Python script to download covid genome !
...but they require you to sign up import requests import yaml seqs = yaml.load(requests.get("https://www.ncbi.nlm.nih.gov/core/assets/genbank/files/ncov-sequences.yaml").text)...1126 days ago
Install BLAST in Ubuntu/Linux and Window !
...h.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-win64.exe #Run this installer using the defaults, it should put BLAST under C:\Program Files\NCBI\blast-2.7.1+1137 days ago
2906 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
...are repleced with the\n". "specified character. e.g. -m '?' will place ? to the ambigous characters.\n" . "If multiple files are given, sequences in all files are marged. If no \n"....2904 days ago
Converting from Windows-style to UNIX-style line endings with dos2unix
...s2unix amd64 7.3.4-3 [351 kB] Fetched 351 kB in 3s (130 kB/s) Selecting previously unselected package dos2unix. (Reading database ... 177704 files and directories currently ins...1167 days ago
Perl subroutine to read and write files
# Input output (InOut) the file # usage: # @array = InOut('read',$file) # $string = InOut('read',$file) # InOut('write',$file,\$string) # InOut('write',$file,\@a...2856 days ago
Install ATOM editor on Elemantory OS / Ubuntu
...atom amd64 1.54.0 [126 MB] Fetched 845 kB in 4s (219 kB/s) Selecting previously unselected package gconf2-common. (Reading database ... 194272 files and directories currently ins...1166 days ago
Extract fasta sequence from a multifasta file with coordinates
...:Fasta; # Create database from a directory of Fasta files my $db = Bio::DB::Fasta->new('/path/to/fasta/files/'); my @ids = $db->ge...access my $fh = Bio::DB::Fasta->newFh('/path/to/fasta/files/'); while (my $seq = ) {...2522 days ago
Download the genome from NCBI using bash script/command
...tp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_viral #Read the url from file and download FILES=$(pwd)/* for f in $FILES do echo "Processing $f fi...2522 days ago
Unzip all the genome file and remove all fasta header except first one
#!/bin/bash gzip -d *.gz FILES=$(pwd)/* for f in $FILES do echo "Processing $f file..." if [[ $f =~ \.fna$ ]]; then awk ' /^>/ && FNR > 1 {next} {print $0} ' $f | sed '/^>/{s/ /_...2521 days ago