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 > --
