Perl script to insert the DNA string in genome
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; my $file = $ARGV[0]; # input fasta file (genome file) my $out = $ARGV[1]; # output fast...2656 days ago
Calculate ATGC percentage in parallel with perl
#!/usr/bin/perl use strict; use Parallel::ForkManager; use Bio::SeqIO; #usage: perl testParallel.pl my %sequences; my $seqio = Bio::SeqIO->new(-file => "$AR...2653 days ago
BASH script for SelfBLAST a genome
#!/bin/bash #self BLAST a genome -- Expecting you have blast and samtools installed in your system #Author: Jitendra Narayan #USAGE: ./selfBlast.sh extract #USAGE...2649 days ago
Calculate some statistics for a DNA alignment with Perl
use Bio::AlignIO; use Bio::Align::DNAStatistics; my $stats = Bio::Align::DNAStatistics->new(); my $alignin = Bio::AlignIO->new(-format => 'emboss',...2646 days ago
Extracting FASTA sequences based on position with perl script !!
#!/usr/bin/env perl #Uses: perl sub-seq.pl input.txt range use strict; use warnings; my $end = pop; my $start = pop; local $/ = '>'; while () {...2618 days ago
Palindrome Simulation commands !
(base) ➜ palindromeAssemblySim more allCommands 3315 mutate.sh in= mutant15CH101.fasta out=mutant153CH101.fasta id=97 3316 mutate.sh in=mutant15CH101.fasta out=m...1732 days ago
Extract fasta sequence from a multifasta file with coordinates
#!/usr/bin/perl use Bio::DB::Fasta; #USAGE perl extractFASTAwithSIZE.pl finalSample_filtered.fa 0 1000 > aaaaaa.fa my $fastaFile = shift; my $querySizeST = sh...2529 days ago
Calculate Dinucleotide Frequency with Perl
#!/usr/bin/perl -w use strict; my ($genome, $head, $tail); my (%mono_nt, %di_nt); $/ = ">"; open my $fasta, '2335 days ago
Extract the fastq sequence with range in Perl
use Bio::DB::Fasta; open(POSITIONS,"positions.txt"); while(){ chomp; my ($seqName,$begin,$end) = split(/\s/); my $db = Bio::DB::Fasta->new('allGenomeContacted.fa'); my $seq = $db->seq("$seqName", $begin => $end); print "$seq\n"; } close(POSITIONS);2465 days ago
Convert newline formated sequence into fasta format with perl
use strict; use warnings; my $filename = $ARGV[0]; open(my $fh, '2367 days ago