Convert newline formated sequence into fasta format with perl
use strict; use warnings; my $filename = $ARGV[0]; open(my $fh, '2363 days ago
Extract fasta sequence with Ids with Bash script
#!/bin/bash while IFS='' read -r line || [[ -n "$line" ]]; do echo "Text read from file: $line" samtools faidx ONT.fasta $line > $line.faa done < "$1"2347 days ago
Fill up the form and blast with perl
...e; use strict; use warnings; my $mech = WWW::Mechanize->new; my $sequence = 'GCCCGCGGTCTCAGAGATCTCGATAT...=> 'blastx', 'BlastTargetSet' => 'ATH1_pep', 'QueryText' => $sequence, }, ); print $mech->co...2318 days ago
Insert the sequence at desire location in multi-fasta file with Perl
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; use File::Copy; #ARGV[0] should be in following format --- Keep the coordinate sorted b...2307 days ago
Create genome scaffolding with Perl
...WKMHBDVXN-/; # work on masked sequences as well $seq =~ tr/acgtuy...y" => 0, # contig file for query sequences "prefix" => "psl_scaffol...} print(STDERR "Loading query sequences into memory..."); open(my $...$replacementSeqs{$sName}{sequence} = $alConsensus; # p...2301 days ago
Perl script to convert fastq to fasta file
...Bio::Factory::EMBOSS->new; my $seqret = $factory->program('seqret'); # $seqret is a Bio::Tools::Run::EMBOSSApplication object $seqret->run({-sequence => $infile, -s...2244 days ago
Plot custom gene density with R
library(karyoploteR) pp2243 days ago
Perl script to read multi fasta sequence one by one
...fastaSeq{$key}\n"; } sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2214 days ago
Perl script to find coding regions in DNA sequences
...rint "dnaloglkh.pl codontable DNAsequence\n"; exit(1); } # creat...ecodontable = $ARGV[0]; my $filesequence = $ARGV[1]; # open the f...################ # open the DNA sequence (second file) if (!open(SE...f the codons in # the input DNA sequence. To split the sequence in seg...2148 days ago
Biological Sequence handling with Perl !
package Sequence::Generic; # File: Sequence/Generic.pm use strict; us...} # Return the type of the sequence as a human readable string s...lass) if ref($class); my ($sequence,$type) = @_; my $self =...if ref($seq); return new Sequence::Alignment(src=>$seq,target=>...2174 days ago