Re^3: how to combine these two scripts in perl?

If you have unwanted files left over, the solution to that is easy.

# script 1
use strict;
use warnings;
use Storable;

my $storable_file = 'store.file';
$var = complicated multilevel structure;
store(\$var,$storable_file);

# script 2
use strict;
use warnings;
use Storable;

my $storable_file = 'store.file';
my $var = retrieve($storable_file);
unlink $storable_file;

open my $outfile,'>','output.file';
print $outfile $var;
close $outfile;
[download]

Only file created will be output.file.

But God demonstrates His own love toward us, in that while we were yet sinners, Christ died for us. Romans 5:8 (NASB)

Comment on Re^3: how to combine these two scripts in perl? Download Code

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Re^4: how to combine these two scripts in perl? by dimitris852 (Acolyte) on Mar 15, 2016 at 16:25 UTC
please excuse me for the confusion. I edited my previous comment. I have 3 different things in my mind: I want to highlight also that `$aln` at the last line of the first script has the alignment. #I tried at first to pass this alignment to the `my $alnio = Bio::AlignIO` but didn't succeed it. ##My second try was changing `$factory` and outputting a file`(out_file)` from `my $factory = Bio::Tools::Run::Alignment::Clustalw->new(-matrix => 'BLOSUM','outfile' => 'out_file','outype'=clustalw);` in order to use it in `my $alnio = Bio::AlignIO->new('-file'=> 'out_file','-format' => 'clustalw');` This is what I was searching to do through a variable and not a file ###Thrird, now I'm thinking of finding a way to delete the file `out_file` after it is used from `my $alnio = Bio::AlignIO` but seems me not the right way.	[reply] [d/l] [select]
Re^5: how to combine these two scripts in perl? by poj (Abbot) on Mar 15, 2016 at 17:11 UTC
I know nothing about bioinformatics but have you tried using the object returned by `->align` in the iterator loop ? `#!perl my $factory = Bio::Tools::Run::Alignment::Clustalw ->new(-matrix => 'BLOSUM'); . . . my $alnio = $factory->align($seq_array_ref); while( my $aln = $alnio->next_aln ) { . . }` [download] poj	[reply] [d/l] [select]