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package Bio::MUST::Apps::TwoScalp::Seq2Seq; |
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# ABSTRACT: internal class for two-scalp tool |
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$Bio::MUST::Apps::TwoScalp::Seq2Seq::VERSION = '0.211710'; |
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10
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use Moose; |
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9
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7464
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use namespace::autoclean; |
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1
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23
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6
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7
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91
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use autodie; |
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3
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1
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11
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5808
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use feature qw(say); |
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4
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97
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1
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1
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12
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use Smart::Comments -ENV; |
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21
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12
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1
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2049
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use List::AllUtils qw(part); |
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5
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68
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use Bio::MUST::Core; |
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33
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use Bio::MUST::Core::Constants qw(:gaps); |
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195
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7
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use Bio::MUST::Core::Utils qw(secure_outfile); |
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4
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1
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63
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639
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use Bio::MUST::Drivers; |
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2190244
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103
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use aliased 'Bio::MUST::Core::Ali'; |
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use aliased 'Bio::MUST::Core::Ali::Temporary'; |
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184
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use aliased 'Bio::MUST::Core::Seq'; |
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1
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202
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use aliased 'Bio::MUST::Core::SeqId'; |
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22
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174
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use aliased 'Bio::MUST::Core::SeqMask'; |
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3
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1
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4
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1
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1
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193
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use aliased 'Bio::MUST::Apps::SlaveAligner::Local'; |
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2
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1
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4
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24
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25
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26
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has 'coverage_mul' => ( |
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is => 'ro', |
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isa => 'Num', |
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default => 1.1, |
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); |
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32
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has 'single_hsp' => ( |
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is => 'ro', |
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isa => 'Bool', |
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default => 0, |
36
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); |
37
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38
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has 'out_suffix' => ( |
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is => 'ro', |
40
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isa => 'Maybe[Str]', |
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default => '-ts', |
42
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); |
43
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44
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has 'ali' => ( |
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is => 'ro', |
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isa => 'Bio::MUST::Core::Ali', |
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required => 1, |
48
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coerce => 1, |
49
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); |
50
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51
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has 'lookup' => ( |
52
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is => 'ro', |
53
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isa => 'Bio::MUST::Core::IdList', |
54
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init_arg => undef, |
55
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writer => '_set_lookup', |
56
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); |
57
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58
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has 'new_ali' => ( |
59
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is => 'ro', |
60
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isa => 'Bio::MUST::Core::Ali', |
61
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init_arg => undef, |
62
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writer => '_set_new_ali', |
63
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); |
64
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65
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has 'integrator' => ( |
66
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is => 'ro', |
67
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isa => 'Bio::MUST::Apps::SlaveAligner::Local', |
68
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init_arg => undef, |
69
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writer => '_set_integrator', |
70
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); |
71
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72
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has 'blastdb' => ( |
73
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is => 'ro', |
74
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isa => 'Bio::MUST::Drivers::Blast::Database::Temporary', |
75
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init_arg => undef, |
76
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writer => '_set_blastdb', |
77
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); |
78
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79
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has 'query_seqs' => ( |
80
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is => 'ro', |
81
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isa => 'Bio::MUST::Core::Ali::Temporary', |
82
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init_arg => undef, |
83
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writer => '_set_query_seqs', |
84
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); |
85
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86
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87
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sub _align_seqs { |
88
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0
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0
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my $self = shift; |
89
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90
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0
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my $args->{-outfmt} = 5; |
91
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0
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$args->{-max_target_seqs} = 5; |
92
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93
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0
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my $blastdb = $self->blastdb; |
94
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0
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my $query_seqs = $self->query_seqs; |
95
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0
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my $parser = $blastdb->blast($query_seqs, $args); |
96
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#### [S2S] XML BLASTP/N: $parser->filename |
97
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98
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0
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my $bo = $parser->blast_output; |
99
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0
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0
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return unless $bo; |
100
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101
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0
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0
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my $sort_method = $self->single_hsp ? 'score' : 'hit_start'; |
102
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103
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QUERY: |
104
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0
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for my $query ( $bo->all_iterations ) { |
105
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106
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0
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my $query_id = $query_seqs->long_id_for( $query->query_def ); |
107
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##### [S2S] Aligning: $query_id |
108
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109
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0
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my @templates; |
110
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my @template_seqs; |
111
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0
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my $best_coverage = 0; |
112
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113
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TEMPLATE: |
114
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0
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for my $template ( $query->all_hits ) { |
115
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116
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# compute query coverage by template HSPs |
117
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0
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my $mask = SeqMask->empty_mask( $query->query_len ); |
118
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$mask->mark_block( $_->query_start, $_->query_end ) |
119
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0
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for $template->all_hsps; |
120
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0
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my $coverage = $mask->coverage; |
121
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122
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0
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0
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last TEMPLATE if $coverage |
123
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< $best_coverage * $self->coverage_mul; |
124
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0
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$best_coverage = $coverage; |
125
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126
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# fetch template full_id |
127
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0
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my $template_id = SeqId->new( |
128
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full_id => $blastdb->long_id_for( $template->def ) |
129
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); |
130
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131
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###### [S2S] template: $template_id->full_id |
132
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###### [S2S] coverage: $coverage |
133
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134
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# fetch and cache aligned template seq from Ali |
135
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0
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push @templates, $template; |
136
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0
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push @template_seqs, $self->ali->get_seq( |
137
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$self->lookup->index_for( $template_id->full_id ) |
138
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); |
139
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} |
140
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141
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0
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0
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unless (@templates) { |
142
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##### [S2S] skipped alignment due to lack of suitable template |
143
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0
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next QUERY; |
144
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} |
145
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146
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0
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0
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@templates = ( $templates[-1] ) if $self->single_hsp; |
147
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148
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TEMPLATE: |
149
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0
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for my $template (@templates) { |
150
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151
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# use each template in turn for BLAST alignment |
152
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0
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my $template_seq = shift @template_seqs; |
153
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0
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0
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last TEMPLATE unless $template_seq; |
154
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155
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# sort HSPs by descending start coordinate on template or by |
156
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# descending score depending on --single-hsp option |
157
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my @hsps = sort { |
158
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0
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$b->$sort_method <=> $a->$sort_method |
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0
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159
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} $template->all_hsps; |
160
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161
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HSP: |
162
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0
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for my $hsp (@hsps) { |
163
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164
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# build HSP id from query id (and template/HSP ranks) |
165
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0
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my $hsp_id = $query_seqs->long_id_for( $query->query_def ); |
166
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0
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0
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$hsp_id .= '.H' . $template->num . '.' . $hsp->num |
167
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unless $self->single_hsp; |
168
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0
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$hsp_id .= '#NEW#'; |
169
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170
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# build HSP seq from BLASTX report |
171
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0
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(my $hsp_seq = $hsp->qseq) =~ s{\*}{$FRAMESHIFT}xmsg; |
172
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0
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my $new_seq = Seq->new( |
173
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seq_id => $hsp_id, |
174
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seq => $hsp_seq |
175
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); |
176
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177
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# fetch aligned template seq from HSP (= subject) |
178
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0
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my $subject_seq = Seq->new( |
179
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seq_id => $template_seq->seq_id, |
180
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seq => $hsp->hseq |
181
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); |
182
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183
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# reverse complement seqs if template on reverse in BLASTN |
184
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0
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0
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0
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if ($query_seqs->type eq 'nucl' && $blastdb->type eq 'nucl' |
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0
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185
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&& $hsp->hit_strand == -1) { |
186
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0
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$new_seq = $new_seq->reverse_complemented_seq; |
187
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0
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$subject_seq = $subject_seq->reverse_complemented_seq; |
188
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} |
189
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190
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# align new_seq on template_seq using subject_seq as a guide |
191
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$self->new_ali->add_seq( |
192
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0
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$self->integrator->align( |
193
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new_seq => $new_seq, |
194
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subject => $subject_seq, |
195
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template => $template_seq, |
196
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start => $hsp->hit_start, |
197
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) |
198
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); |
199
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200
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0
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0
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last HSP if $self->single_hsp; |
201
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} |
202
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} |
203
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} |
204
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205
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0
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return; |
206
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} |
207
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208
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209
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sub display { ## no critic (RequireArgUnpacking) |
210
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0
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0
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0
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return join "\n--- ", q{}, @_ |
211
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} |
212
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213
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214
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sub BUILD { |
215
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0
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0
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my $self = shift; |
216
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217
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0
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my $ali = $self->ali; |
218
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#### [ALI] #seqs: $ali->count_seqs |
219
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0
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0
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unless ($ali->count_seqs) { |
220
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#### [ALI] empty file; skipping! |
221
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0
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return; |
222
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} |
223
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224
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# Note: this class maintains DRY through a single BUILD |
225
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# hence the writers instead of the usual builders |
226
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227
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0
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$self->_set_lookup( $ali->new_lookup ); |
228
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229
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# TODO: fix bug with 'aligned' seqs only composed of trailing spaces |
230
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my ($unaligned_seqs, $aligned_seqs) |
231
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0
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0
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0
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|
= part { $_->is_aligned ? 1 : 0 } $ali->all_seqs; |
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0
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232
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#### [S2S] seqs to align: display( map { $_->full_id } @{$unaligned_seqs} ) |
233
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234
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0
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|
$self->_set_blastdb( Bio::MUST::Drivers::Blast::Database::Temporary->new( |
235
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seqs => $aligned_seqs ) |
236
|
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); |
237
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0
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|
|
$self->_set_query_seqs( Temporary->new( seqs => $unaligned_seqs ) ); |
238
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239
|
0
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|
|
my $new_ali = Ali->new( seqs => $aligned_seqs ); |
240
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0
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|
|
$self->_set_new_ali($new_ali); |
241
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242
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0
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|
|
my $integrator = Local->new( ali => $new_ali ); |
243
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0
|
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|
|
|
$self->_set_integrator($integrator); |
244
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245
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0
|
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|
|
|
$self->_align_seqs; |
246
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247
|
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|
|
#### [S2S] Making delayed indels... |
248
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0
|
|
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|
|
|
$integrator->make_indels; |
249
|
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|
250
|
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|
|
#### [S2S] Writing updated file... |
251
|
0
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|
|
|
my $outfile = secure_outfile($ali->filename, $self->out_suffix); |
252
|
0
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|
|
|
|
|
$new_ali->store($outfile); |
253
|
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254
|
0
|
|
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|
|
|
return; |
255
|
|
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|
|
|
|
} |
256
|
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|
257
|
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258
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|
|
__PACKAGE__->meta->make_immutable; |
259
|
|
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|
|
1; |
260
|
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|
261
|
|
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|
|
__END__ |
262
|
|
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|
|
|
|
263
|
|
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|
|
=pod |
264
|
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|
|
265
|
|
|
|
|
|
|
=head1 NAME |
266
|
|
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|
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|
|
|
267
|
|
|
|
|
|
|
Bio::MUST::Apps::TwoScalp::Seq2Seq - internal class for two-scalp tool |
268
|
|
|
|
|
|
|
|
269
|
|
|
|
|
|
|
=head1 VERSION |
270
|
|
|
|
|
|
|
|
271
|
|
|
|
|
|
|
version 0.211710 |
272
|
|
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|
273
|
|
|
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|
|
=head1 AUTHOR |
274
|
|
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|
|
|
|
275
|
|
|
|
|
|
|
Denis BAURAIN <denis.baurain@uliege.be> |
276
|
|
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|
|
|
|
|
277
|
|
|
|
|
|
|
=head1 COPYRIGHT AND LICENSE |
278
|
|
|
|
|
|
|
|
279
|
|
|
|
|
|
|
This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN. |
280
|
|
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|
|
|
|
|
281
|
|
|
|
|
|
|
This is free software; you can redistribute it and/or modify it under |
282
|
|
|
|
|
|
|
the same terms as the Perl 5 programming language system itself. |
283
|
|
|
|
|
|
|
|
284
|
|
|
|
|
|
|
=cut |