Re: using guile like a awk filter in a C program.

[Pjotr Prins <pjotr.public12@thebird.nl>]

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
> 

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