[Biopython] error with entrez id code

[Peter Cock]

On Thursday, October 6, 2011, Dilara Ally <dilara.ally at gmail.com> wrote:
> Hi All
>
> I've written a program to identify Entrez gene ids from a blastall that I
performed.  The code is as follows:
>
> from Bio import SeqIO
> from Bio import Entrez
> ...
>
> The code seemed to run fine on my first file for the first 1287 lines but
then I got this error
>
>> raceback (most recent call last):
>>  File "Ally_EntrezID_Search_Final_Script.py", line 38, in <module>
>>    record=SeqIO.read(handle,"genbank")
>>  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/SeqIO/__init__.py",
line 604, in read
>>    first = iterator.next()
>>  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/SeqIO/__init__.py",
line 532, in parse
>>    for r in i:
>>  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/GenBank/Scanner.py",
line 440, in parse_records
>>    record = self.parse(handle, do_features)
>>  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/GenBank/Scanner.py",
line 423, in parse
>>    if self.feed(handle, consumer, do_features):
>>  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/GenBank/Scanner.py",
line 400, in feed
>>    misc_lines, sequence_string = self.parse_footer()
>>  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/GenBank/Scanner.py",
line 921, in parse_footer
>>    line = self.handle.readline()
>>  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py",
line 447, in readline
>>    data = self._sock.recv(self._rbufsize)
>>  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py",
line 533, in read
>>    return self._read_chunked(amt)
>>  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py",
line 586, in _read_chunked
>>    value.append(self._safe_read(amt))
>>  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py",
line 637, in _safe_read
>>    raise IncompleteRead(''.join(s), amt)
>> httplib.IncompleteRead: IncompleteRead(707 bytes read, 3147 more
expected)
>
> I'm new to python and biopython programming.  So any advice would be
extremely appreciated.

Is it always the same record that breaks? If so, what is the ID so we can
try it out.

If not, then it looks like a random network error, maybe you can stick a
try/except in to refetch the data?

Peter