App-Fasops

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lib/App/Fasops/Command/axt2fas.pm  view on Meta::CPAN

* <infiles> are paths to axt files, .axt.gz is supported
* infile == stdin means reading from STDIN
* Without query chr.sizes file, positions on negative strand of query will be wrong

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    return $desc;
}

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

    if ( !@{$args} ) {
        my $message = "This command need one or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

* <infiles> are paths to axt files, .axt.gz is supported
* infile == stdin means reading from STDIN
* <genome.fa> is one multi fasta file contains genome sequences

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    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";

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

* <infile> is the path to blocked fasta file, .fas.gz is supported
* infile == stdin means reading from STDIN
* <name.list> is a file with a list of names to keep, one per line
* Names in the output file will following the order in <name.list>

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    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";

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

* <infile> are paths to blocked fasta files, .fas.gz is supported
* infile == stdin means reading from STDIN
* `poa` is used for creating consensus sequences

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    return $desc;
}

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

    if ( @{$args} != 1 ) {
        my $message = "This command need one input file.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

    $desc .= <<'MARKDOWN';

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

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    return $desc;
}

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

    if ( !@{$args} ) {
        my $message = "This command need one or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

    $desc .= ucfirst(abstract) . ".\n";
    $desc .= <<'MARKDOWN';

* Need `samtools` in $PATH

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    return $desc;
}

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

    if ( !@{$args} ) {
        my $message = "This command need one or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

    $desc .= <<'MARKDOWN';

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

MARKDOWN

    return $desc;
}

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

    if ( !@{$args} ) {
        my $message = "This command need one or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

    $desc .= <<'MARKDOWN';

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

MARKDOWN

    return $desc;
}

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

    if ( !@{$args} ) {
        my $message = "This command need one or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

lib/App/Fasops/Command/maf2fas.pm  view on Meta::CPAN

    $desc .= <<'MARKDOWN';

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

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    return $desc;
}

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

    if ( !@{$args} ) {
        my $message = "This command need one or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

* infile == stdin means reading from STDIN

    cat 1.csv 2.csv | egaz mergecsv -f 0 -f 1
    egaz mergecsv -f 0 -f 1 1.csv 2.csv

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    return $desc;
}

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

    if ( @{$args} < 1 ) {
        my $message = "This command need one or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

    $desc .= <<'MARKDOWN';

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

MARKDOWN

    return $desc;
}

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

    if ( !@{$args} ) {
        my $message = "This command need one or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

    * clustalw
    * none: means skip realigning
* <infile> are paths to blocked fasta files, .fas.gz is supported
* infile == stdin means reading from STDIN

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    return $desc;
}

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

    if ( @{$args} != 1 ) {
        my $message = "This command need one input file.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

        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

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    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";

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

    $desc .= <<'MARKDOWN';

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

MARKDOWN

    return $desc;
}

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

    if ( !@{$args} ) {
        my $message = "This command need one or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

* <infiles> are paths to axt files, .axt.gz is supported
* infile == stdin means reading from STDIN
* <runlist.yml> is a App::RL dump

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";

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

    $desc .= <<'MARKDOWN';

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

MARKDOWN

    return $desc;
}

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

    if ( !@{$args} ) {
        my $message = "This command need one or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

    $desc .= <<'MARKDOWN';

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

MARKDOWN

    return $desc;
}

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

    if ( @{$args} != 1 ) {
        my $message = "This command need one input file.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

* <infile> is the path to blocked fasta file, .fas.gz is supported
* infile == stdin means reading from STDIN
* <name.list> is a file with a list of names to keep, one per line
* Names in the output file will following the order in <name.list>

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";

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

    $desc .= <<'MARKDOWN';

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

MARKDOWN

    return $desc;
}

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

    if ( @{$args} != 1 ) {
        my $message = "This command need one input file.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

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

    $desc .= <<'MARKDOWN';

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

MARKDOWN

    return $desc;
}

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

    if ( @{$args} != 1 ) {
        my $message = "This command need one input file.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";