Results for "Perl Modules"
Bio-Scripts
$ sudo apt-get install rakudo [sudo] password for jit: Reading package lists... Do...sing triggers for libc-bin (2.27-3ubuntu1) ... $ perl6 -v This is Rakudo version 2...18.03 built on MoarVM version 2018.03 implementing Perl 6....1564 days ago
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving environment: done ## Package Plan ## environment...a pbcore: 1.6.5-py27_0 bioconda perl:...2003 days ago
Perl script to split fasta sequence and create overlaps
#!/usr/bin/perl use strict; use warnings; my $len = 5000; my $over = 200; my $seq_id=$ARGV[0]; my $seqFile = $ARGV[1]; my $seq; open(my $fh, "1985 days ago
Perl script to count occurrence of a character !
#!/usr/bin/env perl # -*- coding: utf-8 -*- #!/usr/bin/perl use strict; use warnings; my %count_of; while ( ) { my @val = split "\t", $_; #my ( $word) = m/(\w+...1914 days ago
- my @tests = ( ["FOO", "BAR"], ["CRATE", "TRACE"], ["CRATE", "CRATE"], ["TRACE", "CRATE"], ["CREATE", "TRACT"], ["DWAYNE", "DUANE"], ); for my $word_pair (@...
1814 days ago
- #!/bin/bash cd `pwd` perl ~/apps/SSPACE-1.2_linux-x86_64/SSPACE_v1-2.pl \ -l libraries.txt \ -s Contigs_over200_nocp.fasta \ -k 5 \ -a 0.7 \ -x 1 \ -m 30 \ -o 20 \ -b Rayk31_scaffolds_extension
1736 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManager; use Bio::SeqIO; my ($sequence_data_ref) = parse_genome_files($ARGV[0]); my %genome=%{$seq...1700 days ago
Find and replace in multifasta or fasta header with perl onliner
You have a fasta file and you want to replace: "|" You are told to replace that by "_" perl -i -p -e "s/\|/_/g" genome.fasta -i = inplace editing -p = loop over lines and print each line (after processing) -e = command line script1629 days ago
- # $1 = vcf file # $2 = input bam file # $3 = output QV file module load samtools NUM_BP=`samtools depth $2 | perl -e '$c = 0; while(){chomp; @s...)}} END { print SUM}'` echo "num snp: "$NUM_SNP perl -e...
1618 days ago
- ...ace-expansion node-builtin-modules node-combined-stream node-con...c/universe amd64 node-builtin-modules all 1.1.1-1 [3,338 B] Get:11...selected package node-builtin-modules. Preparing to unpack .../09-...... Setting up node-builtin-modules (1.1.1-1) ... Processing tri...
1566 days ago
