Comments with newlines at start of newick file

[Yan Wong]

I'm commenting my newick files with a line in square brackets at the start, e.g.

[My comments here]

(((CYCLOSTOMATA,GNATHOSTOMATA)Vertebrata,Tunicates)ChordataMinusAmphioxus,CEPHALOCHORDATA);

on the assumption that "Whitespace elsewhere is ignored" (https://en.wikipedia.org/wiki/Newick_format). But Bio::Phylo::Parsers::Newick seems to die if there are newlines at the start of the newick file.  Is there a switch I can use when parsing to read these in correctly, or should I just strip newline before reading?

Cheers

Yan (apologies for all the posts!)

[Rutger Vos]

Hi Yan,

to the best of my knowledge, this should work. Note that the comments are stripped out by the reader, so you won't have access to them by way of the tree objects you get out of the newick (though they will of course still be there in the file), but they shouldn't cause problems. Can you try the attached script and tell me what you get because I can't reproduce the issue on my end?

Rutger

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[Yan Wong]

On Friday, 27 June 2014 09:19:46 UTC+1, Rutger Vos wrote:

 Can you try the attached script and tell me what you get because I can't reproduce the issue on my end?

Your script works fine for me. But after a little debugging on my end and I think the problem comes because I undefined $/ so that I could read multiple files in using a single while(<>) loop. So for instance, this dies for me

#!/usr/bin/perl

use strict;

use warnings;

use Bio::Phylo::IO 'parse_tree';

$/ = undef;

my $tree = parse_tree(

    -string => "[My comments here]

(((CYCLOSTOMATA,GNATHOSTOMATA)Vertebrata,Tunicates)ChordataMinusAmphioxus,CEPHALOCHORDATA);",

    -format => 'newick'

);

print $tree->to_newick;

[Rutger Vos]

Er, yes, don't mess with the global special variables :-)

If you must play around with $/ you want to do that with the 'local' keyword so that the rest of the world outside your specific block stays the same.

[Yan Wong]

On Friday, 27 June 2014 11:49:37 UTC+1, Rutger Vos wrote:

Er, yes, don't mess with the global special variables :-)

Fair point!

 

If you must play around with $/ you want to do that with the 'local' keyword so that the rest of the world outside your specific block stays the same.

Hmm, difficult in this case because the Bio::Phylo code is inside the while(<>) block which I'm using with undef $/ to read multiple files. I guess I'll have to save the previous value and set it just before using Bio::Phylo::IO->parse_tree.

Thanks

Yan

[Rutger Vos]

I don't fully understand the use case. You know you can read multiple trees from the same file in one go, right? Or is that not what you're trying? You could also in a separate block slurp the contents of multiple files and pass that into parse() as a string.

--

[Yan Wong]

On Friday, 27 June 2014 13:41:40 UTC+1, Rutger Vos wrote:

You could also in a separate block slurp the contents of multiple files and pass that into parse() as a string.

I've got trees in multiple files. I want to pass all the filenames to the perl script and iterate over each tree. You're right there's probably a better way to do it than undef $/; while(<>) {parse($_)}

By the way, I've just installed the github version, and I can't get unnamed nodes out of $tree->resolve(1). This just seems to name the nodes "NodeX", "NodeY" etc rather than rx, ry:

#!/usr/bin/perl

use Bio::Phylo::IO 'parse_tree';

srand(1);

my $tree = parse_tree(

'-format' => 'newick',

'-handle' => \*DATA,

);

$tree->resolve(1);

print $tree->to_newick(-nodelabels=>1);

#can't get e.g ((D,((A,B)mynode1),C)mynode2,E);

#or even ((D,((A,B)mynode1):0.0,C)mynode2,E);

__DATA__

(((A,B)mynode1,C,D)mynode2,E);