Extract a range from genome file with perl.
#!/usr/bin/perl use strict; use warnings; use Bio::Seq...= Bio::SeqIO->new ( -file => $in_file, -format => 'fasta'); my $out = Bio::SeqIO->new( -file => ">$in_file.out", -format => 'fasta'); while (my $seq = $in-...2639 days ago
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Perl script to remove the duplicate sequences from multifasta file
use strict; use Bio::SeqIO; my %unique; my $file = "m...eqio = Bio::SeqIO->new(-file => $file, -format => "fasta"); my $outseq = Bio::SeqIO->new(-file => ">$file.uniq", -format => "fasta"); while(my $seqs = $seqio...2702 days ago
Perl script to insert the DNA string in genome
#!/usr/bin/perl use warnings; use strict; use...Bio::Seq; my $file = $ARGV[0]; # input fasta file (genome file) my $out = $ARGV[1]; # output fasta file my $chr="test"; #inse...y $seq_in = Bio::SeqIO->new( -format => 'fasta',-file => $file); my $seq_ou...2671 days ago
Calculate ATGC percentage in parallel with perl
#!/usr/bin/perl use strict; use Parallel::ForkManager; use Bio::SeqIO; #usage:...my %sequences; my $seqio = Bio::SeqIO->new(-file => "$ARGV[0]", -format => "fasta"); while(my$seqobj = $seqio-...2668 days ago
BASH script for SelfBLAST a genome
#!/bin/bash #self BLAST a genome -- Expecting you hav...USAGE: ./selfBlast.sh all #Common settings FASTAFILE=MergedContigs.fasta MYDB=myDB OUTFILE=seeRES T...astDB named $MYDB for you"; makeblastdb -in $FASTAFILE -parse_seqids -dbtype nuc...2664 days ago
Calculate some statistics for a DNA alignment with Perl
use Bio::AlignIO; use Bio::Align::DNAStatistics; my $stats = Bio::Align::DNASta...us /nonsynonymous substitutions ## my $in = Bio::AlignIO->new(-format => 'fasta',...2661 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 () {...2634 days ago
Palindrome Simulation commands !
(base) ➜ palindromeAssemblySim more allCom...3315 mutate.sh in= mutant15CH101.fasta out=mutant153CH101.fasta id=97 3316 mutate.sh in=mu...ate_pass_FAH31515.faa mutant3CH101.fasta mutant15CH101.fasta mutant153...a interleavedPE.fq > interleavedPE.fasta 3323 ~/Tools/BWISE/Bwise.p...1748 days ago