Results for "r"
Bio-Scripts
Perl script to run awk inside perl
#!/usr/local/bin/perl eval 'exec /usr/local/bin/perl -S $0 ${1+"$@"}' if $running_under_some_shell; # this emulates #! processing on NIH machines. # (remove #! line above if indiges...itches $, = ' '; # set output field separator $\ = "\n"; # set output...1227 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtils::Installed; use LWP::Simple; use Archive::Extract; # # First, check if all the required modules have been inst...e $_ OK!\n";} } # end 'for' } # end 'BEGIN' block #B...y_DB/silvaDB/SILVA_138.1_LSUParc_tax_silva.fasta' ); #In...1224 days ago
- #use strict; use warnings; use ExtUtils::Installed; use LWP::Simple; use Archive::Extract; # # First, check if all the required modules have been inst...base # BEGIN { my @import_modules = ( 'Cwd',...e $_ OK!\n";} } # end 'for' } # end 'BEGIN' block #B...
1222 days ago
Perl script to check modules installed !
#use strict; use warnings; use ExtUtils::Installed; # # First, check if all the required mo...ystem # BEGIN { my @import_modules = ( 'Cwd',...OSIX', 'Tie::File', 'Try::Tiny', 'Data::Dumper',...etopt::Long', 'Statistics::R', 'Math::Round', 'F...1219 days ago
Install htop in elementary/Ubuntu OS !
...~$ sudo apt-get install htop Reading package lists... Done Building dependency tree Reading state infor...one The following packages were automatically installed and...l be installed: htop 0 upgraded, 1 newly installed, 0 to...6684 files and directories currently installed.) Preparing t...1216 days ago
- ...JitMetaENV) ➜ setu git:(master) ✗ conda install -c bioconda ragout Collecting package metadata (current_repodata.json): done Sol...flexible solve. Solving environment: failed with repodata f...##################### | 100% ragout-2.3 | 2.8 MB...
1212 days ago
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "comp...require you to sign up import requests import yaml seq...= seqs['genbank-sequences'] print("got %d sequences" % len(s...seq[nm] = ''.join(dna) import json with open("data/allseq...1200 days ago
Install NCBI entrez-direct and esearch using conda !
$ conda install -c bioconda entrez-direct Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. 13....################################ | 100% Preparing transaction: done Ver...1165 days ago
Download genome using NCBI esearch command line !
...nd line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -form...fasta > seq1.fa esearch -db nucleotide -query "CP003784.1" | efetch -forma...ize -o fastani.out #Plot using sequences Rscript plotSeq.R seq1.fa seq2....1165 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-f...=commandArgs(TRUE)[1] subject_fasta=commandArgs(TRUE)[2] fastANI_visual_fi...1165 days ago
