1210 days ago
2137 days ago
Palindrome Simulation commands !
(base) ➜ palindromeAssemblySim more allCommands...allPalindromeSimulated.fa 3319 ~/Tools/art_bin_MountRainier/art_illu...-m 300 -s 10 -o paired_dat 3320 ~/Tools/art_bin_MountRainier/art_illu...leavedPE.fasta 3326 cd masurca; ~/Tools/MaSuRCA-3.2.3/bin/masurca sim...1728 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 }2518 days ago
Loop over with all files in a directory in bash
#!/bin/bash FILES=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/* ref=/media/Compara...bi-genomes-2017-11-13/GCA_000196735.1_ASM19673v1_genomic.fna path=/home/urbe/Tools/SATSUMA/satsuma-code-0 for f...2324 days ago
Perl script to convert fastq to fasta file
#!/usr/bin/env perl use strict; use warnings; use Bio::Factory::EMBOSS; my $usage...:EMBOSS->new; my $seqret = $factory->program('seqret'); # $seqret is a Bio::Tools::Run::EMBOSSApplication objec...2244 days ago
2144 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for S...$tarfile = "renamedAdinetaV2.fa"; #Ur target file my $satsumaLoc="/home/urbe/Tools/SATSUMA/satsuma-code-0"; # Lo...2133 days ago
2130 days ago
2120 days ago