Results for "B"
Bio-Scripts
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...all the required modules have been installed in the system and download the mandatory database # BEGIN { my @impor...'Data::Dumper', 'File::Basename', 'Bio::SeqIO',...>extract( to => 'third_party_DB/silvaDB/SILVA_138.1_LSUParc_t...1218 days ago
- ...check if all the required modules have been installed in the system and download the mandatory database # BEGIN { my @impor...iny', 'Data::Dumper', 'File::Basename', 'Bio::SeqIO',...OK!\n";} } # end 'for' } # end 'BEGIN' block #Bash script el...
1216 days ago
Perl script to check modules installed !
...st, check if all the required modules have been installed in the system # BEGIN { my @import_modules...y::Tiny', 'Data::Dumper', 'File::Basename', 'Bio::SeqIO',...'Math::Round', 'File::Find', 'Bio::DB::Taxonomy', 'Pod::...1213 days ago
Install htop in elementary/Ubuntu OS !
...htop Reading package lists... Done Building dependency tree...onger required: gir1.2-vte-2.91 libido3-0.1-0 libllvm6.0 libwayla...em. The following NEW packages will be installed: htop 0 upgrad...selected package htop. (Reading database ... 176684 files and direc...1210 days ago
- ...setu git:(master) ✗ conda install -c bioconda ragout Collecting pac...ial frozen solve. Retrying with flexible solve. Solving environment...wnloading and Extracting Packages sibelia-3.0.7 | 24.8 MB...| 100% ragout-2.3 | 2.8 MB | ########################...
1206 days ago
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https:...ww.gisaid.org/ has more (1200?), but they require you to sign up...load(requests.get("https://www.ncbi.nlm.nih.gov/core/assets/genb...", nm) dna = Entrez.efetch(db='nucleotide',id=nm, rettype =...1194 days ago
Install NCBI entrez-direct and esearch using conda !
$ conda install -c bioconda entrez-direct Collecting package metadata...A newer version of conda exists. 13.9-pl5262he881be0_2 Proceed ([y]/n)? y...d Extracting Packages entrez-direct-13.9 | 5.2 MB | ########################...1159 days ago
Download genome using NCBI esearch command line !
...line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -query "CP003784.1...or alignment free comparision #conda install -c bioconda fastani fastANI -q...1159 days ago
R script to visualize fastANI core-genome comparison
...org #Parse command line arguments query_fasta=commandArgs(TRUE)[1] subject_fasta=commandArgs(TRUE)[2] fastANI_visual_file=commandArgs(TRUE)[3] library(genoPlotR) #Read fastA...1159 days ago
- ...k@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda/label/cf201901 canu Collecting p...environment: done ==> WARNING: A newer version of conda exists. bioconda/label/cf201901 Pr...
1112 days ago
