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Re: using guile like a awk filter in a C program.
From: |
Pjotr Prins |
Subject: |
Re: using guile like a awk filter in a C program. |
Date: |
Thu, 30 May 2024 09:50:21 +0200 |
Note that the scheme shell (scsh) has an awk implementation using
macros. Maybe the code helps:
https://carlstrom.com/publications/scsh-manual.pdf
On Fri, May 10, 2024 at 03:55:58PM +0200, Pierre LINDENBAUM wrote:
>
> Hi all,
>
> I tried to learn guile a few years ago with a side project that went
> nowhere.
>
> I'm now back with guile that I would like to use as a filter, just like awk,
> for my data.
> I've got question about the general design of such program.
>
> My program uses a C library ( https://github.com/samtools/htslib ) scanning
> mutations/variants in large VCF files (
> https://en.wikipedia.org/wiki/Variant_Call_Format ).
>
> A typical C program looks like (pseudo code) ;
>
> ```
> header = read_header(input);
> variant = new_variant();
> while(read_variant(input,header,variant)) {
> do_something(header,variant)
> }
> dispose_variant(variant)
> dispose_header(header)
> ```
>
> I would like to use guile to filter VCF using a custom user GUILE
> expression/program . So my program would now look like
>
> ```
> header = read_header(input);
> guile_context = my_initialize_guile(header, argc_argv_user_script)
> variant = new_variant();
> while(read_variant(input,header,variant)) {
> if(!my_guile_test(guile_context,header,variant)) {
> continue;
> }
> do_something(header,variant)
> }
> dispose_variant(variant)
> my_dispose_guile(guile_context)
> dispose_header(header)
> ```
>
> and would may be be invoked like:
>
> ```
> ./a.out -e '(and (variant-is-snp? ) (equals? (variant-allele-count) 2))'
> input.vcf > output.vcf
> ```
>
> where `variant-is-snp` would test if the current variant in the 'while' loop
> is a 'single nucleotide polylmorphism' using `bcf_is_snp`
> https://github.com/samtools/htslib/blob/develop/htslib/vcf.h#L889
>
>
> So my questions are:
>
> - is it possible to use guile for such task ? More precisely, can I compile
> the guile script just once in `my_initialize_guile` and use it in the while
> loop without having to recompile it.
> - furthermore, what's the best practice to include the user's script in a
> larger script that would include the definitions of `variant-is-snp?` ,
> `variant-allele-count`, etc...
> - is there any implementation that works like this (something like a AWK
> script in guile) ?
> - is there any way to make the program stateless ? I mean, any invocation of
> `my_guile_test` would erase the definition of the previous variant
>
> Thanks for your answers,
>
> Pierre L
>
--