Results for "C"
Bio-Scripts
#Create a conda environment. #Install a Python package in the terminal using conda. $ conda create -n myen...reate -n myenv Python=3.7 $ conda env create -f environment...onda activate myenv #Update Conda Environments Using a YAML...mpy #List Installed Dependencies Within an Environment (my...1020 days ago
Commands to Remove White Space In Text Or String Using Awk And Sed In Linux
text=" ATGGTV AGTGACCTAGAGTGATGA G GGRTTT" echo "$text" | sed 's/ //g' OR echo "$text" |...gsub(/ /,""); print }' Return: ATGGTVAGTGACCTAGAGTGATGAGGGRTTT echo "$...echo "$text" | sed 's/ \$//g' #Multiple space cat /tmp/test.txt | sed 's/...1014 days ago
Trim the reads in loop using Trimmomatic !
...*_1.fastq.gz do base=$(basename ${infile} _1.fastq.gz) trimmomatic PE ${infile} ${base}_2.fastq....2un.trim.fastq.gz \ SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:NexteraPE-PE.fa:2:40:15...1013 days ago
Oneliner to convert lower-case to sequence masked with Ns
perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna awk '{if(/^[^>]/)gsub(/[a-z]/,"N");print $0}' genomic.fna > genomic.N-masked.fna1008 days ago
Perl script for Smith-Waterman Algorithm
...usage statement die "usage: $0 \n" unless @ARGV == 2; # get sequences from command line my ($seq1, $seq2)...@ARGV; # scoring scheme my $MATCH = 1; # +1 for letters that match my $MISMATCH = -1; # -1 for...1008 days ago
- ...: 0 = pairwise, 1 = query-anchored showing identities, 2 =...ut, 9 = Tabular output with comments [Integer] default...uired region in query (-1 indicates end of query) [Integer]...efault = hit_file -T Produce HTML output [T/F] defau...
1008 days ago
Command line to create blast uniref database !
#The NCBI BLAST+ distribution does not include 'blastpgp', it has been replaced by the 'psiblast' program. The 'blastpgp' program is available in the legacy NCBI BLAST package (no longe...ef90filt -i uniref90filt #When using NCBI BLAST+ the 'formatdb' comma...1008 days ago
Inreractive SCP / File transfer !
...bin/bash #next line prints hearer of script echo "Interactive Script to Copy File (files) / Directory using scp" #next line ch...finishes while loop done #next line check if entered value is not n...filename filename='null' #next line check if entered value is null,...1008 days ago
- #using : after a switch variable means it requires some input (ie, t: req...othing. while getopts “ht:r:p:v” OPTION do case $OPTION in h)...usage exit ;; esac done if [[ -z $TEST ]] ||...
1007 days ago
Get the Linux system information !
...ystem information program DIALOG_CANCEL=1 DIALOG_ESC=255 HEIGHT=0...dialog --title "$1" \ --no-collapse \ --msgbox "$resu...itle "Menu" \ --clear \ --cancel-label "Exit" \ --me...;; $DIALOG_ESC) clear echo "Program abor...1006 days ago
