[Biopython] Issue in retrieving Pubmed Ids

[Lenna Peterson]

If your file has blank lines as shown, then the second iteration is calling
`data = Entrez.esearch(db="pubmed",term = "\n")`

When reading files I often have a check like this:

line = line.strip()
if not line:
    continue

Hope that helps.

Cheers,

Lenna


On Fri, Aug 9, 2013 at 3:12 PM, sai nitin <sainitin7 at gmail.com> wrote:

> Hi all,
>
> I have set of genes ( ASCL1, AEBP1, MLF1) i want to search PUBMED for
> literature in glioma. Means i want to get Pubmed Ids for these genes in
> glioma. To achieve this i tried biopython script as follows. First i stored
> this terms in file as follows
>
> ASCL1 and glioma
>
> AEBP1 and glioma
>
> .....
>
> infile = "file.txt"
>
> for line in infile.readlines():
>
>   single_id = line
>
>   #Retreiving information
>
>   data = Entrez.esearch(db="pubmed",term = single_id)
>
>   res=Entrez.read(data)
>
>   PMID = res["IdList"]
>
>   print "%s" %(PMID)
>
>   out_put.write("%s\n" %(PMID))
>
> out_put.close()
>
> It reads only first line ASCL1 and glioma ... and gives result as follows
>
> ['22859994', '18796682', '18636433', '17146289', '17124508', '16103883',
> '11433425']
>
> Traceback (most recent call last):
>
>   File "PUBMED.py", line 13, in <module>
>
>     res=Entrez.read(data)
>
>   File "/Library/Python/2.7/site-packages/Bio/Entrez/__init__.py", line
> 367, in read
>
>     record = handler.read(handle)
>
>   File "/Library/Python/2.7/site-packages/Bio/Entrez/Parser.py", line 184,
> in read
>
>     self.parser.ParseFile(handle)
>
>   File "/Library/Python/2.7/site-packages/Bio/Entrez/Parser.py", line 322,
> in endElementHandler
>
>     raise RuntimeError(value)
>
> RuntimeError: Empty term and query_key - nothing todo
>
>
> It looks like it does not read second line..in file.txt..Can any body tell
> how to solve this issue..
>
>
> Thanks,
>
> --
>
> Sainitin D
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