Talk:SeqIO
(Difference between revisions)
(Question on 'embl' parser support) |
(Question on 'embl' parser support) |
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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') |
| − | >>> | + | >>>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
