1217 days ago
Perl script to check modules installed !
#use strict; use warnings; use ExtUtils::Installed; # # First, check if all the required modules...my @import_modules = ( 'Cwd', 'File::chdir',...in', 'File::Remove', 'Capture::Tiny', 'File::Tem...# end 'for' } # end 'BEGIN' block1214 days ago
Install htop in elementary/Ubuntu OS !
...apt-get install htop Reading package lists... Done Building dependency tree Reading state i...following packages were automatically installed and are no long...aded. Need to get 80.0 kB of archives. After this operation,...tting up htop (2.1.0-3) ... Processing triggers for desktop-fi...1211 days ago
1207 days ago
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://...seqs = yaml.load(requests.get("https://www.ncbi.nlm.nih.gov/core/assets/gen...seqs['genbank-sequences'] print("got %d sequences" % len(seqs)) from Bio i...1195 days ago
Install NCBI entrez-direct and esearch using conda !
$ conda install -c bioconda entrez-direct Collecting package metadata (current_repodata.json):...nt: done ==> WARNING: A newer version of conda exists. 13.9-pl5262he881...([y]/n)? y Downloading and Extracting Packages entrez-direct-13.9 |...1160 days ago
Download genome using NCBI esearch command line !
#Download using command line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -query "CP003...lignment free comparision #conda install -c bioconda fastani fastANI -...1160 days ago
R script to visualize fastANI core-genome comparison
####### # Purpose: Visualize fastANI core-genome comparison # Usage: Rscript # Output: .pdf # Uses genoPlotR package: http://genoplotr.r-forge...#Parse command line arguments query_fasta=commandArgs(TRUE)[1] subject_f...1160 days ago
1113 days ago
1113 days ago