[BioPython] said Your XML file was empty in parsing blast records but can see the results in the saved xml file

[Hongwu Ma]

Thanks, Peter. I tried to reopen the xml file and it was working. I also 
tried to parse the result before reading as below:

  ...

    blast_records = NCBIXML.parse(result_handle)
    bres=result_handle.read()

  ...

I found I still got the problem, a good xml file but empty 
blast_records. Why the later read() function affect the parse before it?

> On Thu, Nov 13, 2008 at 11:18 AM, Hongwu Ma <hma2 at staffmail.ed.ac.uk> wrote:
>   
>>  Sometimes when I parse the blast records in biopython using the following
>> program I get the error "Your XML file was empty" but there are actually
>> some results in the saved xml files. Anyone know what is the problem?
>> Thanks in advance.
>> Hongwu
>>
>>  ...
>>  bres=result_handle.read()
>>  save_file = open(myfolder+file[:3]+'orfre.xml', "w")
>>  save_file.write(bres)
>>  save_file.close()
>>  blast_records = NCBIXML.parse(result_handle)
>>  for blast_record in blast_records:
>>  ...
>>     
>
> When you do result_handle.read() it reads in all the data in the
> handle - leaving it empty (pointing at the end of the file).  When the
> parser tries to read more data from the handle there isn't any, which
> is why the parser says the file seems to be empty.  You'll have to
> "reset" the handle to the beginning.
>
> One way would be to open the file you just wrote to disk:
>
> ...
> save_file.close()
> result_handle = open(...)
> blast_records = NCBIXML.parse(result_handle)
> ...
>
> Peter
>
>   


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