how to output the final Tree into a file?

dimitris852 has asked for the wisdom of the Perl Monks concerning the following question:

After executing the script, a Tree in newick form is generated (form a fasta file given). How can I output this result into a file and not just leave it in my command promt? Thanks!

#!/usr/bin/perl

$ENV{CLUSTALDIR} = 'C:\\\\\\\\\\\\\\\\\\\\;
use Bio::Tools::Run::Alignment::Clustalw;

my $file = <>; # Get file name (fasta file) from command prompt.

#  Build a clustalw alignment factory
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(-matrix => 'BL
+OSUM',-outfile=>'out', -output =>'clustalw'); 
my $ktuple = 2;
$factory->ktuple($ktuple);

my $inseq = Bio::SeqIO->new(
                    -file=> "<$file",
                    -format=> 'fasta'
                   );
my $seq;
my @seq_array;
while ($seq = $inseq->next_seq) {
    push(@seq_array, $seq);
}
# Now we do the actual alignment.
my $seq_array_ref = \@seq_array;
my $aln = $factory->align($seq_array_ref);

#constarcting the Tree
my $alnio = Bio::AlignIO->new(-file => 'out', -format=>'clustalw');

my $dfactory = Bio::Tree::DistanceFactory->new(-method => 'NJ');

my $stats = Bio::Align::ProteinStatistics->new;

my $treeout = Bio::TreeIO->new(-format => 'newick');

while( my $aln = $alnio->next_aln ) 
{
 my $mat = $stats->distance(-method => 'Kimura',
                            -align  => $aln);
 my $tree = $dfactory->make_tree($mat);
 $treeout->write_tree($tree);
}

exit;
[download]

Comment on how to output the final Tree into a file? Download Code

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Re: how to output the final Tree into a file? by Mr. Muskrat (Canon) on Mar 15, 2016 at 22:27 UTC
You can open a file for writing and pass the file handle into Bio::TreeIO->new. `... my $outfile = '/path/to/file/to/create'; open my $fh, '>', $outfile or die "Cannot create $outfile, $!\n"; my $treeout = Bio::TreeIO->new(-format => 'newick', -fh => $fh); ...` [download] Alternately, you can simply pass a filename to Bio::TreeIO->new. `... my $outfile = '/path/to/file/to/create'; my $treeout = Bio::TreeIO->new(-format => 'newick', -file => ">$outfil +e"); ...` [download]	[reply] [d/l] [select]
Re^2: how to output the final Tree into a file? by 1nickt (Canon) on Mar 16, 2016 at 00:40 UTC
Hmm, I've not used it myself, but the docs seemed pretty clear that the file/filehandle is for reading, and that Bio::TreeIO doesn't have a print method, but relies on you to print the contents of the tree. From the DESCRIPTION: `This is the driver module for Tree reading from data streams and flatf +iles. This is intended to be able to create Bio::Tree::TreeI objects.` [download] and the SYNOPSIS: `{ use Bio::TreeIO; my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'globin.dnd'); while( my $tree = $treeio->next_tree ) { print "Tree is ", $tree->number_nodes, "\n"; } }` [download] In this case the OP has created his tree with Bio::TreeIO and it's held in `$treeout`. The way forward always starts with a minimal test.	[reply] [d/l] [select]
Re^2: how to output the final Tree into a file? by dimitris852 (Acolyte) on Mar 15, 2016 at 23:46 UTC
I did that `my $outfile = 'C:\Users\Ioulia\Desktop\outree.tre'; my $treeout = Bio::TreeIO->new(-format => 'newick', -file => ">$outfil +e");` [download] But I get this: "my" variable $treeout masks earlier declaration in same scope at....line 50. Then I can normaly run the script but an empty file outree.tre is created. please excuse me but I m really new and it takes me a long time to understand many things	[reply] [d/l]
Re^3: how to output the final Tree into a file? by Anonymous Monk on Mar 15, 2016 at 23:58 UTC
please excuse me but I m really new and it takes me a long time to understand many things :) fragments which don't reproduce the error message, don't reproduce the error message -- you can't learn about the error message from those :) diagnostics/perldiag/splain perl -we" my $foo = 1; my $foo = 2; " "my" variable $foo masks earlier declaration in same scope at -e line +1. $ perl -Mdiagnostics -we" my $foo = 1; my $foo = 2; " "my" variable $foo masks earlier declaration in same scope at -e line +1 (#1) (W misc) A "my", "our" or "state" variable has been redeclared in +the current scope or statement, effectively eliminating all access to +the previous instance. This is almost always a typographical error. +Note that the earlier variable will still exist until the end of the sc +ope or until all closure referents to it are destroyed. [download]	[reply] [d/l]
Re^4: how to output the final Tree into a file? by dimitris852 (Acolyte) on Mar 16, 2016 at 00:33 UTC
Re^5: how to output the final Tree into a file? by 1nickt (Canon) on Mar 16, 2016 at 00:41 UTC
Re^5: how to output the final Tree into a file? by Anonymous Monk on Mar 16, 2016 at 00:54 UTC
Some notes below your chosen depth have not been shown here
Re: how to output the final Tree into a file? by 1nickt (Canon) on Mar 15, 2016 at 21:23 UTC
Based on http://www.bioperl.org/wiki/HOWTO:Trees#Reading_and_Writing_Trees, it seems you need something like: `open my $fh, '>', 'filename' or die $!; while ( my $tree = $treeout->next_tree ) { for my $node ( $tree->get_nodes ) { printf $fh "id: %s bootstrap: %s\n", $node->id \|\| '', $node->b +ootstrap \|\| '', "\n"; } } close $fh or die $!;` [download] Hope this helps! Edit: fix typo The way forward always starts with a minimal test.	[reply] [d/l]
Re^2: how to output the final Tree into a file? by dimitris852 (Acolyte) on Mar 16, 2016 at 01:32 UTC
hi!.i thinks this codes is just for nodes and bootstrap values.i cant use it to print the tree in newick form into a file.it just reads a file with newick form.	[reply]