Talk:SeqIO

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(Question on 'embl' parser support)
 
(Question on 'embl' parser support)
Line 2: Line 2:
 
I tested Bio.SeqIO.parse on EMBL formated miRNA.dat from the microRNA Registry. But I got an error. Is the EMBL format supported fully?
 
I tested Bio.SeqIO.parse on EMBL formated miRNA.dat from the microRNA Registry. But I got an error. Is the EMBL format supported fully?
 
As:
 
As:
>>> from Bio import SeqIO
+
 
>>> handle = open('/home/liang/Desktop/miRNA.dat','rU')
+
>>>from Bio import SeqIO
>>> record_iterator = SeqIO.parse(handle,'embl')
+
>>>handle = open('/home/liang/Desktop/miRNA.dat','rU')
>>> first_record=record_iterator.next()
+
>>>record_iterator = SeqIO.parse(handle,'embl')
 +
>>>first_record=record_iterator.next()
 
Traceback (most recent call last):
 
Traceback (most recent call last):
 
   File "<stdin>", line 1, in <module>
 
   File "<stdin>", line 1, in <module>

Revision as of 09:49, 19 May 2007

Hi, I am a newbie of Biopython. I tested Bio.SeqIO.parse on EMBL formated miRNA.dat from the microRNA Registry. But I got an error. Is the EMBL format supported fully? As:

>>>from Bio import SeqIO >>>handle = open('/home/liang/Desktop/miRNA.dat','rU') >>>record_iterator = SeqIO.parse(handle,'embl') >>>first_record=record_iterator.next() Traceback (most recent call last):

 File "<stdin>", line 1, in <module>
 File "/usr/lib/python2.5/site-packages/Bio/GenBank/Scanner.py", line 410, in parse_records
   record = self.parse(handle)
 File "/usr/lib/python2.5/site-packages/Bio/GenBank/Scanner.py", line 393, in parse
   if self.feed(handle, consumer) :
 File "/usr/lib/python2.5/site-packages/Bio/GenBank/Scanner.py", line 360, in feed
   self._feed_first_line(consumer, self.line)
 File "/usr/lib/python2.5/site-packages/Bio/GenBank/Scanner.py", line 540, in _feed_first_line
   assert len(fields) == 7

AssertionError

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