20210223

Contents

1. 1. Working directories
2. 2. BLAST display
3. 3. Primer BLAST
4. 4. HEV
5. 5. R
   1. 5.1. ggtree installation

Working directories

i=/media/ht/ht_5T/Database/Virus/Herpesvirus/Herpesviridae; pcmanfm -n ${i}; cd ${i}
#
i=/media/ht/ht_5T/Database/Virus/Herpesvirus
pcmanfm -n ${i}; cd ${i}
#
i=/media/ht/ht_5T/Database/Virus/Herpesvirus/Herpesvirales_RefSeq.fas
FasCount ${i} # Output, 61
#
i=/media/ht/ht_5T/Database/Virus/Herpesvirus/Herpesviridae/Herpesviridae_RefSeq_20150320.fas
FasCount ${i} # Output, 73
#
i=/media/ht/ht_5T/Work/Projects/Herpesvirus_Project/EBV_CMV_Detect/20210219
pcmanfm -n ${i}; cd ${i}
#
i=/media/ht/ht_5T/Work/Projects/Herpesvirus_Project/EBV_CMV_Detect/20210219
pcmanfm -n ${i}; cd ${i}
Query=/media/ht/ht_5T/Work/Projects/Herpesvirus_Project/EBV_CMV_Detect/20210219/Quantitative_multi-target_RNA_profiling_in_EBV_infected_tumor_cells.fas
Subject=/media/ht/ht_5T/Database/Virus/Herpesvirus/Herpesviridae/Herpesviridae_RefSeq_20150320.fas
BLASTn ${Query} ${Subject}

BLAST display

• Display BLAST search results with custom output format - BLAST庐 Command Line Applications User Manual - NCBI Bookshelf

Primer BLAST

##################################################################
# BLASTn XXX YYY
##################################################################
function BLASTn {
  Query=$1; Subject=$2
  QueryBase=`basename ${Query}`; SubjectBase=`basename ${Subject}`; Tag=`date +%Y%m%d_%H%M`
  # blastn -query ${Query} -subject ${Subject} -outfmt 11 > blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.asn -max_hsps 10000 -num_alignments 10000
  # blast_formatter -archive blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.asn -outfmt 6 -out blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.csv; blast_formatter -archive blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.asn -line_length 100 -outfmt 0 -out blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.txt
  blastn -query ${Query} -subject ${Subject} -outfmt 6 > blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.csv -max_target_seqs 10000 -word_size 7
  blastn -query ${Query} -subject ${Subject} -outfmt 0 -line_length 100 > blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.txt -max_hsps 10000 -num_alignments 10000 -word_size 7
  blastn -query ${Query} -subject ${Subject} -outfmt 17 > blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.sam -max_target_seqs 10000 -word_size 7
  Query=$2; Subject=$1
  QueryBase=`basename ${Query}`; SubjectBase=`basename ${Subject}`
  # blastn -query ${Query} -subject ${Subject} -outfmt 11 > blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.asn -max_hsps 10000 -num_alignments 10000
  # blast_formatter -archive blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.asn -outfmt 6 -out blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.csv; blast_formatter -archive blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.asn -line_length 100 -outfmt 0 -out blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.txt
  blastn -query ${Query} -subject ${Subject} -outfmt 6 > blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.csv -max_target_seqs 10000 -word_size 7
  blastn -query ${Query} -subject ${Subject} -outfmt 0 -line_length 100 > blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.txt -max_hsps 10000 -num_alignments 10000 -word_size 7
  blastn -query ${Query} -subject ${Subject} -outfmt 17 > blastn_${QueryBase%.*}_vs_${SubjectBase%.*}_${Tag}.sam -max_target_seqs 10000 -word_size 7
  echo -e ${Green}'============================================'${NoColor}
  echo -e ${Green}'=============== BLASTn was Done ! ==============='
  echo -e ${Green}'============================================'${NoColor}
}

HEV

Subject=/media/ht/ht_5T/Work/Funding/2017_重大专项/Management/Administration/09_02_63_HEV/Seq/HEV_25.fasta
Query=/media/ht/ht_5T/Work/Funding/2017_重大专项/Management/Administration/09_02_63_HEV/Seq/20210223/HEV_20210131_Filtrated.fas # Extracted w/ location and sampling date
#
BLASTn ${Query} ${Subject}
#
i=/media/ht/ht_5T/Work/Funding/2017_重大专项/Management/Administration/09_02_63_HEV/Seq/HEV_25.fasta
cat ${i} | ag '>'
cat ${i} | ag '>' | wc -l

R

install.packages(c("boot", "broom", "cachem", "cli", "cluster", "crayon", "crul", "data.table", "dbplyr", "deldir", "dotCall64", "dplyr", "gert", "ks", "lifecycle", "MASS", "mgcv", "mime", "nlme", "pillar", "pkgKitten", "promises", "qpcR", "rappdirs", "RcppArmadillo", "rgdal", "rgl", "rJava", "rmarkdown", "segmented", "sf", "SparseM", "spatstat.data", "spdep", "testthat", "usethis", "waldo", "xfun", "XLConnect"))

ggtree installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ggtree")

赏

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