App-Egaz

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README.md  view on Meta::CPAN

    Available commands:

          commands: list the application's commands
              help: display a command's help screen

         blastlink: link sequences by blastn
        blastmatch: matched positions by blastn in genome sequences
            blastn: blastn wrapper between two fasta files
        exactmatch: exact matched positions in genome sequences
           fas2vcf: list variations in blocked fasta file
           formats: formats of files use in this project
             lastz: lastz wrapper for two genomes or self alignments
           lav2axt: convert .lav files to .axt
           lav2psl: convert .lav files to .psl
            lpcnam: the pipeline of pairwise lav-psl-chain-net-axt-maf
         maskfasta: soft/hard-masking sequences in a fasta file
            multiz: multiz step by step
         normalize: normalize lav files
         partition: partitions fasta files by size
           prepseq: preparing steps for lastz

lib/App/Egaz.pm  view on Meta::CPAN

    Available commands:

          commands: list the application's commands
              help: display a command's help screen

         blastlink: link sequences by blastn
        blastmatch: matched positions by blastn in genome sequences
            blastn: blastn wrapper between two fasta files
        exactmatch: exact matched positions in genome sequences
           fas2vcf: list variations in blocked fasta file
           formats: formats of files use in this project
             lastz: lastz wrapper for two genomes or self alignments
           lav2axt: convert .lav files to .axt
           lav2psl: convert .lav files to .psl
            lpcnam: the pipeline of pairwise lav-psl-chain-net-axt-maf
         maskfasta: soft/hard-masking sequences in a fasta file
            multiz: multiz step by step
         normalize: normalize lav files
         partition: partitions fasta files by size
           prepseq: preparing steps for lastz

lib/App/Egaz/Command/blastn.pm  view on Meta::CPAN

sub usage_desc {
    return "egaz blastn [options] <infile> <genome.fa>";
}

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

* <infile> should be a blocked fasta file (*.fas)
* <genome.fa> is a multi-sequence fasta file contains genome sequences
* `makeblastdb` and `blastn` should be in $PATH

MARKDOWN

    return $desc;
}

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

lib/App/Egaz/Command/fas2vcf.pm  view on Meta::CPAN

package App::Egaz::Command::fas2vcf;
use strict;
use warnings;
use autodie;

use App::Egaz -command;
use App::Egaz::Common;

sub abstract {
    return 'list variations in blocked fasta file';
}

sub opt_spec {
    return (
        [ "outfile|o=s", "Output filename. [stdout] for screen", { default => "stdout" }, ],
        [ "list=s",      "a list of names to keep, one per line", ],
        [ "verbose|v",   "verbose mode", ],
        { show_defaults => 1, }
    );
}

lib/App/Egaz/Command/raxml.pm  view on Meta::CPAN

sub usage_desc {
    return "egaz raxml [options] <infile> [more infiles]";
}

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

* <infile> should be a blocked fasta file (*.fas)
* use `fasops concat` to create a temp relaxed phylip file
* `raxmlHPC` or `raxmlHPC-*` should be in $PATH
* `raxml` is very sensitive to CPU resources. Any competitions on cores will dramatically slow down it.

MARKDOWN

    return $desc;
}

sub validate_args {