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use clap::*;
use intspan::*;
use std::collections::BTreeMap;
use std::io::Write;
// Create clap subcommand arguments
pub fn make_subcommand() -> Command {
Command::new("slice")
.about("Extract alignment slices")
.after_help(
r###"
* <infiles> are paths to block fasta files, .fas.gz is supported
* infile == stdin means reading from STDIN
"###,
)
.arg(
Arg::new("runlist.json")
.required(true)
.index(1)
.num_args(1)
.help("Set the runlist file to use"),
)
.arg(
Arg::new("infiles")
.required(true)
.num_args(1..)
.index(2)
.help("Sets the input files to use"),
)
.arg(
Arg::new("name")
.long("name")
.num_args(1)
.help("According to this species. Default is the first one"),
)
.arg(
Arg::new("outfile")
.long("outfile")
.short('o')
.num_args(1)
.default_value("stdout")
.help("Output filename. [stdout] for screen"),
)
}
// command implementation
pub fn execute(args: &ArgMatches) -> anyhow::Result<()> {
//----------------------------
// Args
//----------------------------
let mut writer = writer(args.get_one::<String>("outfile").unwrap());
let json = read_json(args.get_one::<String>("runlist.json").unwrap());
let set = json2set(&json);
let mut name = if args.contains_id("name") {
args.get_one::<String>("name").unwrap().to_string()
} else {
"".to_string()
};
//----------------------------
// Operating
//----------------------------
for infile in args.get_many::<String>("infiles").unwrap() {
let mut reader = reader(infile);
while let Ok(block) = next_fas_block(&mut reader) {
// the first name of the first block
if name.is_empty() {
name = block.names.first().unwrap().to_string();
}
let idx = block.names.iter().position(|x| x == &name);
if idx.is_none() {
continue;
}
let trange = block.entries.get(idx.unwrap()).unwrap().range().clone();
// chr present
if !set.contains_key(trange.chr()) {
continue;
}
if set.get(trange.chr()).unwrap().is_empty() {
continue;
}
// has intersect
let i_ints_chr = trange.intspan().intersect(set.get(trange.chr()).unwrap());
if i_ints_chr.is_empty() {
continue;
}
// target sequence intspan
let t_ints_seq = seq_intspan(block.entries.get(idx.unwrap()).unwrap().seq());
// every sequence intspans
let mut ints_seq_of = BTreeMap::new();
// all indel region
let mut indel_ints = IntSpan::new();
for (i, name) in block.names.iter().enumerate() {
let seq = block.entries.get(i).unwrap().seq();
ints_seq_of.insert(name.to_string(), seq_intspan(seq));
indel_ints.merge(&indel_intspan(seq));
}
// there may be more than one subslice intersect this alignment
let mut sub_slices: Vec<_> = vec![];
for (lower, upper) in i_ints_chr.spans() {
// chr positions to align
let ss_start =
chr_to_align(&t_ints_seq, lower, trange.start, trange.strand()).unwrap();
let ss_end =
chr_to_align(&t_ints_seq, upper, trange.start, trange.strand()).unwrap();
if ss_start >= ss_end {
continue;
}
let mut ss_ints = IntSpan::from_pair(ss_start, ss_end);
// borders of subslice inside an indel
for n in [ss_start, ss_end] {
if indel_ints.contains(n) {
let island = indel_ints.find_islands_n(n);
ss_ints.subtract(&island);
}
}
sub_slices.push(ss_ints);
}
// write headers and sequences
for ss in &sub_slices {
let ss_start = ss.min();
let ss_end = ss.max();
// align positions to chromosomes of difference species
for (i, name) in block.names.iter().enumerate() {
let range = block.entries.get(i).unwrap().range();
let start = align_to_chr(
ints_seq_of.get(name).unwrap(),
ss_start,
range.start,
range.strand(),
)
.unwrap();
let end = align_to_chr(
ints_seq_of.get(name).unwrap(),
ss_end,
range.start,
range.strand(),
)
.unwrap();
let ss_range =
Range::from_full(range.name(), range.chr(), range.strand(), start, end);
// seq of this sub slice
let ss_seq = &block.entries.get(i).unwrap().seq()
[(ss_start - 1) as usize..ss_end as usize];
//----------------------------
// Output
//----------------------------
writer.write_all(
format!(">{}\n{}\n", ss_range, std::str::from_utf8(ss_seq).unwrap())
.as_ref(),
)?;
}
}
// end of a block
writer.write_all("\n".as_ref())?;
} // block
} // infile
Ok(())
}