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annotate lib/CPT/Bio/GFF_Parsing.pm @ 1:97ef96676b48 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:51:26 +0000
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1 package CPT::Bio::GFF_Parsing;
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2 use Moose;
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3 use autodie;
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4
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5 my $tags = 'allele anticodon artificial_location
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6 bio_material bound_moiety cell_line cell_type chromosome citation
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7 clone clone_lib codon_start collected_by collection_date compare
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8 country cultivar culture_collection db_xref dev_stage direction
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9 EC_number ecotype environmental_sample estimated_length exception
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10 experiment focus frequency function gap_type gene gene_synonym
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11 germline haplogroup haplotype host identified_by inference isolate
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12 isolation_source lab_host lat_lon linkage_evidence locus_tag
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13 macronuclear map mating_type mobile_element_type mod_base mol_type
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14 ncRNA_class note number old_locus_tag operon organelle organism
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15 partial PCR_conditions PCR_primers phenotype plasmid pop_variant
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16 product protein_id proviral pseudo rearranged replace
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17 ribosomal_slippage rpt_family rpt_type rpt_unit_range rpt_unit_seq
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18 satellite segment serotype serovar sex specimen_voucher
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19 standard_name strain sub_clone sub_species sub_strain tag_peptide
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20 tissue_lib tissue_type transgenic translation transl_except
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21 transl_table trans_splicing variety';
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22 my %valid_tags = map { $_ => 1 } split( /\s+/, $tags );
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23
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24 my $keys = "-10_signal -35_signal 3'UTR 5'UTR
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25 CAAT_signal CDS C_region D-loop D_segment GC_signal J_segment LTR
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26 N_region RBS STS S_region TATA_signal V_region V_segment
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27 assembly_gap attenuator enhancer exon gap gene iDNA intron mRNA
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28 mat_peptide misc_RNA misc_binding misc_difference misc_feature
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29 misc_recomb misc_signal misc_structure mobile_element
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30 modified_base ncRNA old_sequence operon oriT polyA_signal
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31 polyA_site precursor_RNA prim_transcript primer_bind promoter
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32 protein_bind rRNA rep_origin repeat_region sig_peptide source
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33 stem_loop tRNA terminator tmRNA transit_peptide unsure variation";
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34 my %valid_keys = map { $_ => 1 } split( /\s+/, $keys );
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35
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36 has 'tag_conv' => ( is => 'ro', isa => 'HashRef', default => sub { return {
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37 #tags
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38 'dbxref' => 'db_xref',
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39 'parent' => 'note',
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40 'name' => 'label',
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41 'Name' => 'label',
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42 'old-name' => 'obsolete_name',
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43 'id' => 'note',
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44 'nat-host' => 'host',
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45 'genome' => 'note',
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46 'region' => 'source',
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47 }; });
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48
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49
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50 sub fix_gff_tag {
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51 my ($self, $tag) = @_;
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52 # Lowercase it
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53 if(defined $tag && defined(${$self->tag_conv()}{lc($tag)})){
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54 return ${$self->tag_conv()}{lc($tag)};
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55 }
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56 return $tag;
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57 }
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58
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59
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60 no Moose;
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61 1;
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62
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63 __END__
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64
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65 =pod
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66
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67 =encoding UTF-8
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68
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69 =head1 NAME
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70
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71 CPT::Bio::GFF_Parsing
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72
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73 =head1 VERSION
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74
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75 version 1.99.4
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76
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77 =head1 AUTHOR
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78
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79 Eric Rasche <rasche.eric@yandex.ru>
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80
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81 =head1 COPYRIGHT AND LICENSE
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82
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83 This software is Copyright (c) 2014 by Eric Rasche.
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84
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85 This is free software, licensed under:
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86
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87 The GNU General Public License, Version 3, June 2007
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88
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89 =cut