[BioPython] Blast parser missing first record

[Jeffrey Chang]

On Jul 16, 2004, at 9:34 PM, Bzy Bee wrote:

> Hi everyone
>
> My program that uses NCBI standalone blast parser
> works just fine, well almost!
>
> The only problem is that it misses first record (i.e.
> all the details and hits of first query sequence) and
> starts from the second query. Has anyone come across
> this one before? Below is a sample code:
>
> ------------------------------------
> from Bio.Blast import NCBIStandalone
> import sys,os,string
>
>
> in_file = 'myblast.txt'
>
> def testp(blast_res):
>     bf = open(blast_res)
>     parser = NCBIStandalone.BlastParser()
>     iter = NCBIStandalone.Iterator(bf, parser)
>     myrec = parser.parse(bf)

Get rid of this line.  You're parsing the results from the first query 
sequence...

>     while 1:
>         myrec = iter.next()
>         if myrec is None:
>             break

... and then immediately discarding it by assigning the second record 
to the same variable.

Jeff