Bash script to extract intronic fragments !
#To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regions from the genic region, we have the intronic region. gunzip -...1380 days ago
Bash script to get intergenic region from genome files !
#For the intergenic region, we will require the size of the chromosomes. wget http://xxx.chrom.sizes cat xxx.chrom.sizes | sed 's/^chr//' | sed 's/Cp/Pt/' > tmp mv...1380 days ago
Bash script to handle Multifasta files
#Convert all lowercase residues to uppercase in a FASTA sequence file $ awk 'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $1}}' input.fasta > output.fasta...1371 days ago
1222 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',...1179 days ago
Perl script to run awk inside perl
#!/usr/local/bin/perl eval 'exec /usr/local/bin/perl -S $0 ${1+"$@"}' if $running_under_some_shell; # this emulates #! processing on NIH machines. # (remove #! line...1177 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...!\n }; #exit 1; } # end 'if' else { print "\n Module $_ OK!\n";} } # end 'for' } # end 'BEGIN' block #Bash script else here print "\nDownloa...1174 days ago
1172 days ago
Perl script to check modules installed !
#use strict; use warnings; use ExtUtils::Installed; # # First, check if all the required modules have been installed in the system # BEGIN { my @import_mo...1170 days ago
Bash script to check installed bioinformatics program !
allTools=(bwa mummer trimomatic) decFlag=0; for name in ${allTools[@]}; do #echo "enter your package name" # read name dpkg -s $name &> /dev/null...1060 days ago