[Biopython] Entrez.efetch

[Michiel de Hoon]

Put a try:/except: block around the call to SeqIO.read, as in:

try:
    seq_record=SeqIO.read(prothandle, "gb")
except ValueError:
    print "INCORRECT ID GIVEN"


--Michiel

--- On Mon, 4/19/10, Olumide Olufuwa <olumideolufuwa at yahoo.com> wrote:

> From: Olumide Olufuwa <olumideolufuwa at yahoo.com>
> Subject: [Biopython] Entrez.efetch
> To: biopython at lists.open-bio.org
> Date: Monday, April 19, 2010, 3:30 AM
> 
> Hello there,
>  
> I wrote a program, I am not awesome in biopython but this
> is what it does: The program code that 
> accepts user defined UNIPROT ID, retrieves the record using
> Entrez.efetch and then it
>  is parsed to obtain the Pubmed ID which i use to search
> Medline for Title, Abstract and other information about the
> entry. 
> The code is simply:
> 
> query_id=str(raw_input("please
> 
> 
> 
>  enter your UNIPROT_ID: ")) #Request UNIPROT ID from user
> Entrez.email="ludax5 at yahoo.com"
> prothandle=Entrez.efetch(db="protein",
> 
> 
> 
>  id=query_id, rettype="gb" #queries Protein DB with the
> given ID
> #The
>  program returns an error here if a wrong ID is given.
> Details of the 
> error is given below
> seq_record=SeqIO.read(prothandle, "gb")
> for
> 
>  record in seq_record.annotations['references']: # To
> obtain Pubmed id 
> from the seqrecord
>    key_word=record.pubmed_id
>    if key_word:
>     
> 
>  handle=Entrez.efetch(db="pubmed",
> 
>  id=key_word, rettype="medline")
>      
> medRecords=Medline.parse(handle)
>      for rec in medRecords: #prints 
> title and Abstract
>          if rec.has_key('AB') and 
> rec.has_key('TI'):
>            print "TITLE: ",rec['TI']
>           
>  print "ABSTRACT: ",rec['AB']
>            print ' '
> 
> 
> THE 
> PROBLEM: The program gives an error if a wrong ID is
> entered or an ID 
> other than UNIPROT ID e.g PDB ID, GSS ID etc. 
> 
> 
> 
> An Example Run with a wrong ID is shown below:
> 
> 
> please enter your UNIPROT_ID:
>  1wio #A PDB ID is given instead
> 
> 
> Traceback (most recent call last):
>   File "file.py", line 11, in 
> <module>
>     seq_record=SeqIO.read(prothandle, "gb")
>   File 
> "/usr/lib/python2.5/site-packages/Bio/SeqIO/__init__.py",
> line 522, in 
> read
>     raise ValueError("No records found in handle")
> ValueError:
> 
> 
>  No records found in handle
> 
> I want to avoid this error, thus i 
> want the program to print "INCORRECT ID GIVEN"  when a
> wrong or an 
> incorrect ID is given.
> 
> 
> Thanks a lot.
> lummy
> 
> 
> 
> 
>       
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