[Bioperl-l] issue writing to pipe with bio sequoia

[Fields, Christopher J]

Sure, should be easy enough to add.

-c

On Jun 1, 2016, at 11:12 AM, Peter Cock <p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>> wrote:

Hi Stephane,

The website source for that page is now here:

https://github.com/bioperl/bioperl.github.io/blob/master/howtos/SeqIO_HOWTO.md<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_bioperl.github.io_blob_master_howtos_SeqIO-5FHOWTO.md&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=YBYjoJM_ao0zxPoNYRS91_ThSa_koTRTKgsS0Av0S1Q&s=8DOZV6TG6X6zXuAmMqyl1E-Ab6rjv6AadFnKlhnw1RU&e=>

You can edit it within the GitHub web interface and make a pull request (remember to check the preview).

Chris etc: Can you apply something like this to add an edit button/link to each page?

https://github.com/biopython/biopython.github.io/issues/14<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_biopython_biopython.github.io_issues_14&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=YBYjoJM_ao0zxPoNYRS91_ThSa_koTRTKgsS0Av0S1Q&s=24MC6pkx9XxQfEvzDynqzirlypHfcZwW8j6ifTf6tbY&e=>
https://github.com/biopython/biopython.github.io/commit/a2b3c5bd551fbfe8b41192d4ae6660b4bb2a68bb<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_biopython_biopython.github.io_commit_a2b3c5bd551fbfe8b41192d4ae6660b4bb2a68bb&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=YBYjoJM_ao0zxPoNYRS91_ThSa_koTRTKgsS0Av0S1Q&s=zA_1muPMjruUJx4FfvO4NwVTm-J6F7El-t2OLmwxheE&e=>

Regards,

Peter

On Wed, Jun 1, 2016 at 9:28 AM, Stephane Plaisance | VIB | <stephane.plaisance at vib.be<mailto:stephane.plaisance at vib.be>> wrote:
Thanks a lot Chris,

Your code example is much more instructive than the text I found on the IO man pages.
If someone has access to (http://bioperl.org/howtos/SeqIO_HOWTO.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioperl.org_howtos_SeqIO-5FHOWTO.html&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=YBYjoJM_ao0zxPoNYRS91_ThSa_koTRTKgsS0Av0S1Q&s=RfPAijOK_XdYIwTnw41qw_2LfbZw9QzGzJHi7Nq-h9M&e=>) and could edit some examples for saving to bgzip it would probably help others.
My code now works like a charm and I generate smaller compressed and tabix index-able bgzip Fasta instead of huge plain files.

THANKS to ALL who helped me

Stephane


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