Install ATOM editor on Elemantory OS / Ubuntu
#Download ATOM deb file from https://atom.io/ https://atom.io/download/deb (base) bioqueen@bioqueen-Lenovo-ideap...te, upgrade, view. Run `apm help ` to see the more details about a specific comm...1189 days ago
2707 days ago
Transpose the file coordinates and plot dendrogram in R
#Save this as tr.awk { for (i=1; i2631 days ago
Download the genome from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome cd genome...URL # USER need to provide the right summary file to curl # Commentline if you are not interested in...2546 days ago
Download the gff files from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome_gff cd ge...URL # USER need to provide the right summary file to curl # Commentline if you are not interested in...2537 days ago
Genetic Algorithms demonstration with word DNA in Perl
#!/usr/bin/perl -w # GA demonstration with word DNA (512 bits) use strict; use Data::Dumper; # individuals in the population my $popsize = 1024; # a good...2385 days ago
Extract fasta sequence with Ids with Bash script
#!/bin/bash while IFS='' read -r line || [[ -n "$line" ]]; do echo "Text read from file: $line" samtools faidx ONT.fasta $line > $line.faa done < "$1"2368 days ago
Reformat the file names with Perl
#!/usr/bin/perl use strict; use warnings; use File::Copy qw(copy);; $| = 1...n USAGE: $0 table\n"; exit;} my $ifh = read_fh($ARGV[0]); while (my $line = ) { next if $line =~ /^#/; #next if $. ==...2349 days ago
Create genome scaffolding with Perl
...ery=s', 'pid=i', 'trimlimit=i', 'prefix=s'); # process remaining command line arguments (hopefully only PSL fi...d2usage({-exitVal => 1, -message => "Error: Unknown command-line option or ". "n...2322 days ago
Remove the duplicated line present only next to each other with Perl
#!/usr/bin/perl use strict; use warnings; { $_ = ; my $next_line; while( $next_line = ) { #print "curren...ne: $next_line$/"; print $_ if $_ ne $next_line; } continue { $...2306 days ago