From: Pierre LINDENBAUM <Pierre.Lindenbaum@univ-nantes.fr>
To: guile-user@gnu.org
Subject: using guile like a awk filter in a C program.
Date: Fri, 10 May 2024 15:55:58 +0200 [thread overview]
Message-ID: <60c7c61c6dea289c9a1d8e59829f9c91@univ-nantes.fr> (raw)
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
next reply other threads:[~2024-05-10 13:55 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2024-05-10 13:55 Pierre LINDENBAUM [this message]
2024-05-17 18:09 ` using guile like a awk filter in a C program Simon Tournier
2024-05-21 13:39 ` Pierre Lindenbaum
2024-05-22 10:39 ` Simon Tournier
2024-05-24 7:31 ` Pierre Lindenbaum
2024-05-28 8:42 ` Zelphir Kaltstahl
2024-06-10 9:08 ` Maxime Devos via General Guile related discussions
2024-05-21 14:58 ` Basile Starynkevitch
2024-05-30 7:50 ` Pjotr Prins
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