<commit_before>=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <<EMAIL>>.

  Questions may also be sent to the Ensembl help desk at
  <<EMAIL>>.

=cut

=head1 NAME

Bio::EnsEMBL::Analysis::Runnable::Pecan - 

=head1 SYNOPSIS

  my $runnable = new Bio::EnsEMBL::Analysis::Runnable::Pecan
     (-workdir => $workdir,
      -fasta_files => $fasta_files,
      -tree_string => $tree_string,
      -program => "/path/to/program");
  $runnable->run;
  my @output = @{$runnable->output};

=head1 DESCRIPTION

Mavid expects to run the program mavid, a global multiple aligner for large genomic sequences,
using a fasta file and a tree file (Newick format), and eventually a constraints file.
The output (multiple alignment) is parsed and return as a Bio::EnsEMBL::Compara::GenomicAlignBlock object.

=head1 METHODS

=cut


# $Source: /tmp/ENSCOPY-ENSEMBL-ANALYSIS/modules/Bio/EnsEMBL/Analysis/Runnable/Pecan.pm,v $
# $Revision: 1.13 $
package Bio::EnsEMBL::Analysis::Runnable::Pecan;

use strict;<commit_msg>source/revision cvs tag removal<commit_after>=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <<EMAIL>>.

  Questions may also be sent to the Ensembl help desk at
  <<EMAIL>>.

=cut

=head1 NAME

Bio::EnsEMBL::Analysis::Runnable::Pecan - 

=head1 SYNOPSIS

  my $runnable = new Bio::EnsEMBL::Analysis::Runnable::Pecan
     (-workdir => $workdir,
      -fasta_files => $fasta_files,
      -tree_string => $tree_string,
      -program => "/path/to/program");
  $runnable->run;
  my @output = @{$runnable->output};

=head1 DESCRIPTION

Mavid expects to run the program mavid, a global multiple aligner for large genomic sequences,
using a fasta file and a tree file (Newick format), and eventually a constraints file.
The output (multiple alignment) is parsed and return as a Bio::EnsEMBL::Compara::GenomicAlignBlock object.

=head1 METHODS

=cut


package Bio::EnsEMBL::Analysis::Runnable::Pecan;

use strict;
{'fraction_non_alphanumeric': 0.10147172734314484, 'fraction_numerical': 0.012006196746707979, 'mean_word_length': 4.282208588957055, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 23, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '245275', 'n_tokens_mistral': 883, 'n_tokens_neox': 811, 'n_words': 268}