[Biopython] Fwd: BlastParsing gives Value Error: Invalid header?

[Peter Cock]

On Wed, May 9, 2012 at 7:01 PM, Martin Mokrejs
<mmokrejs at fold.natur.cuni.cz> wrote:
> Hi Brad,
>  I just got bitten by this myself as well. Could be the legacy blast parser
> improved to give clearer error message? E.g. that it failed to find the LOCUS
> line or whatever was it looking for? With the legacy BLAST documentation being
> gone from current Tutorial it is easy to pick the wrong parser. ;)
>
>  And BTW, please do not drop support for legacy BLAST. I just cannot make BLAST+
> give me same alignment, no matter what arguments I use to adjust for the (it gives me
> wider alignment than wanted and I can make it a look shorter, but shortening it just
> a bit like legacy BLAST output .. is not doable).

Have you contacted the NCBI about this possible regression?

>  And, took me a while to find old biopython-1.52.tar.gz to lookup the old docs.
> Could there be a hyperlink from Tutorial to these unpacked, browseable sources? ;)
> I am speaking about http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc85 .
> Thanks,
> Martin

Could you clarify if you are talking about documentation for calling
the 'legacy'
BLAST command line tools (e.g. blastall), or documentation for parsing the
plain text human readable output (which still exists in BLAST+)?

On a related point, Bow's just done a bit of work updating our plain
text parser to
cope with BLAST+ (specifically changes in BLAST 2.2.25+ and/or 2.2.26+).

One of the aims of Bow's GSoC project will make dealing with the different
BLAST formats a lot simpler.

Peter