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obiaddtaxids error/ doc error
#1
Hey everyone,

I wanted to use the obiaddtaxids script to annotate my fasta Reference file obtained from UNITE.
It fails to annotate my UNITE files when using the command:
Code:
obiaddtaxids -d taxDB -f UNITE_FULL UNITE_public_31.01.2016.fasta
with the Error:
Code:
 File "/usr/bin/obiaddtaxids", line 402, in <module>
   species_name = s['species_name']
TypeError: string indices must be integers, not str
any suggestions on why this is happening? it should work with the UNITE/INSD ITS Release, right?

Also, while going through the documentation, i noticed that there is an example using a -T parameter, which is not actually available. the documentation should probably fixed...

thanks and regards,
max
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#2
Hi, it looks like the UNITE file wasn't correctly parsed. Could you copy here a few lines of the file so I can check what's happening?
Thanks!
Céline

ps. I corrected the documentation, it will appear in the next released version of the obitools!
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#3
Hi Céline,
I used the official UNITE General FASTA release, here is the head of that file.

Thanks,
Max


.txt   head_UNITE.fasta.txt (Size: 11.96 KB / Downloads: 2)
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#4
Hi,
Thanks, there was a bug to read files of that format, I fixed it, you can update your installation of the OBITools to get the fixed version (1.2.3)!
Céline
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