Re: Regular expression

[Fredrik Lundh]

Beema shafreen wrote:

How do I write a regular expression for this kind of sequences
>

>gi|158028609|g b|ABW08583.1| CG8385-PF, isoform F [Drosophila melanogaster]

MGNVFANLFKGLFGK KEMRILMVGLDAAGK TTILYKLKLGEIVTT IPTIGFNVETVE

line.split("|") ?

it's a bit hard to come up with a working RE with only a single sample;
what are the constraints for the different fields? is the last part
free form text or something else, etc.

have you googled for existing implementations of the format you're using?

</F>

[bearophileHUGS@lycos.com]

Re: Regular expression

On Jul 16, 4:14 pm, Fredrik Lundh <fred...@python ware.comwrote:

Beema shafreen wrote:

How do I write a regular expression for this kind of sequences

>

>gi|158028609|g b|ABW08583.1| CG8385-PF, isoform F [Drosophila melanogaster]

MGNVFANLFKGLFGK KEMRILMVGLDAAGK TTILYKLKLGEIVTT IPTIGFNVETVE

>
line.split("|") ?
>
it's a bit hard to come up with a working RE with only a single sample;
what are the constraints for the different fields? is the last part
free form text or something else, etc.
>
have you googled for existing implementations of the format you're using?

That'a a fasta file, so for the header line this is enough:
[part.strip() for part in line.split("|")]
But better is to use the biopython libs that already perform all such
things better.

Bye,
bearophile