Check overlapping range with Perl
#!/usr/bin/perl use strict; use warnings; my @ranges = 0; push @ranges, $ranges[-1] + 1 + int rand 200 for 1..10000; my @tests = map int rand $ranges[-1], 0..1...2639 days ago
Extract ids from file with perl
#!/usr/bin/perl use strict; use warnings; my $fh=read_fh("fin.txt"); my %idHash; my $lastKey; while () { chomp $_; my @cells = split /\t/, $_; $idHash{...2620 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 = shift; my...2544 days ago
Download the genome from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome cd genome # Look for genome assembly summary and extract the URL...2544 days ago
Read a tab delimited file and search with perl
use strict; use warnings; use Data::Dumper; use Text::CSV; use IO::Handle; my $file = "/home/urbe/Tools/Alienomics_v0.1/Alienomics/output/intermediate_files/rRNA/refGene.megablast"; open my $fh, "[0]\n"; warn Dumper $row; # To see the structure }2537 days ago
Download the gff files from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome_gff cd genome_gff # Look for genome assembly summary and extract...2535 days ago
Extract fasta sequence from a multifasta file with fasta header Ids
#!/usr/bin/perl use strict; use warnings; #Usage: perl my $list = shift @ARGV; my $fasta = shift @ARGV; my $out = shift @ARGV; my %select; open LIST, "$list" or d...2530 days ago
2506 days ago
Compress and decompress the sequence with perl
use strict; use warnings; my @char; while () { @char = split //; } comp(\@char); #--------------------- my $com= "r0a3m4a4j0"; my @com = split //, $com; dcomp (\@com); #dcomp sub here sub dcomp { my ($com_ref)=@_; my @com=@$com_ref; my $car; for (my $aa=0; $aa2527 days ago
2525 days ago