Bio-Palantir

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META.yml  view on Meta::CPAN

  DBD::SQLite: '0'
  DBI: '0'
  Data::UUID: '0'
  File::Basename: '0'
  File::ShareDir: '0'
  File::Temp: '0'
  Getopt::Euclid: '0'
  JSON::Create: '0'
  JSON::Parse: '0'
  List::AllUtils: '0'
  Modern::Perl: '0'
  Moose: '0'
  Moose::Role: '0'
  POSIX: '0'
  Path::Class: '0'
  Smart::Comments: '0'
  Template: '0'
  Test::Most: '0'
  XML::Bare: '0.53'
  XML::Hash::XS: '0'
  aliased: '0'

Makefile.PL  view on Meta::CPAN

    "DBD::SQLite" => 0,
    "DBI" => 0,
    "Data::UUID" => 0,
    "File::Basename" => 0,
    "File::ShareDir" => 0,
    "File::Temp" => 0,
    "Getopt::Euclid" => 0,
    "JSON::Create" => 0,
    "JSON::Parse" => 0,
    "List::AllUtils" => 0,
    "Modern::Perl" => 0,
    "Moose" => 0,
    "Moose::Role" => 0,
    "POSIX" => 0,
    "Path::Class" => 0,
    "Smart::Comments" => 0,
    "Template" => 0,
    "Test::Most" => 0,
    "XML::Bare" => "0.53",
    "XML::Hash::XS" => 0,
    "aliased" => 0,

Makefile.PL  view on Meta::CPAN

  "DBD::SQLite" => 0,
  "DBI" => 0,
  "Data::UUID" => 0,
  "File::Basename" => 0,
  "File::ShareDir" => 0,
  "File::Temp" => 0,
  "Getopt::Euclid" => 0,
  "JSON::Create" => 0,
  "JSON::Parse" => 0,
  "List::AllUtils" => 0,
  "Modern::Perl" => 0,
  "Moose" => 0,
  "Moose::Role" => 0,
  "POSIX" => 0,
  "Path::Class" => 0,
  "Smart::Comments" => 0,
  "Template" => 0,
  "Test::Most" => 0,
  "XML::Bare" => "0.53",
  "XML::Hash::XS" => 0,
  "aliased" => 0,

bin/draw_bgc_maps.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: draw_bgc_maps.pl
# ABSTRACT: This script draws NRPS/PKS BGC clusters maps in PNG
# CONTRIBUTOR: Denis BAURAIN <denis.baurain@uliege.be>

use Modern::Perl '2011';
use autodie;

use Carp;
use GD::Simple;
use Getopt::Euclid qw(:vars);
use POSIX;

use Bio::Palantir;
use Bio::MUST::Core;

bin/explore_bgc_domains.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: explore_bgc_domains.pl
# ABSTRACT: Reports all detected domain signatures for a NRPS/PKS gene cluster
# CONTRIBUTOR: Denis BAURAIN <denis.baurain@uliege.be>

use Modern::Perl '2011';
use autodie;

use Getopt::Euclid qw(:vars);
use JSON::Create qw(create_json);

use aliased 'Bio::Palantir::Explorer::ClusterFasta';

my (%json_for, $i);

my $cluster = ClusterFasta->new( file => $ARGV_fasta_file );

bin/export_bgc_sql_tables.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: export_bgc_sql_tables.pl
# ABSTRACT: Exports SQL tables of BGC data (Palantir and antiSMASH annotations)
# CONTRIBUTOR: Denis BAURAIN <denis.baurain@uliege.be>

use Modern::Perl '2011';
use autodie;
use Smart::Comments;

use Carp;
use Const::Fast;
use Data::UUID;
use DBI;
use GD::Simple;
use Getopt::Euclid qw(:vars);
use File::Basename qw(fileparse);

bin/extract_bgc_sequences.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: extract_bgc_sequences.pl
# ABSTRACT: Extracts protein sequences for different BGC scales into a FASTA file
# CONTRIBUTOR: Denis BAURAIN <denis.baurain@uliege.be>

use Modern::Perl '2011';
use autodie;

use Smart::Comments;

use Carp;
use Getopt::Euclid qw(:vars);

use aliased 'Bio::Palantir::Parser';
use aliased 'Bio::Palantir::Refiner::ClusterPlus';

bin/generate_bgc_dnz_table.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: generate_bgc_dnz_table.pl
# ABSTRACT: Generates a denormalized table for BGC data
# CONTRIBUTOR: Denis BAURAIN <denis.baurain@uliege.be>

use Modern::Perl '2011';
use autodie;

use Smart::Comments;

use Carp;
use File::Basename qw(fileparse);
use Getopt::Euclid qw(:vars);
use Path::Class qw(dir file);

use aliased 'Bio::Palantir::Parser';

bin/generate_bgc_report.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: generate_bgc_report.pl
# ABSTRACT: Generates PDF/Word reports from antiSMASH results
# CONTRIBUTOR: Denis BAURAIN <denis.baurain@uliege.be>

use Modern::Perl '2011';
use autodie;

use Smart::Comments;

use Carp;
use Const::Fast;
use File::Basename qw(fileparse);
use File::ShareDir qw(dist_dir);
use File::Temp;
use Getopt::Euclid qw(:vars);