[Biopython-dev] rebase and regexp

Jeffrey Chang jchang at SMI.Stanford.EDU
Sun Jul 16 00:39:47 EDT 2000

Great!  Glad you're interested in adding rebase.

Yes, we can add this if it's really needed.  However, I've purposefully
left it out mostly to discourage the use of regular expressions for
performance reasons.  Is this something that you can do with either the
'start' and/or 'contains' parameters?

For example, in the Blast.NCBIStandalone module, I inserted the whitespace
directly into the string:
       read_and_call(uhandle, consumer.score, start=' Score')
       read_and_call(uhandle, consumer.identities, start=' Identities')

Alternative ways to do this might be:
       read_and_call(uhandle, consumer.score, contains='Score')

       read_and_call(uhandle, consumer.score, start=' ', contains='Score')

Please let me know.


On Sat, 15 Jul 2000, Cayte wrote:

>    I was thinking about using the parser/consumer template to parse a
> rebase file.  It would be useful if _fail_condition in ParserSupport.py
> could handle regular expressions.  The rebase tags are indented, so
> white space needs to be skipped before the start field.
>                                                             Cayte
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