20210206

Contents
  1. 1. Working directories
  2. 2. CPU of mobile device
  3. 3. Check RNA-Seq from Wang Jiao
    1. 3.1. Basic information of sequencing package
      1. 3.1.1. Directories in .zip file
      2. 3.1.2. Document list
      3. 3.1.3. FPKM documents
  4. 4. RNA-Seq pipeline
  5. 5. HEV sequence downloading/Yin Wenjiao
    1. 5.1. Database selection
    2. 5.2. Nucleotide database access
    3. 5.3. SRA
    4. 5.4. HEVnet | RIVM
  6. 6. NCBI Virus
    1. 6.1. Download with command line
  7. 7. command line - Convert .xls/.xlsx spreadsheets to multiple .csv’s based on a list - Ask Ubuntu
    1. 7.1. in2csv — csvkit 1.0.2 documentation
    2. 7.2. vba - fast way to batch convert multiple csv files into excel files - Stack Overflow
    3. 7.3. Armin / csv2xlsx · GitLab
    4. 7.4. gnumeric
    5. 7.5. LibreOffice
    6. 7.6. unoconv

Working directories

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i=/media/ht/ht_5T/Work/Projects/NFE/Ab/Selected_Ab.pdf # Ab list for Nrf2 related work
#
####################################################################
# HGNC added
####################################################################
#
i=/media/${USER}/ht_5T/Database/Management/Database.Rmd; setsid chromium-browser ${i%.Rmd}.html
subl ${i}
#
i=/media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106
pcmanfm -n ${i}; cd ${i} # Check RNA-Seq from Wang Jiao
#
i=/media/ht/ht_5T_5/HLA-G/SRA/E-MTAB-1733/GZ
pcmanfm -n ${i}; cd ${i} # "Truncated_Rev" analysis in progress/Dell
#
i=/media/ht/ht_5T/Work/Projects/NFE/Summary/NFE2_Sum_Large.pptx
setsid wpp ${i} # B95-8-Nrf2 revised

CPU of mobile device

Check RNA-Seq from Wang Jiao

To be deleted

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i=/media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106
pcmanfm -n ${i}; cd ${i}

Basic information of sequencing package

Directories in .zip file

  • differential
    • Caski-VS-Caski_FL2/, Demo
      • Caski-VS-Caski_FL2.all.xls
      • Caski-VS-Caski_FL2.diff.png
      • Caski-VS-Caski_FL2.diff.xls
    • control-VS-FL2/
    • control-VS-tBHQ/
    • HeLa-VS-HeLa_FL2/
    • HeLa-VS-HeLa_tBHQ/
    • SiHa-VS-SiHa_FL2/
    • SiHa-VS-SiHa_tBHQ/
  • expression
    • Caski_FL2.fpkm.xls
    • Caski.fpkm.xls
    • count_table.xls
    • HeLa_FL2.fpkm.xls
    • HeLa.fpkm.xls
    • HeLa_tBHQ.fpkm.xls
    • SiHa_FL2.fpkm.xls
    • SiHa.fpkm.xls
    • SiHa_tBHQ.fpkm.xls
  • fastqc_clean
  • fastqc_raw
  • GO
    • Caski-VS-Caski_FL2/, Demo
      • diff.go.BP.dotplot.pdf
      • diff.go.BP.dotplot.tiff
      • diff.go.CC.dotplot.pdf
      • diff.go.CC.dotplot.tiff
      • diff.go.MF.dotplot.pdf
      • diff.go.MF.dotplot.tiff
      • enrich-GO-BP.xls
      • enrich-GO-CC.xls
      • enrich-GO-MF.xls
    • control-VS-FL2/
    • control-VS-tBHQ/
    • HeLa-VS-HeLa_FL2/
    • HeLa-VS-HeLa_tBHQ/
    • SiHa-VS-SiHa_FL2/
    • SiHa-VS-SiHa_tBHQ/
  • KEGG, seven (7) sub-directories
    • Caski-VS-Caski_FL2/, Demo
      • diff.kegg.dotplot.pdf
      • diff.kegg.dotplot.tiff
      • enrich-kegg.xls
    • control-VS-FL2/
    • control-VS-tBHQ/
    • HeLa-VS-HeLa_FL2/
    • HeLa-VS-HeLa_tBHQ/
    • SiHa-VS-SiHa_FL2/
    • SiHa-VS-SiHa_tBHQ/
  • mapping, .xls, simple document, mapping log
    • C33A-FL2-mapping.xls
    • Caski_FL2-mapping.xls
    • Caski-mapping.xls
    • HeLa_FL2-mapping.xls
    • HeLa-mapping.xls
    • HeLa_tBHQ-mapping.xls
    • mapping-stats.xls
    • SiHa_FL2-mapping.xls
    • SiHa-mapping.xls
    • SiHa_tBHQ-mapping.xls
  • SNP, colleciton of .vcf documents
    • C33A-FL2.vcf
    • Caski_FL2.vcf
    • Caski.vcf
    • HeLa_FL2.vcf
    • HeLa_tBHQ.vcf
    • HeLa.vcf
    • SiHa_FL2.vcf
    • SiHa_tBHQ.vcf
    • SiHa.vcf
    • SNP_stats.xls

Document list

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i=/media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/Doc.list
subl ${i}

Extensions of documents

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i=/media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/Doc.list
cat ${i} | awk -F'.' ' { print $NF} ' | sort | uniq
File extension description
  • fo, xml document of FASTQC
  • html, output of FASTQC
  • pdf
  • png
  • tiff
  • txt
  • vcf # bcftools_filterCommand=filter -O v -o SiHa_FL2.vcf -i ‘%QUAL>30 && (DP4[2]+DP4- [3]) >2’ SiHa_FL2.bcf
  • xls
    • ./differential/
      • .diff.xls
      • .all.xls
    • ./mapping/
      • -mapping.xls
      • mapping-stats.xls
    • ./GO/
      • enrich-GO-CC.xls
      • enrich-GO-BP.xls
      • enrich-GO-MF.xls
    • ./KEGG/, -kegg.xls
    • ./SNP/
    • ./expression/, .fpkm.xls
      • /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/Caski.fpkm.xls
      • /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/Caski_FL2.fpkm.xls
      • /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/HeLa.fpkm.xls
      • /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/HeLa_FL2.fpkm.xls
      • /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/HeLa_tBHQ.fpkm.xls
      • /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/SiHa.fpkm.xls
      • /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/SiHa_FL2.fpkm.xls
      • /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/SiHa_tBHQ.fpkm.xls
  • xlsx
    • ./fastqc_clean/QC_stas.xlsx
    • ./fastqc_raw/QC_stas.xlsx

FPKM documents

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i=/media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/
find ${i} -type f | ag '.fpkm.xls'
find ${i} -type f | ag '.fpkm.xls' | sed "s|^|setsid et |"
find ${i} -type f | ag '.fpkm.xls' | sed "s|^|setsid wps |"
FPKM Tables 
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setsid et /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/Caski.fpkm.xls
setsid et /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/Caski_FL2.fpkm.xls
setsid et /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/HeLa.fpkm.xls
setsid et /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/HeLa_FL2.fpkm.xls
setsid et /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/HeLa_tBHQ.fpkm.xls
setsid et /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/SiHa.fpkm.xls
setsid et /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/SiHa_FL2.fpkm.xls
setsid et /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/SiHa_tBHQ.fpkm.xls
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setsid wps /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/Caski.fpkm.xls
setsid wps /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/Caski_FL2.fpkm.xls
setsid wps /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/HeLa.fpkm.xls
setsid wps /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/HeLa_FL2.fpkm.xls
setsid wps /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/HeLa_tBHQ.fpkm.xls
setsid wps /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/SiHa.fpkm.xls
setsid wps /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/SiHa_FL2.fpkm.xls
setsid wps /media/ht/ht_5T/Work/Projects/NFE/RNA-Seq_20201106/expression/SiHa_tBHQ.fpkm.xls

RNA-Seq pipeline

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i=/media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/NGS_Softs/RNA-Seq/
pcmanfm -n ${i}; cd ${i} # new directory created
#
i=/media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/NGS_Softs/RNA-Seq/RNA-Seq_Learning.md
subl ${i} # collection of selected publication

HEV sequence downloading/Yin Wenjiao

Keyword of “txid12461[Organism:exp] “ was worked in web searching in NCBI database.

Database selection

Nucleotide database access

SRA

HEVnet | RIVM

Members of HEVnet
  • Stephan Aberle, Medical University of Vienna, Vienna, Austria
  • Lorenzo Subissi, Sciensano, Brussels, Belgium
  • Vanessa Suin, Sciensano, Brussels, Belgium
  • Sofie Midgley, Virus surveillance and research, Statens Serum Institut, Copenhagen, Denmark
  • Tatiana Kuznetsova, Department of Virology and Immunology, National Institute for Health Development, Tallinn, Estonia
  • Jacques Izopet, Federative Intitute of Biology, National Reference Center for Hepatitis E virus, Toulouse, France
  • Nicole Pavio, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
  • Christine Baechlein, University of Veterinary Medicine Hannover, Hannover, Germany
  • Sally A. Baylisa, Paul-Ehrlich-Institut (PEI), Langen, Germany
  • Victor M. Corman, Institute of Virology Charité – Universitätsmedizin Berlin, Berlin, Germany
  • Mirko Fabera, Robert Koch-Institut, Berlin, Germany
  • Reimar Johne, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
  • Christel Kamp, Paul-Ehrlich-Institut (PEI), Langen, Germany
  • Juergen J. Wenzel, Institute of Clinical Microbiology and Hygiene, Regensburg University Medical Center, Regensburg, Germany
  • Suzie Coughlan, National virus reference laboratory, University College Dublin, Dublin, Ireland
  • Ilaria Di Bartolo, Istituto Superiore di Sanità, Rome, Italy
  • Roberto Bruni, Istituto Superiore Di Sanità, Rome, Italy
  • Anna Rita Ciccaglionea, Istituto Superiore di Sanità, Rome, Italy
  • Anna Rosa Garbuglia, Laboratory of virology INMI Spallanzani IRCCs Italy
  • Elisabetta Suffredini, Department of Food safety, Nutrition and Veterinary public health, Istituto Superiore di Sanità, Rome, Italy
  • Ingeborg Boxman, the Netherlands Food and Consumer Product Safety Authority (NVWA), the Netherlands
  • Boris Hogema, Sanquin Blood Supply Foundation, Amsterdam, the Netherlands
  • Wim van der Poel, Wageningen BioVeterinary Research, Wageningen, the Netherlands
  • Hans Zaaijera, Sanquin Blood Supply Foundation, Amsterdam, the Netherlands
  • Rita de Sousaa, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
  • Branko Velebit, Institute of Meat Hygiene and Technology, Serbia
  • Ana Avellóna, Viral Hepatitis Reference and Research Laboratory National Center of Microbiology Carlos III Health Institute, Madrid, Spain
  • Maria Buti, Hospital Universitario Valle Hebron, Barcelona, Spain
  • Rosina Girones, Section of Microbiology, Virology and Biotechnology Department of Genetics, Microbiology and Statistics Faculty of Biology University of Barcelona, Barcelona, Spain
  • Josep Quer, Vall d’Hebron Institut Research, Barcelona, Spain
  • Frederik Widén, National Veterinary Institute (SVA), Uppsala, Sweden
  • Heléne Norder, Sahlgrenska University Hospital, Gothenburg, Sweden
  • Kristina Nyström, Sahlgrenska University Hospital, Gothenburg, Sweden
  • Claudia Bachofen, Institute of Virology, Vetsuisse Faculty of the University of Zürich, Zürich, Switzerland
  • Roland Sahli, Institute of microbiology, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, SwitzerlandHarry Daltona, Royal Cornwall Hospital, Treliske, UK
  • Samreen Ijaza, Public Health England, London, UK
  • Samantha Treagus, CEFAS, University of Exeter, UK
  • Michael Kulka, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Unites States of America
  • Valentina Rizzi, European Food Safety Authority (EFSA), Unit of Biological Hazards and Contaminants, Parma, Italy

HEVnet

NCBI Virus

  1. Visit NCBI Virus
  2. Click nucleotide
  • taxid:2697049
  • 61,835 hits

Downloaded

Download with command line

Note showed in NCBI_Learning.html.

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ls /media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/NCBI/Summary/NCBI_Learning.html

command line - Convert .xls/.xlsx spreadsheets to multiple .csv’s based on a list - Ask Ubuntu

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#!/usr/bin/env perl
use strict;
use warnings;
use autodie;
# CPAN modules required:
use Spreadsheet::Write;
use Text::CSV;

my $xlsx_file = shift @ARGV;
$xlsx_file .= ".xlsx" unless $xlsx_file =~ /\.xlsx$/;
my $xlsx = Spreadsheet::Write->new(file => $xlsx_file);
my $csv = Text::CSV->new({binary => 1});

for my $csv_file (@ARGV) {
    my @rows = ();
    open my $fh, "<:encoding(utf8)", $csv_file;
    while (my $row = $csv->getline($fh)) {
        push @rows, $row;
    }
    $csv->eof or $csv->error_diag();
    close $fh;  

    (my $sheet_name = $csv_file) =~ s/\.[^.]+$//;   # strip extension
    $xlsx->addsheet($sheet_name);
    $xlsx->addrows(@rows);
}
$xlsx->close();
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/path/to/create_xlsx.pl file.xlsx *.csv
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while IFS= read -r file; do
    while IFS= read -r sheet; do
        in2csv --sheet "$sheet" "$file" > "${file%.*}-${sheet}.csv"
    done < <(in2csv -n "$file")
done < <(find . -name '*.xls' -o -name '*.xlsx')
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shopt -s globstar  # enable recursive globbing
for f in **/*.xls{,x}  # for files ending in .xls or .xlsx
do
    in2csv -n "$f" |   # get the sheetnames
      xargs -I {} bash -c 'in2csv --sheet "$2" "$1" > "${1%.*}"-"$2".csv' _ "$f" {} # {} will be replaced with the sheetname
done
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find . -name '*.xls' -o -name '*.xlsx' -exec in2csv --write-sheets "-" {} \;

in2csv — csvkit 1.0.2 documentation

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sudo apt install csvkit

vba - fast way to batch convert multiple csv files into excel files - Stack Overflow

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Sub CSVtoXLSB2()
Dim wb As Workbook
Dim CSVPath As String
Dim sProcessFile As String

CSVPath = "C:\your_path_here\"
sProcessFile = Dir(CSVPath & "*.csv")
Do Until sProcessFile = ""   ' Loop until no file found.
    Set wb = Application.Workbooks.Open(CSVPath & sProcessFile)
    wb.SaveAs CSVPath & Split(wb.Name, ".")(0) & ".xlsb", FileFormat _
        :=50, Password:="", WriteResPassword:="", ReadOnlyRecommended:=False, _
        CreateBackup:=False
    wb.Close
    sProcessFile = Dir()   ' Get next entry.
Loop
Set wb = Nothing
End Sub

Armin / csv2xlsx · GitLab

gnumeric

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ssconvert file.csv file.xls

LibreOffice

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--convert-to output_file_extension[:output_filter_name] [-outdir ouput_dir] files
      Batch convert files.
      If -outdir is not specified then current working dir is used as output_dir.
      Eg. -convert-to pdf *.doc
          -convert-to pdf:writer_pdf_Export -outdir /home/user *.doc

unoconv

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unoconv -f xls foo.csv bar.csv
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{% if theme.mermaid.enable %} {% endif %}

tag:

    缺失模块。
    1、请确保node版本大于6.2
    2、在博客根目录（注意不是yilia根目录）执行以下命令：
    npm i hexo-generator-json-content --save

    3、在根目录_config.yml里添加配置： 

      jsonContent:
    meta: false
    pages: false
    posts:
      title: true
      date: true
      path: true
      text: false
      raw: false
      content: false
      slug: false
      updated: false
      comments: false
      link: false
      permalink: false
      excerpt: false
      categories: false
      tags: true

Step by step.