Results for "C"
Bio-Scripts
#use strict; use warnings; use ExtUtil...led; use LWP::Simple; use Archive::Extract; # # First, check if all t...my @import_modules = ( 'Cwd', 'File::chdir',...', 'File::Remove', 'Capture::Tiny', 'File::Tem...end 'for' } # end 'BEGIN' block #Bash script else here...1215 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' block1212 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...1208 days ago
- ...taENV) ➜ setu git:(master) ✗ conda install -c bioconda ragout Collecting package metadata (current_repodata.json): done S...nt: failed with repodata from current_repodata.json, will ret...################### | 100% decorator-4.3.0 | 10 KB...
1204 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...1193 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 |...1158 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 -...1158 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...1158 days ago
- ...d-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda/label/cf201901 canu Collecting package metadata (current_repodata.json): done S.... bioconda/label/cf201901 Proceed ([y]/n)? y Downloadin...######### | 100% Preparing transaction: done Verifying transact...
1111 days ago
- vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda shasta Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.
1111 days ago
