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lib/App/Fasops/Command/replace.pm  view on Meta::CPAN

package App::Fasops::Command::replace;
use strict;
use warnings;
use autodie;

use App::Fasops -command;
use App::RL::Common;
use App::Fasops::Common;

sub abstract {
    return 'replace headers from a blocked fasta';
}

sub opt_spec {
    return ( [ "outfile|o=s", "Output filename. [stdout] for screen." ], { show_defaults => 1, } );
}

sub usage_desc {
    return "fasops replace [options] <infile> <replace.tsv>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= <<'MARKDOWN';

* <infiles> are paths to axt files, .axt.gz is supported
* infile == stdin means reading from STDIN

* <replace.tsv> is a tab-separated file containing more than one fields

        original_name   replace_name    more_replace_name

    * With one field will delete the whole alignment block
    * With three or more fields will duplicate the whole alignment block

MARKDOWN

    return $desc;
}

sub validate_args {
    my ( $self, $opt, $args ) = @_;

    if ( @{$args} != 2 ) {
        my $message = "This command need two input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";
        if ( !Path::Tiny::path($_)->is_file ) {
            $self->usage_error("The input file [$_] doesn't exist.");
        }
    }

    if ( !exists $opt->{outfile} ) {
        $opt->{outfile} = Path::Tiny::path( $args->[0] )->absolute . ".fas";
    }
}

sub execute {
    my ( $self, $opt, $args ) = @_;

    my $replace = App::Fasops::Common::read_replaces( $args->[1] );

    my $in_fh;
    if ( lc $args->[0] eq "stdin" ) {
        $in_fh = *STDIN{IO};
    }
    else {
        $in_fh = IO::Zlib->new( $args->[0], "rb" );
    }

    my $out_fh;
    if ( lc( $opt->{outfile} ) eq "stdout" ) {
        $out_fh = *STDOUT{IO};
    }
    else {
        open $out_fh, ">", $opt->{outfile};
    }

    {
        my $content = '';    # content of one block
        while (1) {
            last if $in_fh->eof and $content eq '';
            my $line = '';
            if ( !$in_fh->eof ) {
                $line = $in_fh->getline;
            }
            if ( ( $line eq '' or $line =~ /^\s+$/ ) and $content ne '' ) {
                my $info_of = App::Fasops::Common::parse_block_header($content);
                $content = '';

                my @ori_names = keys %{$info_of};

                my @replace_names
                    = grep { exists $info_of->{$_} } keys %{$replace};

                if ( @replace_names == 0 ) {    # block untouched
                    for my $header (@ori_names) {