treefix tree output format conversion

Question

[arunprasanna83]

Hello,

I have trees from treefix. The format in tree is a kind of stacked version of newick format. Like this:

                        (
                          Taxon_A,
                          Taxon_B
                         );

How to convert this into normal newick format ? (Taxon_A,Taxon_B);. Is there any existing method?

Thanks in Advance,

AP

[jhc]

ete3 can read newick files even if there are new lines and spaces in it. use tree.write() to export back in a clean newick string.

Answer 1

[Brice Sarver]

This is simple: replace all newlines with nothing. Something like this using sed.

[arunprasanna83]

I forgot to mention that, there are ~12k files !

[Brice Sarver]

Not a problem! Loop, remove newlines, and combine with >>.

Answer 2

[dago]

Did you give it a try here?