Opened 16 years ago
Closed 15 years ago
#148 closed task (fixed)
Check Newick tree exporter
Reported by: | fog | Owned by: | devel |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | ARB_NTREE | Version: | release_20071207 |
Keywords: | Cc: |
Description
There was a complain by someone using the LTP in newick format.
He tried to parse it with the Bioperl parser and it did not work.
Here is his report:
The $node→id is written by ARB in the format:
‘spec_tax, accession, genus_tax’ to the newick .
I am using:
my $treeio = new Bio::TreeIO(-format ⇒ 'newick', -file ⇒ $file);
to get the .
if I examine $node→id when traversing the
, it is like this
‘spec_tax
Bioperl
1) Does not recognize single quote as a quote, but rather as a part of id
2) Ergo, treats subsequent comma as a “newick” delimiter between branches
If I replace single quote by double quote and comma by greater-than (>), it parses fine. (It does not like semicolon either, BTW)
“>” is a little unorthodox, so if you are going to change the export, please use more conventional delimiter that is still parsable by BIOPERL
Change History (3)
comment:1 Changed 16 years ago by fog
comment:2 Changed 16 years ago by fog
- Component changed from ARB to ARB_NTREE
- Version changed from stable-2007 to release_20071207
comment:3 Changed 15 years ago by westram
- Resolution set to fixed
- Status changed from new to closed
- fixed by [6066]
- added options for quoting style and char-removal
see also Ticket #153: Problem with the ARB Newick Tree Exporter