Bio SwissProt.read() broken in Python 3.5 (biopython 1.66 np110py35_0) #773
Description
Windows7 Python 3.5.1 Anaconda 2.5.0 biopython 1.66 np110py35_0
(in jupyter)
from Bio import ExPASy
handle = ExPASy.get_sprot_raw("P75952")
from Bio import SwissProt
record = SwissProt.read(handle)
results in:
---------------------------------------------------------------------------
IncompleteRead Traceback (most recent call last)
<ipython-input-1-11c8db89238e> in <module>()
3 print(handle)
4 from Bio import SwissProt
----> 5 record = SwissProt.read(handle)
6 print(record)
C:\Anaconda3\lib\site-packages\Bio\SwissProt\__init__.py in read(handle)
135 ##print(handle.url," ",handle," ",handle.fp)
136 ##handle.fp = None
--> 137 remainder = handle.read()
138 print(remainder)
139 if remainder:
C:\Anaconda3\lib\http\client.py in read(self, amt)
446 else:
447 try:
--> 448 s = self._safe_read(self.length)
449 except IncompleteRead:
450 self._close_conn()
C:\Anaconda3\lib\http\client.py in _safe_read(self, amt)
596 print(chunk, "\n")
597 if not chunk:
--> 598 raise IncompleteRead(b''.join(s), amt)
599 s.append(chunk)
600 amt -= len(chunk)
IncompleteRead: IncompleteRead(0 bytes read, 6066 more expected)
from what I can tell (not much experience here)
it seems something changed in how lines are read in __init__.py of SwissProt
such that when handle.read() of http/client is called,
different values are sent than were before.
The Python 3.5.1 version (biopython 1.66 np110py35_0) passes http/client.read a header with
length = 6066 and fp = <_io.BufferedReader name=1156>
whereas Python 3.4.4 (biopython 1.66 np110py34_0) version passes a header with
length = 0 and fp = None