Re: Regular expression

[Fredrik Lundh]

Beema shafreen wrote:

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

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

MGNVFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIG FNVETVE

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]

On Jul 16, 4:14 pm, Fredrik Lundh <[e-mail]:

Beema shafreen wrote:

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

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

MGNVFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIG FNVETVE

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