Results for "Perl Modules"
Bio-Scripts
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 above if...1215 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtils::...# # First, check if all the required modules have been installed in the sy...database # BEGIN { my @import_modules = ( 'Cwd', 'File::c...Installed->new(); my (@installed_modules) = $inst->modules(); f...1212 days ago
- #use strict; use warnings; use ExtUtils:...# # First, check if all the required modules have been installed in the sy...database # BEGIN { my @import_modules = ( 'Cwd', 'File::c...Installed->new(); my (@installed_modules) = $inst->modules(); f...
1211 days ago
Perl script to check modules installed !
#use strict; use warnings; use ExtUtils:...# # First, check if all the required modules have been installed in the system # BEGIN { my @import_modules = ( 'Cwd', 'File::c...Installed->new(); my (@installed_modules) = $inst->modules(); f...1208 days ago
- ...ntltool jq libalgorithm-merge-perl libarchive-cpio-perl libasan4 libatomic1 libblas-d...ntltool jq libalgorithm-merge-perl libarchive-cpio-perl libasan4...4 libfile-stripnondeterminism-perl all 0.040-1.1~build1 [13.8 kB...in amd64 libsys-hostname-long-perl all 1.5-1 [11.7 kB]...
1106 days ago
Install grabseqs using conda !
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1106 days ago
Perl onliner to print fasta headers !
#Save all your fasta in seq.fa and run the following ... perl -ne 'print if /^>/' seq.fa #Print header with line number perl -ne 'print "$. $_" if /^>/ ' seq.fa1048 days ago
- Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/$ sudo apt install jellyfish...linux-image-4.15.0-147-generic linux-image-4.15.0-151-generic linux-modules-4.15.0-144-generic linux-modules-4.15.0-147-generic linux-modu...
1033 days ago
Oneliner to convert lower-case to sequence masked with Ns
perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna awk '{if(/^[^>]/)gsub(/[a-z]/,"N");print $0}' genomic.fna > genomic.N-masked.fna1002 days ago
Perl script for Smith-Waterman Algorithm
# Smith-Waterman Algorithm # usage statement die "usage: $0 \n" unless @ARGV == 2; # get sequences from command line my ($seq1, $seq2) = @ARGV; # scoring s...1002 days ago
