On Wed, Nov 20, 2013 at 7:10 PM, Dooley, Damion <damion.doo...@bccdc.ca> wrote:
> I'm doing a 1 step generic reporting tool along the lines of the "BLAST
> XML to tabular" script by Peter. I was just about to ask about this line,
> which looked pretty much like a bug:
>
> sallseqid = ";".join(name.split(None,1)[0] for name in
> hit_def.split(" >"))
>
> Then I found the patch from Nov 7th 2013:
>
>
> https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/blastxml_to_tabular.py
>
> try:
> sallseqid = ";".join(name.split(None,1)[0] for name in
> hit_def.split(" >"))
> except IndexError as e:
> stop_err("Problem splitting multuple hits?\n%r\n--> %s" %
> (hit_def, e))
>
> Yay! But what I've seen in recent XML output reports is that the ">"
> content has been changed to ">" . E.g.
>
>
> https://github.com/biopython/biopython/blob/master/Tests/Blast/mirna.xml
>
> <Hit>
> <Hit_num>66</Hit_num>
> <Hit_id>gi|195029385|ref|XR_047134.1|</Hit_id>
> <Hit_def>Drosophila grimshawi miR-7-RA (Dgri\mir-7), ncRNA
> >gi|195336156|ref|XR_048470.1| Drosophila sechellia miR-7-RA (Dsec\mir-7),
> ncRNA >gi|195585143|ref|XR_050309.1| Drosophila simulans miR-7-RA
> (Dsim\mir-7), ncRNA</Hit_def>
> <Hit_accession>XR_047134</Hit_accession>
> ...
>
> So perhaps a stop_err() could be avoided, if test is for ">" instead?
> I assume that no variants of python ElementTree.iterparse() will
> unescape content when returned via the iterator?
>
> Damion
On Wed, Nov 20, 2013 at 7:31 PM, Dooley, Damion <damion.doo...@bccdc.ca> wrote:
> Woops - I realize now findtext() must be unescaping all ">", so Peter
> was trying to address other non-splitting occurances of " >" as per his
> patch notes. But perhaps a stop_err() isn't merrited in this case?
>
> So ignore my test for ">" comment.
>
> Regards,
>
> Damion
OK - good. I was worried that there might be some inconsistency
between different databases of versions of BLAST about how
the > was encoded.
As to why I treat this as a fatal error (calling stop_err), the
alternative would be to issue a warning to stderr, and guess
what the data ought to look like? That just seems like asking
for trouble - a big red error should ensure I hear bug reports ;)
Zen of Python: Errors should never pass silently.
Peter
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