Bio-MUST-Core
38 results

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META.yml  view on Meta::CPAN 

  Graphics::ColorNames: '0'
  Graphics::ColorNames::HTML: '0'
  Graphics::ColorNames::WWW: '0'
  HTTP::Request::Common: '0'
  IPC::System::Simple: '0'
  LWP::Protocol::https: '0'
  LWP::Simple: '0'
  LWP::UserAgent: '0'
  List::AllUtils: '0.12'
  List::Compare: '0'
  Modern::Perl: '0'
  Moose: '0'
  Moose::Role: '0'
  Moose::Util::TypeConstraints: '0'
  MooseX::NonMoose: '0'
  MooseX::SemiAffordanceAccessor: '0'
  MooseX::Storage: '0'
  POSIX: '0'
  Path::Class: '0'
  Scalar::Util: '0'
  Smart::Comments: '0'

Makefile.PL  view on Meta::CPAN 

    "Graphics::ColorNames" => 0,
    "Graphics::ColorNames::HTML" => 0,
    "Graphics::ColorNames::WWW" => 0,
    "HTTP::Request::Common" => 0,
    "IPC::System::Simple" => 0,
    "LWP::Protocol::https" => 0,
    "LWP::Simple" => 0,
    "LWP::UserAgent" => 0,
    "List::AllUtils" => "0.12",
    "List::Compare" => 0,
    "Modern::Perl" => 0,
    "Moose" => 0,
    "Moose::Role" => 0,
    "Moose::Util::TypeConstraints" => 0,
    "MooseX::NonMoose" => 0,
    "MooseX::SemiAffordanceAccessor" => 0,
    "MooseX::Storage" => 0,
    "POSIX" => 0,
    "Path::Class" => 0,
    "Scalar::Util" => 0,
    "Smart::Comments" => 0,

bin/ali2phylip.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: ali2phylip.pl
# ABSTRACT: Convert (and filter) ALI files to PHYLIP files for tree building
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
# CONTRIBUTOR: Raphael LEONARD <rleonard@doct.uliege.be>

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

use Getopt::Euclid qw(:vars);
use List::Compare;
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::IdList';

bin/app-len-ids-ali.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: app-len-ids-ali.pl
# ABSTRACT: Appends seq lengths to ids in ALI files (as SCaFoS)

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(secure_outfile);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::IdMapper';

bin/change-ids-ali.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: change-ids-ali.pl
# ABSTRACT: Abbreviate or restore the org component of full seq ids in ALI files

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix secure_outfile);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::IdMapper';

bin/classify-ali.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: classify-ali.pl
# ABSTRACT: Classify ALI files based on taxonomic filters

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

use Config::Any;
use File::Basename;
use File::Find::Rule;
use Getopt::Euclid qw(:vars);
use Path::Class qw(dir file);
use Smart::Comments;

use Bio::MUST::Core;

bin/export-itol.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: export-itol.pl
# ABSTRACT: Download formatted trees from iTOL
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>

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

use Getopt::Euclid qw(:vars);
use Smart::Comments '###';

use Config::Any;
use HTTP::Request::Common;
use LWP::UserAgent;

use Bio::MUST::Core;

bin/extract-ali.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: extract-ali.pl
# ABSTRACT: Extract sequences from a FASTA database file based on id lists

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix);
use aliased 'Bio::MUST::Core::Ali::Stash';
use aliased 'Bio::MUST::Core::IdList';

bin/fasta2ali.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: fasta2ali.pl
# ABSTRACT: Convert FASTA files to ALI files

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix);
use aliased 'Bio::MUST::Core::Ali';

bin/fetch-tax.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: fetch-tax.pl
# ABSTRACT: Fetch (and format) information from the NCBI Taxonomy database

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

use Getopt::Euclid qw(:vars);
use List::AllUtils qw(apply each_array);
use Scalar::Util qw(looks_like_number);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Constants qw(:ncbi);
use Bio::MUST::Core::Utils qw(change_suffix);

bin/format-tree.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: format-tree.pl
# ABSTRACT: Format (and annotate) trees for printing
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;
use Try::Tiny;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(:filenames secure_outfile);
use aliased 'Bio::MUST::Core::IdList';
use aliased 'Bio::MUST::Core::IdMapper';

bin/idealize-ali.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: idealize-ali.pl
# ABSTRACT: Discard (nearly) gap-only sites from ALI files

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(secure_outfile);
use aliased 'Bio::MUST::Core::Ali';

bin/import-itol.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: import-itol.pl
# ABSTRACT: Upload trees and associate metadata files to iTOL
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>

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

use Getopt::Euclid qw(:vars);
use Smart::Comments '###';

use Archive::Zip qw(:ERROR_CODES :CONSTANTS);
use File::Basename;
use File::Find::Rule;
use HTTP::Request::Common;
use LWP::UserAgent;

bin/inst-abbr-ids.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: inst-abbr-ids.pl
# ABSTRACT: Abbreviate seq ids in FASTA files (optimized)
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>

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

use File::Basename;
use Getopt::Euclid qw(:vars);
use Path::Class qw(dir file);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Constants qw(:seqids);
use Bio::MUST::Core::Utils qw(secure_outfile);

bin/inst-qual-filter.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: inst-qual-filter.pl
# ABSTRACT: Discard low-quality nt seqs in FASTA files (optimized)
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Constants qw(:seqtypes);
use Bio::MUST::Core::Utils qw(secure_outfile);
use aliased 'Bio::MUST::Core::Ali';

bin/inst-split-seqs.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: inst-split-seqs.pl
# ABSTRACT: Split sequences of FASTA files into shorter sequences (optimized)
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>

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

use Getopt::Euclid qw(:vars);
use Smart::Comments '###';

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(secure_outfile);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::Seq';

bin/inst-tax-filter.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: inst-tax-filter.pl
# ABSTRACT: Apply a taxonomic filter to a (UniProt) FASTA database (optimized)
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>

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

use File::Basename;
use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(secure_outfile);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::SeqId';

bin/jack-ali-dir.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: jack-ali-dir.pl
# ABSTRACT: Jackknife a directory of ALI files

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use File::Find::Rule;
use List::AllUtils qw(shuffle);
use Path::Class qw(file dir);
use POSIX;

bin/list2mapper.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: list2mapper.pl
# ABSTRACT: Build final id mapper from id list using the NCBI Taxonomy database

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix);
use aliased 'Bio::MUST::Core::IdList';
use aliased 'Bio::MUST::Core::Taxonomy';

bin/mask-ali.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: mask-ali.pl
# ABSTRACT: Mask an ALI file according to BLOCKS file(s)

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

use File::Basename;
use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(insert_suffix);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::SeqMask';

bin/phylip2ali.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: phylip2ali.pl
# ABSTRACT: Convert PHYLIP files to ALI files

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::IdMapper';

bin/prune-ali.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: prune-ali.pl
# ABSTRACT: Prune sequences from ALI files based on id lists

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix secure_outfile);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::IdList';

bin/prune-tree.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: prune-tree.pl
# ABSTRACT: Prune tips from TREE files based on id lists

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

use File::Basename;
use Getopt::Euclid qw(:vars);
use Smart::Comments;
use Try::Tiny;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix insert_suffix secure_outfile);
use aliased 'Bio::MUST::Core::IdList';

bin/rest-ids-ali.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: rest-ids-ali.pl
# ABSTRACT: Change (restore) full seq ids in ALI files

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix secure_outfile);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::IdMapper';

bin/setup-taxdir.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: setup-taxdir.pl
# ABSTRACT: Setup a local mirror of the NCBI Taxonomy (or GTDB) database

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use aliased 'Bio::MUST::Core::Taxonomy';

unless ($ARGV_update_cache) {
    my %args;

bin/split-matrix.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: split-matrix.pl
# ABSTRACT: Extract individual gene ALIs from a SCaFoS supermatrix

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

use File::Basename;
use Getopt::Euclid qw(:vars);
use Path::Class qw(dir file);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Constants qw(:files);
use aliased 'Bio::MUST::Core::Ali';

bin/split-rates-ali.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: split-rates-ali.pl
# ABSTRACT: Split ALI files into subsets of sites based on site-wise statistics

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix secure_outfile);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::SeqMask';

bin/stock2ali.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: stock2ali.pl
# ABSTRACT: Convert STOCKHOLM files to ALI files

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix);
use aliased 'Bio::MUST::Core::Ali';

bin/subs-forest.pl  view on Meta::CPAN 

#!/usr/bin/env perl
# PODNAME: subs-forest.pl
# ABSTRACT: Subsample forest (multiple trees) files (and restore ids)

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

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix secure_outfile);
use aliased 'Bio::MUST::Core::IdMapper';
use aliased 'Bio::MUST::Core::Tree::Forest';

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