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0
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1 =pod
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2
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3 =head1 LICENSE
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4
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5 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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6 Genome Research Limited. All rights reserved.
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7
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8 This software is distributed under a modified Apache license.
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9 For license details, please see
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10
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11 http://www.ensembl.org/info/about/code_licence.html
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12
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13 =head1 CONTACT
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14
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15 Please email comments or questions to the public Ensembl
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16 developers list at <dev@ensembl.org>.
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17
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18 Questions may also be sent to the Ensembl help desk at
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19 <helpdesk@ensembl.org>.
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::Pipeline::FASTA::CopyDNA
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24
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25 =head1 DESCRIPTION
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26
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27 Performs a find in the DNA dumps directory, for the given species, in the
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28 previous release FTP dump directory. Any files matching the normal gzipped
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29 fasta extension will be copied over to this release's directory.
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30
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31 Previous release is defined as V<release-1>; override this class if your
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32 definition of the previous release is different.
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33
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34 Allowed parameters are:
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35
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36 =over 8
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37
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38 =item release - Needed to build the target path
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39
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40 =item previous_release - Needed to build the source path
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41
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42 =item ftp_dir - Current location of the FTP directory for the previous
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43 release. Should be the root i.e. the level I<release-XX> is in
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44
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45 =item species - Species to work with
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46
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47 =item base_path - The base of the dumps; reused files will be copied to here
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48
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49 =back
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50
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51 =cut
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52
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53 package Bio::EnsEMBL::Pipeline::FASTA::CopyDNA;
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54
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55 use strict;
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56 use warnings;
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57
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58 use base qw/Bio::EnsEMBL::Pipeline::FASTA::Base/;
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59
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60 use File::Copy;
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61 use File::Find;
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62 use File::Spec;
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63
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64 sub fetch_input {
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65 my ($self) = @_;
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66 my @required = qw/release ftp_dir species/;
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67 foreach my $key (@required) {
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68 $self->throw("Need to define a $key parameter") unless $self->param($key);
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69 }
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70 return;
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71 }
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72
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73 sub run {
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74 my ($self) = @_;
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75
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76 my $new_path = $self->new_path();
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77 #Remove all files from the new path
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78 $self->unlink_all_files($new_path);
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79
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80 my $files = $self->get_dna_files();
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81 foreach my $old_file (@{$files}) {
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82 my $new_file = $self->new_filename($old_file);
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83 $self->fine('copy %s %s', $old_file, $new_file);
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84 copy($old_file, $new_file) or $self->throw("Cannot copy $old_file to $new_file: $!");
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85 }
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86
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87 return;
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88 }
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89
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90 sub new_filename {
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91 my ($self, $old_filename) = @_;
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92 my ($old_volume, $old_dir, $old_file) = File::Spec->splitpath($old_filename);
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93 my $old_release = $self->param('previous_release');
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94 my $release = $self->param('release');
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95 my $new_file = $old_file;
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96 $new_file =~ s/\.$old_release\./.$release./;
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97 my $new_path = $self->new_path();
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98 return File::Spec->catfile($new_path, $new_file);
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99 }
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100
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101 sub new_path {
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102 my ($self) = @_;
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103 return $self->fasta_path('dna');
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104 }
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105
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106 sub get_dna_files {
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107 my ($self) = @_;
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108 my $old_path = $self->old_path();
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109 my $filter = sub {
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110 my ($filename) = @_;
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111 return ($filename =~ /\.fa\.gz$/ || $filename eq 'README') ? 1 : 0;
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112 };
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113 my $files = $self->find_files($old_path, $filter);
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114 return $files;
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115 }
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116
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117 1;
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