[Biopython-dev] FormatIO and SwissProt
Yves Bastide
Yves.Bastide at irisa.fr
Thu Jul 3 05:43:28 EDT 2003
Jeffrey Chang wrote:
> On Wednesday, July 2, 2003, at 10:03 AM, Yves Bastide wrote:
>
>> Hi,
>>
>> FormatIO doesn't seem to handle SwissProt files well...
>>
>> bionix:~/src/bio/biopython/Tests% python
>> Python 2.2.2 (#1, Feb 14 2003, 12:23:31)
>> [GCC 3.2 20020903 (Red Hat Linux 8.0 3.2-7)] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>>
>>>>> from Bio import SeqRecord
>>>>> sequence_iterator = SeqRecord.io.readFile(open("SwissProt/sp008"))
>>
>> Traceback (most recent call last):
>> File "<stdin>", line 1, in ?
>> File "/.amd/archipel/export/archive/d08/symbiose/ybastide/src/bio/
>> biopython/build/lib.linux-i686-2.2/Bio/FormatIO.py", line 97, in
>> readFile
>> raise TypeError("Could not determine file type")
>> TypeError: Could not determine file type
>>
>> [OK, there are two Swissprot parsers. Erm, why
>> */build/lib-*/Bio/FormatIO.py?
>> It's certainly not in my path :)]
>
>
> Is this related to the patch you sent in? This also fails on my
> system, but the path points to my usual python path (i.e. not
> ../build...).
Strange. No, don't see how it could be because of my patch: I didn't
use run_test nor play with sys.path
>
> And yes, you've hit the problem right on the nose. There are two
> Swiss-Prot parsers. The FormatIO one is still considered experimental,
> and is not maintained as well. I'd recommend using the
> Bio/SwissProt/SProt parser instead.
There are three SP parsers: Bio/SwissProt/SProt and two for FormatIO
(../Bio/expressions/swissprot/sprot{38,40}.py)
I'd like to use FormatIO because
1. It's cool to use the same code whether I'm accessing nr or sprot or
something else
2. Bio.SeqRecord: to insert into a database. One can't get a
Bio.SeqRecord from SProt, I think
About GenBank:
GenBank.FeatureParser uses a nice Martel parser, FormatIO an
experimental-unmaintened one; couldn't FormatIO use the good one? (OTOH
Bio.SwissProt.SProt is not Martel-based)
>
> Jeff
yves
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