[Biopython] Issue in retrieving Pubmed Ids
sai nitin
sainitin7 at gmail.com
Fri Aug 9 19:12:39 UTC 2013
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
More information about the Biopython
mailing list