GNU bug report logs - #51792
coreutils - csplit - feature request

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Rodolfo Aramayo <raramayo <at> tamu.edu>
To: bug-coreutils <at> gnu.org
Subject: coreutils - csplit - feature request
Date: Fri, 12 Nov 2021 11:05:09 -0600

[Message part 1 (text/plain, inline)]

Dear Coreutils Maintainers,

First, thank you for your work. I use coreutils daily both for my research
and teaching. It is a great set of tools.

Second, I recently needed to extract Coding Sequences information from a
GenBank file. GenBank files are used in Computational
Genomics/Bioinformatics extensively. I used csplit, and it works like a
charm.

The command I used is:

csplit -sz -n 5 --prefix=02_ 01_00001
/[[:space:]][[:space:]][[:space:]][[:space:]][[:space:]]CDS[[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]]/
{*};

I was unable to declare: "[[:space:]]\+" as I expected for POSIX aware code.

My question is: Is csplit POSIX compatible? and if it is not, can we make
it POSIX compatible?

Many Thanks

Rodolfo

--
Dr. Rodolfo Aramayo, PhD
Faculty of Biology and Genetics
Department of Biology, Texas A&M University

[Message part 2 (text/html, inline)]

Message #8 received at 51792 <at> debbugs.gnu.org (full text, mbox):

From: Pádraig Brady <P <at> draigBrady.com>
To: Rodolfo Aramayo <raramayo <at> tamu.edu>, 51792 <at> debbugs.gnu.org
Subject: Re: bug#51792: coreutils - csplit - feature request
Date: Fri, 12 Nov 2021 18:23:37 +0000

On 12/11/2021 17:05, Rodolfo Aramayo wrote:
> Dear Coreutils Maintainers,
> 
> First, thank you for your work. I use coreutils daily both for my research
> and teaching. It is a great set of tools.
> 
> Second, I recently needed to extract Coding Sequences information from a
> GenBank file. GenBank files are used in Computational
> Genomics/Bioinformatics extensively. I used csplit, and it works like a
> charm.
> 
> The command I used is:
> 
> csplit -sz -n 5 --prefix=02_ 01_00001
> /[[:space:]][[:space:]][[:space:]][[:space:]][[:space:]]CDS[[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]]/
> {*};
> 
> I was unable to declare: "[[:space:]]\+" as I expected for POSIX aware code.
> 
> My question is: Is csplit POSIX compatible? and if it is not, can we make
> it POSIX compatible?


Well POSIX defines BRE and ERE, with csplit supporting the former.
From the code we have:

  re_syntax_options =
    RE_SYNTAX_POSIX_BASIC & ~RE_CONTEXT_INVALID_DUP & ~RE_NO_EMPTY_RANGES;

Generally one can replace '+' functionality from ERE, with '\{1,\}' in BRE.
So you'd be using something like:

  [[:space:]]\{1,\}CDS[[:space:]]\{1,\}

We might add an option to use ERE, though there isn't a big need
for that I think for csplit use cases.

cheers,
Pádraig

Message #11 received at 51792 <at> debbugs.gnu.org (full text, mbox):

From: Rodolfo Aramayo <raramayo <at> tamu.edu>
To: Pádraig Brady <p <at> draigbrady.com>
Cc: Rodolfo Aramayo <raramayo <at> tamu.edu>, 51792 <at> debbugs.gnu.org
Subject: Re: bug#51792: coreutils - csplit - feature request
Date: Wed, 17 Nov 2021 13:33:24 -0600

[Message part 1 (text/plain, inline)]

Pádraig,

Thank you for your response

Unfortunately, even the command pattern you are proposing as an alternative:

  [[:space:]]\{1,\}CDS[[:space:]]\{1,\}

does not work, therefore I have to conclude that csplit is neither BRE
and ERE compatible

Thanks for your help

R




On Fri, Nov 12, 2021 at 12:23 PM Pádraig Brady <P <at> draigbrady.com> wrote:

> On 12/11/2021 17:05, Rodolfo Aramayo wrote: > Dear Coreutils Maintainers,
> > > First, thank you for your work. I use coreutils daily both for my
> research > and teaching. It is a great set of tools. > > Second, I recently
> needed ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
> This message came from outside your organization.
> ZjQcmQRYFpfptBannerEnd
>
> On 12/11/2021 17:05, Rodolfo Aramayo wrote:
> > Dear Coreutils Maintainers,
> >
> > First, thank you for your work. I use coreutils daily both for my research
> > and teaching. It is a great set of tools.
> >
> > Second, I recently needed to extract Coding Sequences information from a
> > GenBank file. GenBank files are used in Computational
> > Genomics/Bioinformatics extensively. I used csplit, and it works like a
> > charm.
> >
> > The command I used is:
> >
> > csplit -sz -n 5 --prefix=02_ 01_00001
> > /[[:space:]][[:space:]][[:space:]][[:space:]][[:space:]]CDS[[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]]/
> > {*};
> >
> > I was unable to declare: "[[:space:]]\+" as I expected for POSIX aware code.
> >
> > My question is: Is csplit POSIX compatible? and if it is not, can we make
> > it POSIX compatible?
>
>
> Well POSIX defines BRE and ERE, with csplit supporting the former.
>  From the code we have:
>
>    re_syntax_options =
>      RE_SYNTAX_POSIX_BASIC & ~RE_CONTEXT_INVALID_DUP & ~RE_NO_EMPTY_RANGES;
>
> Generally one can replace '+' functionality from ERE, with '\{1,\}' in BRE.
> So you'd be using something like:
>
>    [[:space:]]\{1,\}CDS[[:space:]]\{1,\}
>
> We might add an option to use ERE, though there isn't a big need
> for that I think for csplit use cases.
>
> cheers,
> Pádraig
>
>

-- 
Dr. Rodolfo Aramayo, PhD
Faculty of Biology and Genetics
Department of Biology, Texas A&M University
PeerJ
PeerJ - the Journal of Life & Environmental Sciences
<https://peerj.com/> Academic
Editor peerj.com/RodolfoAramayo

[Message part 2 (text/html, inline)]

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