m(self, socket, mode, content, copy)\u001b[0m\n\u001b[1;32m    802\u001b[0m         \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 803\u001b[0;31m             \u001b[0mmsg_list\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msocket\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrecv_multipart\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmode\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcopy\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcopy\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    804\u001b[0m         \u001b[0;32mexcept\u001b[0m \u001b[0mzmq\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mZMQError\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n","\u001b[0;32m/usr/local/lib/python3.7/dist-packages/zmq/sugar/socket.py\u001b[0m in \u001b[0;36mrecv_multipart\u001b[0;34m(self, flags, copy, track)\u001b[0m\n\u001b[1;32m    624\u001b[0m         \"\"\"\n\u001b[0;32m--> 625\u001b[0;31m         \u001b[0mparts\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrecv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mflags\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcopy\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcopy\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtrack\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mtrack\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    626\u001b[0m         \u001b[0;31m# have first part already, only loop while more to receive\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n","\u001b[0;32mzmq/backend/cython/socket.pyx\u001b[0m in \u001b[0;36mzmq.backend.cython.socket.Socket.recv\u001b[0;34m()\u001b[0m\n","\u001b[0;32mzmq/backend/cython/socket.pyx\u001b[0m in \u001b[0;36mzmq.backend.cython.socket.Socket.recv\u001b[0;34m()\u001b[0m\n","\u001b[0;32mzmq/backend/cython/socket.pyx\u001b[0m in \u001b[0;36mzmq.backend.cython.socket._recv_copy\u001b[0;34m()\u001b[0m\n","\u001b[0;32m/usr/local/lib/python3.7/dist-packages/zmq/backend/cython/checkrc.pxd\u001b[0m in \u001b[0;36mzmq.backend.cython.checkrc._check_rc\u001b[0;34m()\u001b[0m\n","\u001b[0;31mKeyboardInterrupt\u001b[0m: ","\nDuring handling of the above exception, another exception occurred:\n","\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)","\u001b[0;32m<ipython-input-4-d5df0069828e>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mgoogle\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcolab\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mdrive\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mdrive\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmount\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'/content/drive'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m","\u001b[0;32m/usr/local/lib/python3.7/dist-packages/google/colab/drive.py\u001b[0m in \u001b[0;36mmount\u001b[0;34m(mountpoint, force_remount, timeout_ms, use_metadata_server)\u001b[0m\n\u001b[1;32m    111\u001b[0m       \u001b[0mtimeout_ms\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mtimeout_ms\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    112\u001b[0m       \u001b[0muse_metadata_server\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0muse_metadata_server\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 113\u001b[0;31m       ephemeral=ephemeral)\n\u001b[0m\u001b[1;32m    114\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    115\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n","\u001b[0;32m/usr/local/lib/python3.7/dist-packages/google/colab/drive.py\u001b[0m in \u001b[0;36m_mount\u001b[0;34m(mountpoint, force_remount, timeout_ms, use_metadata_server, ephemeral)\u001b[0m\n\u001b[1;32m    290\u001b[0m       \u001b[0;32mwith\u001b[0m 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\u001b[0mpassword\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    705\u001b[0m         )\n\u001b[1;32m    706\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n","\u001b[0;32m/usr/local/lib/python3.7/dist-packages/ipykernel/kernelbase.py\u001b[0m in \u001b[0;36m_input_request\u001b[0;34m(self, prompt, ident, parent, password)\u001b[0m\n\u001b[1;32m    732\u001b[0m             \u001b[0;32mexcept\u001b[0m \u001b[0mKeyboardInterrupt\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    733\u001b[0m                 \u001b[0;31m# re-raise KeyboardInterrupt, to truncate traceback\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 734\u001b[0;31m                 \u001b[0;32mraise\u001b[0m \u001b[0mKeyboardInterrupt\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    735\u001b[0m             \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    736\u001b[0m                 \u001b[0;32mbreak\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n","\u001b[0;31mKeyboardInterrupt\u001b[0m: "]}],"source":["from google.colab import drive\n","drive.mount('/content/drive')"]},{"cell_type":"markdown","metadata":{"id":"GbPLWTJ05uH4"},"source":["## After running these steps, click on **Runtime** in the menu bar & **Change Runtime Type** to Go, if it hasn't changed yet.\n","\n","This will make Colab starting use a open source go kernel called Gopher Notes.\n","\n","Now we are ready to work."]},{"cell_type":"markdown","metadata":{"id":"flsk3_roXwdM"},"source":["# **Automatic annotation of problematic sequences**"]},{"cell_type":"markdown","metadata":{"id":"34gduXzXl-Nb"},"source":["## **Importing packages and pre-requisites**"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"gQVnSh-tmEvz","vscode":{"languageId":"python"}},"outputs":[],"source":["package main\n","\n","import (\n","\t\"fmt\"\n","\t\"os\"\n","\t\"path/filepath\"\n","\t\"strings\"\n","\t\"strconv\"\n","\t\"sync\"\n","\n","  \"github.com/Open-Science-Global/poly\"\n","\t\"github.com/Open-Science-Global/poly/checks\"\n","\t\"github.com/Open-Science-Global/poly/io/fasta\"\n","\t\"github.com/Open-Science-Global/poly/io/genbank\"\n","\t\"github.com/Open-Science-Global/poly/linearfold\"\n","\t\"github.com/Open-Science-Global/poly/synthesis\"\n","\t\"github.com/Open-Science-Global/poly/transform\"\n","\t\"github.com/Open-Science-Global/poly/transform/codon\"\n","\t\"github.com/Open-Science-Global/poly/finder\"\n",")"]},{"cell_type":"markdown","metadata":{"id":"JjOp36MzMUfw"},"source":["## **1. Preparations for fixing problematic sequences: functions set up**\n"]},{"cell_type":"markdown","metadata":{"id":"h4csnPYGanNR"},"source":["Run the cells below to generate the function to annotate problematic sequences, based on the sequences of your choice. \n","For example: binding sites of restriction enzymes are problematic because they cannot be in your sequence. For iGEM teams these can be the enzymes of the Biobrick system.\n","\n","\n","**Important points:**\n","*   We have below ONE main function (findProblematicSequences) and 3 subfunctions (forbiddenSeqList, AvoidHairpin and homologySequencesFindProblems) that are inside the main one and also need to be set. \n","*   Overall, you don't need to change anything to save and use these functions in the second step of this tutorial (2. Running), except in the first cell of code below, because note that this is OUR list of forbidden restriction enzyme binding site sequences, so for the next cell of code you will probably have to change some things. Feel free to remove some or add others."]},{"cell_type":"code","execution_count":null,"metadata":{"id":"_-yjSHB6au6m","vscode":{"languageId":"python"}},"outputs":[],"source":["// run this to set up the subfunction 1 (REMOVE OR ADD RESTRICTIONS ENZYMES BINDING SITES AS YOU WISH)\n","func forbiddenSeqList() []string {\n","\tBsaI := \"GGTCTC\"\n","\tBbsI := \"GAAGAC\"\n","\tBtgzI := \"GCGATG\"\n","\tSapI := \"GCTCTTC\"\n","\tBsmbI := \"CGTCTC\"\n","\tAarI := \"CACCTGC\"\n","\tPmeI := \"GTTTAAAC\"\n","\tHindIII := \"AAGCTT\"\n","\tPstI := \"CTGCAG\"\n","\tXbaI := \"TCTAGA\"\n","\tBamHI := \"GGATCC\"\n","\tSmaI := \"CCCGGG\"\n","\tKpnI := \"GGTACC\"\n","\tSacI := \"GAGCTC\"\n","\tSalI := \"GTCGAC\"\n","\tEcoRI := \"GAATTC\"\n","\tSphI := \"GCATGC\"\n","\tAvrII := \"CCTAGG\"\n","\tSwaI := \"ATTTAAAT\"\n","\tAscI := \"GGCGCGCC\"\n","\tFseI := \"GGCCGGCC\"\n","\tPacI := \"TTAATTAA\"\n","\tSpeI := \"ACTAGT\"\n","\tNotI := \"GCGGCCGC\"\n","\tSanDI_A := \"GGGACCC\"\n","\tSanDI_T := \"GGGTCCC\"\n","\tBglII := \"AGATCT\"\n","\tXhoI := \"CTCGAG\"\n","\tClaI := \"ATCGAT\"\n","\n","\tList := []string{\n","\t\tBsaI,\n","\t\tBbsI,\n","\t\tSapI,\n","\t\tBsmbI,\n","\t\tBtgzI,\n","\t\tAarI,\n","\t\tPmeI,\n","\t\tHindIII,\n","\t\tPstI,\n","\t\tXbaI,\n","\t\tBamHI,\n","\t\tSmaI,\n","\t\tKpnI,\n","\t\tSacI,\n","\t\tSalI,\n","\t\tEcoRI,\n","\t\tSphI,\n","\t\tAvrII,\n","\t\tSacI,\n","\t\tSalI,\n","\t\tSwaI,\n","\t\tAscI,\n","\t\tFseI,\n","\t\tPacI,\n","\t\tSpeI,\n","\t\tNotI,\n","\t\tSanDI_A,\n","\t\tSanDI_T,\n","\t\tBglII,\n","\t\tXhoI,\n","\t\tClaI,\n","\t}\n","\n","\treturn List\n","}"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"HpIo_FGFayAY","vscode":{"languageId":"python"}},"outputs":[],"source":["// run this to set up the subfunction 2\n","\n","func AvoidHairpin(stemSize int, hairpinWindow int) func(string) []finder.Match {\n","\treturn func(sequence string) []finder.Match {\n","\t\tvar matches []finder.Match\n","\t\treverse := transform.ReverseComplement(sequence)\n","\t\tfor i := 0; i < len(sequence)-stemSize && len(sequence)-(i+hairpinWindow) >= 0; i++ {\n","\t\t\tword := sequence[i : i+stemSize]\n","\t\t\trest := reverse[len(sequence)-(i+hairpinWindow) : len(sequence)-(i+stemSize)]\n","\t\t\tif strings.Contains(rest, word) {\n","\t\t\t\tlocation := strings.Index(rest, word)\n","\t\t\t\tmatches = append(matches, finder.Match{i, i + hairpinWindow - location - 1, \"Hairpin found in next \" + strconv.Itoa(hairpinWindow) + \"bp in reverse complementary sequence: \" + word})\n","\t\t\t}\n","\t\t}\n","\t\treturn matches\n","\t}\n","}"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"6SWSWIHea2j2","vscode":{"languageId":"python"}},"outputs":[],"source":["// run this to set up the subfunction 3\n","\n","func homologySequencesFindProblems() []string {\n","\t// we don't have to worry about TTTTTT and GGGGGG because I already try to find also by reverse complementary of each sequence in finder\n","\treturn []string{\"AAAAAA\", \"CCCCCC\"}\n","}"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"M4a0RTRKEzhv","vscode":{"languageId":"python"}},"outputs":[],"source":["// run this to set up the MAIN function\n","\n","func findProblematicSequences(sequence poly.Sequence) poly.Sequence{\n","\tvar functions []func(string) []finder.Match\n","\n","\tfunctions = append(functions, finder.ForbiddenSequence(forbiddenSeqList()))\n","\tfunctions = append(functions, finder.ForbiddenSequence(homologySequencesFindProblems()))\n","\tfunctions = append(functions, finder.RemoveRepeat(10))\n","\tfunctions = append(functions, AvoidHairpin(20, 200))\n","\n","\tproblems := finder.Find(strings.ToUpper(sequence.Sequence), functions)\n","\n","\tsequence = finder.AddMatchesToSequence(problems, sequence)\n","\treturn sequence\n","}\n"]},{"cell_type":"markdown","metadata":{"id":"NLv21BpfrMjF"},"source":["# **2. Running**\n"]},{"cell_type":"markdown","metadata":{"id":"v0alIhMUwLdK"},"source":["Upload your sequence file - which in this case we are using a Poly subpackage called genbank, to read files with this format.\n","\n","**Important:**\n","* The \"5_bsubori_pbs72_repa.gb\" is a genbank file that has the sequence (and some annotations) of the repA replication source from Bacillus subtilis. This file can be downloaded in the settings section of this tutorial. You can change it to your own genbank file.;\n","* As this function is about **ANNOTATION**, here you cannot use as input a sequence in fasta format (as this is just sequence name and sequence) rather the genbank file which comes with detailed information of parts within your overall sequence."]},{"cell_type":"markdown","metadata":{"id":"No0ZNn2MVPoB"},"source":["If you don't have your sequence in a genbank file, no problem. Below we created a function called `fasta2Sequence` (run it to save it).\n","\n","Then use it with your fasta file or copy/paste your sequence into it as input."]},{"cell_type":"code","execution_count":null,"metadata":{"id":"HYu34MxW8UAh","vscode":{"languageId":"python"}},"outputs":[],"source":["// run to set up the function\n","\n","func fasta2Sequence(filename string) []poly.Sequence {\n","  var sequences []poly.Sequence\n","  fastaseqs := fasta.Read(filename)\n","  \n","  for _, fastaseq := range fastaseqs {\n","    var sequence poly.Sequence\n","    var feature poly.Feature\n","\t  sequence.Sequence = fastaseq.Sequence\n","    feature.Name = fastaseq.Name\n","\t  feature.SequenceLocation.Start = 0\n","\t  feature.SequenceLocation.End = len(sequence.Sequence)\n","    sequences = append(sequences, sequence)\n","  }\n","  \n","  return sequences\n","}"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"cOWSNj4dVEfL","vscode":{"languageId":"python"}},"outputs":[],"source":["sequences := fasta2Sequence(\"input.fasta\")"]},{"cell_type":"markdown","metadata":{"id":"yY9aSRtjYLxt"},"source":["Remember that fastas are lists of sequences, so if you have more than one in your fasta and want to analyze the first one, do so:"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"Zl1rmj7x4gnf","vscode":{"languageId":"python"}},"outputs":[],"source":["firstSeq := findProblematicSequences(sequences[0])\n","\n","// if you want the second:\n","secondSe2 := findProblematicSequences(sequences[1])\n"]},{"cell_type":"markdown","metadata":{"id":"kS3RI_QlYau7"},"source":["In case you already have your sequence in genbank, keep reading the file and proceed to find the problematic sequences:\n","\n","*(This tutorial will follow with this example data, but you can modify this for your file.)*"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"tYzcxSZnhKFy","vscode":{"languageId":"python"}},"outputs":[],"source":["sequence := genbank.Read(\"5_bsubori_pbs72_repa.gb\")"]},{"cell_type":"markdown","metadata":{"id":"rocoszdXywSJ"},"source":["Run below to find the problematic sequences in your file and then save the annotated object for future inspection. **You can, for example, put this into Benchling to inspect in an easier way and be able to correct for synonymous codons if appropriate.**"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"executionInfo":{"elapsed":364,"status":"ok","timestamp":1634429034092,"user":{"displayName":"Isaac Guerreiro","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14Gibo59sdYK-mXxvtGYnmJyGAQyFx3Ml-_Cizj1www=s64","userId":"12892194237443422762"},"user_tz":180},"id":"Rg2OvDHfj1ct","outputId":"7369e858-dbf3-4ad4-8eb4-0d7aa7d0b6de","vscode":{"languageId":"python"}},"outputs":[{"name":"stdout","output_type":"stream","text":["{{  0 0 0   .       {5:_BsubOri_pBS72_repA 3171 DNA  02-SEP-2021 bp false true} [] map[]}    ACATATACAGTGATGGAAGACCCGGAGTTCCTAAGGGTCTCTAAAAGAATTCAAAGTTTATACCTTACCTGGAACAAATGGTTGAAACATACGAGGCTAATATCGGCTTATTAGGAATAGTCCCTGTACTAATAAAATCAGGTGGATCAGTTGATCAGTATATTTTGGACGAAGCTCGGAAAGAATTTGGAGATGACTTGCTTAATTCCACAATTAAATTAAGGGAAAGAATAAAGCGATTTGATGTTCAAGGAATCACGGAAGAAGATACTCATGATAAAGAAGCTCTAAAACTATTCAATAACCTTACAATGGAATTGATCGAAAGGGTGGAAGGTTAATGGTACGAAAATTAGGGGATCTACCTAGAAAGCCACAAGGCGATAGGTCAAGCTTAAAGAACCCTTACATGGATCTTACAGATTCTGAAAGTAAAGAAACAACAGAGGTTAAACAAACAGAACCAAAAAGAAAAAAAGCATTGTTGAAAACAATGAAAGTTGATGTTTCAATCCATAATAAGATTAAATCGCTGCACGAAATTCTGGCAGCATCCGAAGGGAATTCATATTACTTAGAGGATACTATTGAGAGAGCTATTGATAAGATGGTTGAGACATTACCTGAGAGCCAAAAAACTTTTTATGAATATGAATTAAAAAAAAGAACCAACAAAGGCTGAGACAGACTCCAAACGAGTCTGTTTTTTTAAAAAAAATATTAGGAGCATTGAATATATATTAGAGAATTAAGAAAGACATGGGAATAAAAATATTTTAAATCCAGTAAAAATATGATAAGATTATTTCAGAATATGAAGAACTCTGTTTGTTTTTGATGAAAAAACAAACAAAAAAAATCCACCTAACGGAATCTCAATTTAACTAACAGCGGCCAAACTGAGAAGTTAAATTTGAGAAGGGGAAAAGGCGGATTTATACTTGTATTTAACTATCTCCATTTTAACATTTTATTAAACCCCATACAAGTGAAAATCCTCTTTTACACTGTTCCTTTAGGTGATCGCGGAGGGACATTATGAGTGAAGTAAACCTAAAAGGAAATACAGATGAATTAGTGTATTATCGACAGCAAACCACTGGAAATAAAATCGCCAGGAAGAGAATCAAAAAAGGGAAAGAAGAAGTTTATTATGTTGCTGAAACGGAAGAGAAGATATGGACAGAGGAACAAATAAAAAACTTTTCTTTAGACAAATTTGGTACGCATATACCTTACATAGAAGGTCATTATACAATCTTAAATAATTACTTCTTTGATTTTTGGGGCTATTTTTTAGGTGCTGAAGGAATTGCGCTCTATGCTCACCTAACTCGTTATGCATACGGCAGCAAAGACTTTTGCTTTCCTAGTCTACAAACAATCGCTAAAAAAATGGACAAGACTCCTGTTACAGTTAGAGGCTACTTGAAACTGCTTGAAAGGTACGGTTTTATTTGGAAGGTAAACGTCCGTAATAAAACCAAGGATAACACAGAGGAATCCCCGATTTTTAAGATTAGACGTAAGGTTCCTTTGCTTTCAGAAGAACTTTTAAATGGAAACCCTAATATTGAAATTCCAGATGACGAGGAAGCACATGTAAAGAAGGCTTTAAAAAAGGAAAAAGAGGGACTACCAAAGGTTTTGAAAAAAGAGCACGATGAATTTGTTAAAAAAATGATGGATGAGTCAGAAACAATTAATATTCCAGAGGCCTTACAATATGACACAATGTATGAAGATATACTCAGTAAAGGAGAAATTCGAAAAGAAATCAAAAAACAAATACCTAATCCTACAACATCTTTTGAGAGTATATCAATGACAACTGAAGAGGAAAAAGTAGATAGTACTTTAAAAAGCGAAATGCAAAATCGTGTCTCTAAGCCTTCTTTTGATACCTGGTTTAAAAACACTAAGATCAAAATTGAAAATAAAAATTGTTTATTACTTGTACCGAGTGAATTTGCATTTGAATGGATTAAGAAAAGATATTTAGAAACAATTAAAACAGTCCTTGAAGAAGCTGGATATGTTTTCGAAAAAATCGAACTAAGAAAAGTGCAATAAACTGCTGAAGTATTTCAGCAGTTTTTTTTATTTAGAAATAGTGAAAAAAATATAATCAGGGAGGTATCAATATTTAATGAGTACTGATTTAAATTTATTTAGACTGGAATTAATAATTAACACGTAGACTAATTAAAATTTAATGAGGGATAAAGAGGATACAAAAATATTAATTTCAATCCCTATTAAATTTTAACAAGGGGGGGATTAAAATTTAATTAGAGGTTTATCCACAAGAAAAGACCCTAATAAAATTTTTACTAGGGTTATAACACTGATTAATTTCTTAATGGGGGAGGGATTAAAATTTAATGACAAAGAAAACAATCTTTTAAGAAAAGCTTTTAAAAGATAATAATAAAAAGAGCTTTGCGATTAAGCAAAACTCTTTACTTTTTCATTGACATTATCAAATTCATCGATTTCAAATTGTTGTTGTATCATAAAGTTAATTCTGTTTTGCACAACCTTTTCAGGAATATAAAACACATCTGAGGCTTGTTTTATAAACTCAGGGTCGCTAAAGTCAATGTAACGTAGCATATGATATGGTATAGCTTCCACCCAAGTTAGCCTTTCTGCTTCTTCTGAATGTTTTTCATATACTTCCATGGGTATCTCTAAATGATTTTCCTCATGTAGCAAGGTATGAGCAAAAAGTTTATGGAATTGATAGTTCCTCTCTTTTTCTTCAACTTTTTTATCTAAAACAAACACTTTAACATCTGAGTCAATGTAAGCATAAGATGTTTTTCCAGTCATAATTTCAATCCCAAATCTTTTAGACAGAAATTCTGGACGTAAATCTTTTGGTGAAAGAATTTTTTTATGTAGCAATATATCCGATACAGCACCTTCTAAAAGCGTTGGTGAATAGGGCATTTTACCTATCTCCTCTCATTTTGTGGAATAAAAATAGTCATATTCGTCCATCTACCTATCCTATTATCGAACAGTTGAACTTTTTAATCAAGGATCAGTCCTTTTTTTCATTATTCTTAAACTGTGCTCTTAACTTTAACAACTCGATTTGTTTTTCCAGCACTATCGATAAGGTGAGACCATGGCGTGCGCTGAGTCTTCTGGACACCTCGCGGT [{  misc_feature    map[label:BbsI bind] 16..21  {15 21 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | GAAGAC] 16..21  {15 21 false false false false []}    0xc0002aa540} {  GG    map[label:1] 24..27  {23 27 false false false false []}    0xc0002aa540} {  misc_feature    map[label:BsaI bind] 36..41  {35 41 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | GGTCTC] 36..41  {35 41 false false false false []}    0xc0002aa540} {  GG    map[label:FR] 43..46  {42 46 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | GAATTC] 47..52  {46 52 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | GAATTC] 47..52  {46 52 false false false false []}    0xc0002aa540} {  misc_feature    map[label:EcoRi] 47..52  {46 52 false false false false []}    0xc0002aa540} {  misc_feature    map[label:pBS72 1410] 53..341  {52 341 false false false false []}    0xc0002aa540} {  FR    map[label:pBS72 repA fragment] 53..3119  {52 3119 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAGCTT] 391..396  {390 396 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAGCTT] 391..396  {390 396 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 472..477  {471 477 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | GAATTC] 562..567  {561 567 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | GAATTC] 562..567  {561 567 false false false false []}    0xc0002aa540} {  misc_feature    map[label:Titok 2006 minimal replication origin] 562..2496  {561 2496 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 633..638  {632 638 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 658..663  {657 663 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | TTTTTT] 704..709  {703 709 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TTAAAAAAAA] 709..718  {708 718 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 711..716  {710 716 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 841..846  {840 846 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 852..857  {851 857 false false false false []}    0xc0002aa540} {  misc_feature    map[label:repA CDS] 1039..2002  {1038 2002 false false false false []}    0xc0002aa540} {  CDS    map[label:Translation 1039-2002] 1039..2002  {1038 2002 false false false false []}    0xc0002aa540} {  exon    map[label:Translation 1039-2002] 1039..2002  {1038 2002 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 1129..1134  {1128 1134 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AAGGGAAAGA] 1133..1142  {1132 1142 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AGGGAAAGAA] 1134..1143  {1133 1143 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 1197..1202  {1196 1202 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AAAAAACTTT] 1197..1206  {1196 1206 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AAAAACTTTT] 1198..1207  {1197 1207 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TATACCTTAC] 1230..1239  {1229 1239 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | TTTTTT] 1293..1298  {1292 1298 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 1390..1395  {1389 1395 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 1617..1622  {1616 1622 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 1651..1656  {1650 1656 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TAAAAAAATG] 1674..1683  {1673 1683 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 1675..1680  {1674 1680 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AATCAAAAAA] 1776..1785  {1775 1785 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 1780..1785  {1779 1785 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AAAAAACAAA] 1780..1789  {1779 1789 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AGAAACAATT] 2001..2010  {2000 2010 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | GAAACAATTA] 2002..2011  {2001 2011 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AAACAATTAA] 2003..2012  {2002 2012 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 2045..2050  {2044 2050 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | TTTTTT] 2095..2100  {2094 2100 false false false false []}    0xc0002aa540} {  misc_feature    map[label:Origin Region] 2096..2389  {2095 2389 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TATTTAGAAA] 2102..2111  {2101 2111 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAAAAA] 2117..2122  {2116 2122 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AAAAAAATAT] 2117..2126  {2116 2126 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | ATTTAAAT] 2160..2167  {2159 2167 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | ATTTAAAT] 2160..2167  {2159 2167 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TTTATTTAGA] 2167..2176  {2166 2176 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | ATTTAATGAG] 2211..2220  {2210 2220 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AAAAATATTA] 2236..2245  {2235 2245 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | GGGGGG] 2273..2278  {2272 2278 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | ATTAAAATTT] 2280..2289  {2279 2289 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TTAAAATTTA] 2281..2290  {2280 2290 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TAAAATTTAA] 2282..2291  {2281 2291 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AAAATTTAAT] 2283..2292  {2282 2292 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | CTAATAAAAT] 2319..2328  {2318 2328 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | GGGATTAAAA] 2371..2380  {2370 2380 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | GGATTAAAAT] 2372..2381  {2371 2381 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | GATTAAAATT] 2373..2382  {2372 2382 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | ATTAAAATTT] 2374..2383  {2373 2383 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TTAAAATTTA] 2375..2384  {2374 2384 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TAAAATTTAA] 2376..2385  {2375 2385 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AAAATTTAAT] 2377..2386  {2376 2386 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AAATTTAATG] 2378..2387  {2377 2387 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AATTTAATGA] 2379..2388  {2378 2388 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TTAAGAAAAG] 2405..2414  {2404 2414 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAGCTT] 2412..2417  {2411 2417 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | AAGCTT] 2412..2417  {2411 2417 false false false false []}    0xc0002aa540} {  misc_feature    map[label:pBS72_0020] complement(2449..2955)  {2448 2955 true false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | ATGGAATTGA] 2737..2746  {2736 2746 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TGGAATTGAT] 2738..2747  {2737 2747 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | TTTTTT] 2770..2775  {2769 2775 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AAAACAAACA] 2780..2789  {2779 2789 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AGTCAATGTA] 2802..2811  {2801 2811 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | GTCAATGTAA] 2803..2812  {2802 2812 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TAATTTCAAT] 2835..2844  {2834 2844 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AATTTCAATC] 2836..2845  {2835 2845 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | ATTTCAATCC] 2837..2846  {2836 2846 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TTTCAATCCC] 2838..2847  {2837 2847 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | GAAATTCTGG] 2862..2871  {2861 2871 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | GAAAGAATTT] 2888..2897  {2887 2897 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | TTTTTT] 2895..2900  {2894 2900 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | GGAATAAAAA] 2980..2989  {2979 2989 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | GAATAAAAAT] 2981..2990  {2980 2990 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | AATAAAAATA] 2982..2991  {2981 2991 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | TTTTTT] 3057..3062  {3056 3062 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | TGTTTTTCCA] 3105..3114  {3104 3114 false false false false []}    0xc0002aa540} {  Match    map[label:Repeated sequence | GTTTTTCCAG] 3106..3115  {3105 3115 false false false false []}    0xc0002aa540} {  misc_feature    map[label:ClaI] 3120..3125  {3119 3125 false false false false []}    0xc0002aa540} {  GG    map[label:TS] 3126..3129  {3125 3129 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | GAGACC] 3131..3136  {3130 3136 false false false false []}    0xc0002aa540} {  misc_feature    map[label:Bsai bind] complement(3131..3136)  {3130 3136 true false false false []}    0xc0002aa540} {  GG    map[label:6] 3145..3148  {3144 3148 false false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | GTCTTC] 3151..3156  {3150 3156 false false false false []}    0xc0002aa540} {  misc_feature    map[label:BbsI bind] complement(3151..3156)  {3150 3156 true false false false []}    0xc0002aa540} {  Match    map[label:Forbidden sequence | GGTCTC]   {35 41 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | GAGACC]   {3130 3136 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | GAAGAC]   {15 21 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | GTCTTC]   {3150 3156 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAGCTT]   {390 396 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAGCTT]   {2411 2417 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAGCTT]   {390 396 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAGCTT]   {2411 2417 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | GAATTC]   {46 52 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | GAATTC]   {561 567 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | GAATTC]   {46 52 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | GAATTC]   {561 567 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | ATTTAAAT]   {2159 2167 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | ATTTAAAT]   {2159 2167 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | ATCGAT]   {2490 2496 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | ATCGAT]   {3119 3125 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | ATCGAT]   {2490 2496 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | ATCGAT]   {3119 3125 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {471 477 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {632 638 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {657 663 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {710 716 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {840 846 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {851 857 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {1128 1134 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {1196 1202 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {1389 1395 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {1616 1622 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {1650 1656 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {1674 1680 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {1779 1785 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {2044 2050 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | AAAAAA]   {2116 2122 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | TTTTTT]   {703 709 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | TTTTTT]   {1292 1298 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | TTTTTT]   {2094 2100 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | TTTTTT]   {2769 2775 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | TTTTTT]   {2894 2900 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | TTTTTT]   {3056 3062 false false false false []}    0xc0002aae00} {  Match    map[label:Forbidden sequence | GGGGGG]   {2272 2278 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TTAAAAAAAA]   {708 718 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AAGGGAAAGA]   {1132 1142 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AGGGAAAGAA]   {1133 1143 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AAAAAACTTT]   {1196 1206 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AAAAACTTTT]   {1197 1207 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TATACCTTAC]   {1229 1239 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TAAAAAAATG]   {1673 1683 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AATCAAAAAA]   {1775 1785 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AAAAAACAAA]   {1779 1789 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AGAAACAATT]   {2000 2010 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | GAAACAATTA]   {2001 2011 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AAACAATTAA]   {2002 2012 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TATTTAGAAA]   {2101 2111 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AAAAAAATAT]   {2116 2126 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TTTATTTAGA]   {2166 2176 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | ATTTAATGAG]   {2210 2220 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AAAAATATTA]   {2235 2245 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | ATTAAAATTT]   {2279 2289 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TTAAAATTTA]   {2280 2290 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TAAAATTTAA]   {2281 2291 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AAAATTTAAT]   {2282 2292 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | CTAATAAAAT]   {2318 2328 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | GGGATTAAAA]   {2370 2380 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | GGATTAAAAT]   {2371 2381 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | GATTAAAATT]   {2372 2382 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | ATTAAAATTT]   {2373 2383 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TTAAAATTTA]   {2374 2384 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TAAAATTTAA]   {2375 2385 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AAAATTTAAT]   {2376 2386 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AAATTTAATG]   {2377 2387 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AATTTAATGA]   {2378 2388 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TTAAGAAAAG]   {2404 2414 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | ATGGAATTGA]   {2736 2746 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TGGAATTGAT]   {2737 2747 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AAAACAAACA]   {2779 2789 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AGTCAATGTA]   {2801 2811 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | GTCAATGTAA]   {2802 2812 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TAATTTCAAT]   {2834 2844 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AATTTCAATC]   {2835 2845 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | ATTTCAATCC]   {2836 2846 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TTTCAATCCC]   {2837 2847 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | GAAATTCTGG]   {2861 2871 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | GAAAGAATTT]   {2887 2897 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | GGAATAAAAA]   {2979 2989 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | GAATAAAAAT]   {2980 2990 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | AATAAAAATA]   {2981 2991 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | TGTTTTTCCA]   {3104 3114 false false false false []}    0xc0002aae00} {  Match    map[label:Repeated sequence | GTTTTTCCAG]   {3105 3115 false false false false []}    0xc0002aae00}]}\n"]},{"data":{"text/plain":["24918 <nil>"]},"execution_count":6,"metadata":{},"output_type":"execute_result"}],"source":["annotatedSequence := findProblematicSequences(sequence)\n","fmt.Println(annotatedSequence)"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"8op-7lxCkB8H","vscode":{"languageId":"python"}},"outputs":[],"source":["genbank.Write(annotatedSequence, \"annotatedSequence.gb\")"]}],"metadata":{"colab":{"collapsed_sections":["96PZqanZBAle","3STJpf80Bl9Z"],"name":"#3 - AutomaticAnnotationOfProblematicSequences.ipynb","provenance":[{"file_id":"1NE42_1QHeAyEGTGuAxpsgtGsyJIcIr3I","timestamp":1634684634055},{"file_id":"1JVQfcSFEBoIV4TNCDRYCkcLssQhfp2S2","timestamp":1634426177979},{"file_id":"1GWFFYUcduoykRm08R6Jq7OacGQmDF1BS","timestamp":1634327217511},{"file_id":"1Ts_naBl0P_KfVvwC90Fb-JGWDeP6qjrV","timestamp":1634234790466},{"file_id":"14Bh2CljYULhD03AKCNGlJ3YgM9T5mcRa","timestamp":1627231003334},{"file_id":"1fZTAiBlR5eicaMu4nhhtfeJZEGMUAMHD","timestamp":1626732496856},{"file_id":"1NGDMQi-OGV5-XAbOgz87JWtSc4l2hHyh","timestamp":1626622594804}]},"kernelspec":{"display_name":"Go","name":"gophernotes"}},"nbformat":4,"nbformat_minor":0}