[Biopython-dev] [Bug 2176] XML Blast parser: miscellaneous bug fixes and cleanup

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2176





------- Comment #14 from biopython-bugzilla at maubp.freeserve.co.uk  2009-04-01 07:48 EST -------
I've updated CVS as per comment 12 to also use record.query_length, and comment
13 to also use record.database_length.

Before:

>>> from Bio.Blast import NCBIXML
>>> for record in NCBIXML.parse(open("xbt007.xml")) :
...     print record.query_id
...     print record.query_letters, record.query_length
...     print record.num_letters_in_database, record.database_letters,
record.database_length
... 
gi|585505|sp|Q08386|MOPB_RHOCA
270 None
13958303 None None
gi|129628|sp|P07175.1|PARA_AGRTU
222 None
13958303 None None

Now, with Bio/Blast/NCBIXML.py CVS revision 1.20 or 1.21,

>>> from Bio.Blast import NCBIXML
>>> for record in NCBIXML.parse(open("xbt007.xml")) :
...     print record.query_id
...     print record.query_letters, record.query_length
...     print record.num_letters_in_database, record.database_letters,
record.database_length
... 
gi|585505|sp|Q08386|MOPB_RHOCA
270 270
13958303 None 13958303
gi|129628|sp|P07175.1|PARA_AGRTU
222 222
13958303 None 13958303

We could perhaps deprecate record.database_letters immediately, and at a later
point, record.query_letters


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