Formatting of species.txt

[Thijs Janzen]

I'm currently trying to use the phyloGenerator to build a phylogeny of the cichlid tribe Lamprologini - mainly also because genbank is a mess to manually find DNA files.
In order to do so I use the included species file (Lamprologini.txt). 

It seems however that when phyloGenerator is reading the file, it only recognizes the last species in the file. I have no clue
why this is. I also tried to reformat the species names without the underscores, but this did not improve results...
I use phyloGenerator on OS X 10.10.2, and generated the species name file from an excel file (it is now a tab delimited txt file).

Thanks in advance!

Thijs Janzen 

[Will]

Hello,

Thanks for getting in touch; I'm sorry you're having problems with the program!

I've just tried running this file on my computer and on a Mac computer (OS 10.10.1; thank you for including your OS version!) and I had no problems with it. I think, therefore, the problem is something to do with you being in a different country with some kind of different file encodings. You're in The Netherlands, right?

Can you confirm that this is definitely the file you used? The encodings on this file are 'DOS', which doesn't sound like something you could easily produce on a Mac computer. Could you humour me and download the file you sent round the mailing list and try running that through the program? There's a very good chance that whatever happened to it when it was emailed round fixed the encodings anyway! :D

If that doesn't work... Well, you could try setting your computer to "English", but I appreciate that's not a very nice solution. If you could please, with the downloaded file, open 'Terminal' on your Mac, type 'python' and press enter, and then copy-paste the following into the Python window:

with open("XXX/Lamprologini.txt") as handle:

    for line in handle:

        print line.strip()

...replacing XXX with the location of the file and keeping the new lines in there, and tell me if you get your species list printed out to you. If you do, then I think the only option is for you to build phyloGenerator on your own computer. I am also very happy to send you a copy of the second version (which, honestly, will be released next week :p) where you 100% won't have this problem.

Let me know how you get on, and again, I'm sorry you're having trouble,

Will

---

Need a phylogeny? Try phyloGenerator

Measuring phylogenetic structure? Try install.packages('pez')

Want something to read? Try PEGE journal club or willeerd

Will Pearse
Post-doc, ecology / evolutionary biology
Davies and Peres-Neto labs
Skype: will.pearse
Cell: (+1) 514-973-1987

---

Need a phylogeny? Try phyloGenerator

Measuring phylogenetic structure? Try install.packages('pez')

Want something to read? Try PEGE journal club or willeerd

Will Pearse
Post-doc, ecology / evolutionary biology
Davies and Peres-Neto labs
Skype: will.pearse
Cell: (+1) 514-973-1987

[Thijs Janzen]

Re-downloading the file from here did the trick!

The file was saved from Microsoft Excel for Mac 2011 (hence the DOS encoding).
I was already afraid that somewhere probably the end-line encoding had become messed up, but I couldn't think of a way of testing it. 

Thank you very, very much! 

Now let's see what kind of phylogeny I get :D

Cheers!

Thijs

Op dinsdag 31 maart 2015 11:41:52 UTC+2 schreef Thijs Janzen:

[Will]

Glad I "helped" :D

Bonne chance!

Will

---

Need a phylogeny? Try phyloGenerator

Measuring phylogenetic structure? Try install.packages('pez')

Want something to read? Try PEGE journal club or willeerd

Will Pearse
Post-doc, ecology / evolutionary biology
Davies and Peres-Neto labs
Skype: will.pearse
Cell: (+1) 514-973-1987