Results for "r"
Bio-Scripts
#GffRead: GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more. https://gith...ed / updated specs: - gffread The following package...:_libgcc_mutex-0.1-main gffread bioconda/linux-...transaction: done Executing transaction: done #Run as fol...1267 days ago
Set up WGD environment using conda !
#Wgd cannot be installed directly with bioconda at present, so it is slightly troub...y.whl (82 kB) Collecting coloredlogs>=10.0 Using cached c...any.whl (115 kB) Collecting progressbar2>=3.39 Using cach...1d4eac36dfb206639ce693f Stored in directory: /home/urbe/.c...1267 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
#Need to download i-adhore-3.0.01.tar.gz from https://wdiceryfd4rjn74bjhhtz2k5di--bioinformatic...warn_unused_result [-Wunused-result] system(command.ap...IX.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testse...nvs/wgd/./testset/datasetII/ptr_lists_030210_201/scaffold_119...1267 days ago
Command to create conda environment !
# using pip pip install -r requirements.txt # using Conda conda create --name --file requirements.txt #Using yaml conda env create -f environment.yml #Listing env conda env list #Create env with python36 conda create -n myenv python=3.61264 days ago
Steps to install Conda on Linux !
Download the installer: Miniconda installer for Linux. ( https://docs.conda.io...atest/miniconda.html#linux-installers ) Anaconda installer for Li...llation $ conda -V A few other frequently used commands # l...onment and its dependencies conda remove --name envname --all #...1246 days ago
Converting from Windows-style to UNIX-style line endings with dos2unix
...apt install dos2unix [sudo] password for bioqueen: Reading packa...ency tree Reading state information... Done The following...ayland-egl1-mesa Use 'sudo apt autoremove' to remove them. The fo...kB in 3s (130 kB/s) Selecting previously unselected package do...1241 days ago
Install ATOM editor on Elemantory OS / Ubuntu
#Download ATOM deb file from https://atom.io/ https://a...-egl1-mesa Use 'sudo apt autoremove' to remove them. The fo...ubuntu.com/ubuntu bionic/universe amd64 gconf2-common all 3.2...atom (1.54.0) ... Selecting previously unselected package gc...into a full-fledged IDE (integrated development environment)...1240 days ago
Parse the NCBI taxonomy database with Perl !
use Bio::DB::Taxonomy; use warnings; my $sps="human"; # Get one from a NCBI taxonomy database m...p/names.dmp"); #to check #parseTax('homo_sapiens', 'metazoa...>each_Descendent($nam); #foreach (@taxa) {print $_->scient...ineage; foreach (@lineage) {print $_->scientific_name; print...1236 days ago
Perl script to get all the descendent in a tree !
use warnings; use Bio::DB::Taxonomy; #Rotifera 10190 # Get one from a NCBI taxonomy database my $dbh = Bio::DB::Taxonomy->new(-source => 'flatfile',...a = $dbh->get_all_Descendents($taxon); foreach (@taxa) {print $_->id; pr...1228 days ago
- ...output = open2(\*CHLD_OUT, \*CHLD_IN, 'command arg1 arg2'); It runs a process for both reading and writing and creates a pipe to both STDIN and...pen2(my $out, my $in, 'command arg1 arg2'); OR without using the shell $o...
1227 days ago
