#!/usr/bin/env perl6

# a minimal Stockholm alignment format parser that reads
# ONLY single-line alignments and dumps each sequence (without additional
# gap characters) to a file

use Grammar::Tracer;

grammar StockholmParser {
	token TOP { <header>+ <alignment> <consensus> <sep>? <.eol> }
	token header { ['#'|'#='] [\N]+ <.eol> }
	token alignment { <aln>+  }
	token aln { <id> \s+ <seq> <.eol> }
	token id { [\S+] }
	token consensus { '#=GC SS_cons' <ws> <form> <.eol> }
	token form { <[ ( ) . ]>+ }
	token seq { <[\w\-]>+ }
	token eol { \n [\h*\n]* }
	token sep { '//' }
}

class Stk-actions {
      method seq($/) {make $/.subst(:g, '-','') }
}


sub MAIN ( $filename ){
    say "processing $filename";
    my $result = StockholmParser.parsefile($filename, actions => Stk-actions.new);
 #   note $result;

    for $result<alignment><aln>.flat -> $a {
    my $fh=open "$a<id>.fa", :w;
    $fh.say($a<seq>.made);
    $fh.close
    }
}