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TPS Reserve For Camellia and Tomato Crop

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Anam04anjum edited this page Oct 24, 2021 · 17 revisions

Managed by Anam Anjum

  • SYSTEM DETAILS:

  • Windows edition:

  • Windows 8.1 single language.

  • System:

    • processor: Intel(R)Core(TM)i5-4200u CPU @1.60 GHz
    • Installed RAM: 4.00 GB
    • System Type: 64-bit Operating System, x64-based processor
  • 16/9/2021
  • Make a wikipage (Make sure you have a Github Account log in).
  • After receiving the Github repositories invitation for the specific repository
  • Go to wiki
  • Create New Page option will be seen.
  • Click on that and get started with your content.Markdown Guide

  • 31/8/2021

  • INSTALLATIONS

    • OS-Windows 8.1 6.3 amd64
    • JAVA-6.0.2
    • APACHE MAVEN-3.8.2
    • GIT-2.33.0
    • PYTHON-3.9.5

  • ami and getpapers installation

    • By using the above link ami and getpapers installations can be done in Windows 10 which is very helpful.

  • For path setup go to: Control Panel\System and Security\System.

    • System properties will get open in advanced go to Environment variable
    • Add new path by putting software name in variable name, variable value will be the directory to the bin folder of the respective software or Application (in my case i.e. as below modify it accordingly)
    1. AMI- C:\Windows\System32\ami3\target\appassembler\bin
    2. CMD- C:\windows\system32
    3. GIT- C:\Program Files\Git\cmd
    4. JAVA- C:\Program Files\Java\jre1.8.0_301\bin
    5. JAVA_HOME- C:\Program Files\Java\jdk-16.0.2
    6. MAVEN- C:\Users\kash\Downloads\apache-maven-3.8.2-bin\apache-maven-3.8.2\bin
    7. PYGETPAPERS- C:\Users\kash\AppData\Local\Programs\Python\Python39\Scripts
    8. Path- C:\Users\kash\AppData\Local\Programs\Python\Python39\Scripts;C:\Users\kash\AppData\Local\Programs\Python\Python39
      ;%NVM_HOME%;%NYM_SYMLINK%;%JAVA%;%JAVA_HOME%;%MAVEN%;%GIT%;%AMI%;%CONTENTMINE%;%CMD%;%PYGETPAPERS%;C:\Users\kash\AppData\Local\Programs \Microsoft VS Code\bin

  • In my case path of NVM, python and java was created by my machine during Installation.

  • 2/9/2021

  • Pygetpapers

    • for pygetpapers PYTHON is a necessity which can easily available in the link below:
    • Python and Pygetpapers Installation
    • Download the Pygetpapers which contains Camellia TPS by running this Command on Command Prompt- pygetpapers -q "terpene synthase volatile Camellia AND (((SRC:MED OR SRC:PMC OR SRC:AGR OR SRC:CBA) NOT (PUB_TYPE:"Review")))" -o CamelliaTPS -x -p -s
  • 9/9/2021

  • Dictionary Creation:

    • This dictionary creation contain 80 TPS.
    • After the creation of XLSX worksheet with all the TPS from the papers(pygetpapers) and Google scoping.
  • 12\10\2021
    • Convert the XLSX Worksheet(Camellia_TPS) into .TXT(Camellia_Tps), rename it as gene.txt or replace the name of the file with gene.txt in command line. locate the file into user directory.
    • For Dictionary Creation use the command amidict -v --dictionary eo_Gene --directory gene --input gene.txt create --informat list --outformats xml
    • It will create a Dictionary in the user directory named eo_Gene.
  • eo_CAMSITps
  • eo_tomato
  • eo_Enzyme

  • Testing Dictionary:

    • An error appeared while testing the dictionary java.lang.NullPointerException. Which is resolved using following codes:
    • To update your ami installation, follow these steps:
      1. Navigate to your ami3 directory: cd ami3
      2. Copy latest changes: git pull
      3. Rebuild ami3: mvn clean install -Dmaven.test.skip=true
      • Simply run above commands in Command prompt.
    • full data table is formed in the directory.(.HTML) *Full data table is not well defined.
  • 4\10\2021 Full Data Table Error
  • 19\10\2021

  • Full Data Table Correction:

    1. Edited the Command for Testing Dictionary ami -p "TPSvolatile" search --dictionary eo_Gene.xml
    2. Used this Command Instead ami -p "CamelliaTPS" search --dictionary eo_CAMSITps.xml where CamelliaTPS is corpus folder name and eo_CAMSITpsis Dictionary name.
    3. Make sure your testing Dictionary should be in the user directory(i.e C:\Windows\System32) and a copy of Dictionary into Corpus folder(i.e CamelliaTPS)
  • Correct FULL DATA TABLE

  • 19\09\2021

  • MetaData Analysis Script

  • First of all install Code Editor which redefined and optimized for building and debugging modern web and cloud applications.

  • I downloaded Code Editor

  • After Installation of code editor

  • Make Sure you have Python, open VS code go to EXTENSIONS or type Ctrl+Shift+X. If you already have Python installed, To verify it's installed, create a new terminal (Ctrl + Shift + `) and try running the following command(In the code editor):

  • python --version

  • You should see something similar to the following:

  • Python 3.9.5

  • Now install Excel Viewer. using same Mechanism.

  • 21\09\2021

  • Using VS Code in the New Extension(Ctrl+Shift+X) Install:

  • Scispacy

  • Using pip install scispacy

  • Got the Error:

  • Installing collected packages: nmslib, conllu, scispacy Running setup.py install for nmslib ... error ERROR: Command errored out with exit status 1: command: 'C:\Users\Kash\AppData\Local\Programs\python\python39\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\kash\\AppData\\Local\\Temp\\pip-install-r8541oln\\nmslib_1bb3287db71641a59d5a808f19482206\\setup.py'"'"'; __file__='"'"'C:\\Users\\kash\\AppData\\Local\\Temp\\pip-install-r8541oln\\nmslib_1bb3287db71641a59d5a808f19482206\\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\kash\AppData\Local\Temp\pip-record-o4xzbd_5\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\Kash\AppData\Local\Programs\python\python39\Include\nmslib' cwd: C:\Users\kash\AppData\Local\Temp\pip-install-r8541oln\nmslib_1bb3287db71641a59d5a808f19482206\ Complete output (9 lines): Dependence list: ['pybind11<2.6.2', 'psutil', "numpy>=1.10.0,<1.17 ; python_version=='2.7'", "numpy>=1.10.0 ; python_version>='3.5'"] C:\Users\Kash\AppData\Local\Programs\python\python39\lib\site-packages\setuptools\dist.py:717: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running install running build running build_ext Extra compilation arguments: ['/EHsc', '/openmp', '/O2', '/DVERSION_INFO=\\"2.1.1\\"'] building 'nmslib' extension error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/ ---------------------------------------- ERROR: Command errored out with exit status 1: 'C:\Users\Kash\AppData\Local\Programs\python\python39\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\kash\\AppData\\Local\\Temp\\pip-install-r8541oln\\nmslib_1bb3287db71641a59d5a808f19482206\\setup.py'"'"'; __file__='"'"'C:\\Users\\kash\\AppData\\Local\\Temp\\pip-install-r8541oln\\nmslib_1bb3287db71641a59d5a808f19482206\\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\kash\AppData\Local\Temp\pip-record-o4xzbd_5\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\Kash\AppData\Local\Programs\python\python39\Include\nmslib' Check the logs for full command output.

  • Yake

  • Using pip install yake

  • BS4

  • Using pip install bs4

  • SCOPING FOR S.lycopersicum

  • 26\09\2021

  • Download the pygetpapers for S.lycopersicum using the following command: pygetpapers -q "terpene synthase volatile Solanum lycopersicum AND (((SRC:MED OR SRC:PMC OR SRC:AGR OR SRC:CBA) NOT (PUB_TYPE:"Review")))" -o TomatoTPS -x -p -s

  • It will show the Result showing: Final query is terpene synthase volatile Solanum lycopersicum AND (((SRC:MED OR SRC:PMC OR SRC:AGR OR SRC:CBA) NOT (PUB_TYPE:"Review")))

  • Total hits found out to be 129.

  • It will create a folder "TomatoTPS" containing papers.

  • 7\10\2021

  • After scoping through TomatoTPS pygepapers and searching on Google Search for Solanum lycopersicum Terpene Synthase.

  • This S.lycopersicum_Tps file is obtained.

  • 18\10\2021

  • Created eo_SolycGene Dictionary.

  • 13\10\2021

  • Py4ami Installation

  • Git Clone
  • pip install py4ami
  • Warning: you are using pip version 21.2.4; however version 21.3 is avalaible you should consider upgrading via the C:\Program Files\python 3.9\python.exe pip install --upgrade pip command.
  • Upgraded pip using pip install --upgrade pip
  • pip upgrade
  • command pip install py4ami
  • py4ami installation Error
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