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annotate lib/CPT/Writer/Fasta.pm @ 1:f093e08f21f3 draft default tip

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:47:24 +0000
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1 package CPT::Writer::Fasta;
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2 use Moose;
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3 with 'CPT::Writer';
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4 require Bio::SeqIO;
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5
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6 sub process {
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7 my ($self) = @_;
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8 $self->processed_data( $self->data );
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9 $self->processing_complete(1);
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10 return 1;
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11 }
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12
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13 sub write {
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14 my ($self) = @_;
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15 if ( $self->processing_complete ) {
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16 $self->OutputFilesClass->extension( $self->suffix() );
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17 my $next_output_file = $self->OutputFilesClass->get_next_file();
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18 open( my $filehandle, '>', $next_output_file );
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19 # This is probably a good change but will need testing.
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20 if ( ref( $self->processed_data ) eq 'Bio::PrimarySeqI') {
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21 my $outseq = Bio::SeqIO->new(
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22 -fh => $filehandle,
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23 -format => 'Fasta',
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24 );
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25 $outseq->write_seq( $self->processed_data );
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26 }
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27 elsif ( ref( $self->processed_data ) eq 'ARRAY') {
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28 my $outseq = Bio::SeqIO->new(
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29 -fh => $filehandle,
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30 -format => 'Fasta',
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31 );
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32 foreach my $seq (@{$self->processed_data()}){
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33 $outseq->write_seq( $seq );
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34 }
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35 }
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36 else {
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37 print $filehandle $self->processed_data;
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38 }
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39 close($filehandle);
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40 }
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41 else {
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42 warn "Write called but processing was not marked as complete. Not writing";
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43 }
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44 }
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45
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46 sub suffix {
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47 return 'fa';
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48 }
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49 no Moose;
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50 1;
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51
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52 __END__
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53
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54 =pod
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55
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56 =encoding UTF-8
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57
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58 =head1 NAME
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59
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60 CPT::Writer::Fasta
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61
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62 =head1 VERSION
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63
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64 version 1.99.4
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65
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66 =head1 AUTHOR
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67
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68 Eric Rasche <rasche.eric@yandex.ru>
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69
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70 =head1 COPYRIGHT AND LICENSE
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71
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72 This software is Copyright (c) 2014 by Eric Rasche.
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73
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74 This is free software, licensed under:
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75
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76 The GNU General Public License, Version 3, June 2007
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77
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78 =cut