Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # htt...("got %d sequences" % len(seqs)) from Bio import Entrez allseq = {} for x in seqs:...ccession'] print("downloading", nm) dna = Entrez...1098 days ago
Install NCBI entrez-direct and esearch using conda !
$ conda install -c bioconda entrez-direct Collecting package metadata (current_repodata.json): done Solving..._2 Proceed ([y]/n)? y Downloading and Extracting Packages entrez-direct-13.9 | 5.2 MB | ########...1064 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com) use warnings; use stri...def, verbose => undef, url => 'http://www.ncbi.nlm.nih.gov/entrez...2878 days ago
Perl script to merge LastZ overlaps
#!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '2087 days ago
Commands to install conda in Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ mkdir jittmp jit@jit-HP-Pro-3335-MT:~/Download...PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL ANACONDA, INC. BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL , SPECIAL, EXEMP...1473 days ago
1178 days ago
Installing Covid19 Environment !
...############################################################ | 100% entrez-direct-15.6 | 7.6 MB | ########...would like the taxonomic data stored elsewhere, simply replace this directory with a symlink. For examp...886 days ago
747 days ago