20210307

Contents
  1. 1. Working directories
    1. 1.1. File manager
    2. 1.2. Stopwatch
  2. 2. Download
    1. 2.1. Reactive Oxygen Species
    2. 2.2. Herpesviridae
      1. 2.2.1. Sequence download
    3. 2.3. Datasets - NCBI

Working directories

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i='/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Rev_3'; pcmanfm -n ${i}; cd ${i}
#
i='/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Rev_3/p62_Draft_20210307_2130.docx'; setsid wps ${i} # restart

File manager

Among file managers listed in 30 Best File Managers for Linux Systems, I preferred as below

  • PCManFM/PCMan
  • Thunar
  • XFE File Manager
  • SpaceFM
  • Caja
  • Pantheon

Stopwatch

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man leave
leave +000010 # 10 seconds countdown

Download

Reactive Oxygen Species

Herpesviridae

Taxonomy ID: 10292 (for references in articles please use NCBI:txid10292)

Lineage( full )
Viruses; Duplodnaviria; Heunggongvirae; Peploviricota; Herviviricetes; Herpesvirales

Sequence download

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i='/media/ht/ht_5T/Database/Virus/Herpesvirus/Herpesviridae/20210307'; cd ${i}
#
i='/media/ht/ht_5T/Database/Virus/Herpesvirus/Herpesviridae/20210307/nuccore_result.txt'
ls ${i} # Summary document
#

###################################################
# Single column to three columns
###################################################
Input='nuccore_result.txt'
Number=4
awk -v col=${Number} '{if(NR%col){printf "%5s\t",$0 }else {printf "%s\n",$0}} ' ${Input} > ${Input}.convert
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Input='nuccore_result.txt'
Number=4
awk -v col=${Number} '{if(NR%col){printf "%5s\t",$0 }else {printf "%s\n",$0}} ' ${Input} | sed "s/     /\t/" | sed 's/^\t\t//' > ${Input}.convert

Ref

Datasets - NCBI

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pip install ncbi-datasets-pylib
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      excerpt: false
      categories: false
      tags: true

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