[Biopython-dev] [Bug 2558] Bio.Nexus chokes on TRANSLATE block with superfluous comma

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2558


fkauff at biologie.uni-kl.de changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




------- Comment #2 from fkauff at biologie.uni-kl.de  2008-07-30 08:57 EST -------
I'm all for a little bit of slack in parsers, but this looks in my opinion like
a straightforward syntax error in the nexus file. I work with nexus files
daily, and have never encountered such a trailing comma. What really confuses
me is that there are 58 taxa in the data set, and  no. 59 Lecanorales is in
addition, with no data and no occurence in the tree. I don't think this is
proper nexus format.

Frank



(In reply to comment #1)
> This is an issue in the Bio.Nexus module, so its a job for Frank.  
> 
> Do you know if this affects all the NEXUS files from www.treebase.org? I've
> tried downloading several trees, but their FTP site is just timing out for me. 
> According to http://www.treebase.org/treebase/submit.html the request trees be
> uploaded in the NEXUS file format so its possible that just a minority of their
> trees have this trailing comma.
> 
> Note that this may be an invalid file (a TRANSLATE block with trailing comma),
> but as you say it looks relatively straight forward to cope with.  However, I
> have had a quick look at the Bio.Nexus code, and I don't entirely understand
> what Frank's parser is doing here - so its not going to be a quick fix from me.
> 
> 
> Quick bit of python to show the stack trace:
> 
> >>> from Bio.Nexus import Nexus
> >>> n = Nexus(open("M3579.NX"))
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> TypeError: 'module' object is not callable
> >>> n = Nexus.Nexus(open("M3579.NX"))
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/Users/XXX/repositories/biopython/build/lib.macosx-10.3-i386-2.5/Bio/Nexus/Nexus.py",
> line 552, in __init__
>     self.read(input)
>   File
> "/Users/XXX/repositories/biopython/build/lib.macosx-10.3-i386-2.5/Bio/Nexus/Nexus.py",
> line 614, in read
>     self._parse_nexus_block(title, contents)
>   File
> "/Users/XXX/repositories/biopython/build/lib.macosx-10.3-i386-2.5/Bio/Nexus/Nexus.py",
> line 655, in _parse_nexus_block
>     getattr(self,'_'+line.command)(line.options)
>   File
> "/Users/XXX/repositories/biopython/build/lib.macosx-10.3-i386-2.5/Bio/Nexus/Nexus.py",
> line 922, in _translate
>     raise NexusError,'Format error in line %s.' % options
> Bio.Nexus.Nexus.NexusError: Format error in line 1 'Rolfidium_coccocarpioides',
> 2 'Mycoblastus_sanguinarius', 3 'Protoblastenia_rupestris', 4
> 'Myxobilimbia_sabuletorum', 5 'Byssoloma_leucoblepharum', 6
> 'Stereocaulon_tomentosum', 7 'Scoliciosporum_umbrinum', 8
> 'Haematomma_ochroleucum', 9 'Glyphopeltis_ligustica', 10
> 'Catinaria_atropurpurea', 11 'Miriquidica_garovaglii', 12
> 'Sphaerophorus_globosus', 13 'Lecidea_atrosanguinea', 14
> 'Cladonia_peziziformis', 15 'Stereocaulon_pileatum', 16
> 'Frutidella_caesioatra', 17 'Fellhanera_bouteillei', 18 'Tonina_cinereovirens',
> 19 'Helocarpon_crassipes', 20 'Micarea_alabastrites', 21
> 'Squamarina_lentigera', 22 'Lecanora_intumescens', 23 'Bellemerea_diamarta', 24
> 'Lopadium_disciforme', 25 'Herteliana_taylorii', 26 'Lepraria_lobificans', 27
> 'Psilolechia_leprosa', 28 'Protomicarea_limosa', 29 'Calopadia_foliicola', 30
> 'Fellhanera_subtilis', 31 'Pyrrhospora_quernea', 32 'Lecidella_meiococca', 33
> 'Hypogymnia_physodes', 34 'Ramalina_fastigiata', 35 'Halecania_alpivaga', 36
> 'Platismatia_glauca', 37 'Lepraria_bergensis', 38 'Micarea_micrococca', 39
> 'Lecania_atrynoides', 40 'Crocynia_gossypina', 41 'Psilolechia_lucida', 42
> 'Lecanora_allophana', 43 'Cladonia_digitata', 44 'Schadonia_fecunda', 45
> 'Psorula_rufonigra', 46 'Adelolecia_pilati', 47 'Lecidea_turgidula', 48
> 'Micarea_sylvicola', 49 'Lecidea_fuscoatra', 50 'Psora_rubiformis', 51
> 'Micarea_erratica', 52 'Megalaria_grossa', 53 'Lecidea_silacea', 54
> 'Micarea_intrusa', 55 'Psora_decipiens', 56 'Tephromela_atra', 57
> 'Bacidia_rosella', 58 'Micarea_adnata', 59 'Lecanorales',.
> 


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