Using a path in the output prefix results in false message that there is no tree file

[ak-watson]

When I run FlaGs with tree mode, I receive the message.

'> ETE3 failed to create tree due to lack of valid protein accesions, at least 2 required !'

ETE3 actually succeeded in creating the tree, but the problem is with my output prefix.

I normally used a path in my output prefix to send data to an output directory to organise my data (say if I am using Flags on multiple different gene lists in the same set of genomes).

So my output prefix is something like "outputdir/output_prefix"

Unfortunately this doesn't play nicely with the following test for whether a tree has been sucessfully built by ete3:

if os.path.isfile(args.out_prefix+'_tree/mafft_default-trimal01-none-fasttree_full/'+args.out_prefix+'_tree.fasta.final_tree.nw') == True:

This would mean looking for the treefile in "outputdir/output_prefix_tree/mafft_default-trimal01-none-fasttree_full/outputdir/output_predix_tree.fasta.final_tree.nw'

It might be useful to either have a separate option to allow a user-specified output directory.

Or otherwise, as a quick fix for my own use I have swapped out os.path.isfile for glob.glob which allows wildcards and prevents the need to add a second args.out_prefix argument.

if glob.glob(args.out_prefix+'_tree/mafft_default-trimal01-none-fasttree_full/*fasta.final_tree.nw'): with open(glob.glob(args.out_prefix+'_tree/mafft_default-trimal01-none-fasttree_full/*fasta.final_tree.nw')[0], 'r') as treeIn:
Thanks!
Andrew