Mercurial > repos > cpt > cpt_psm_recombine
comparison lib/CPT/Bio/GFF_Parsing.pm @ 1:97ef96676b48 draft
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author | cpt |
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date | Mon, 05 Jun 2023 02:51:26 +0000 |
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0:b18e8268bf4e | 1:97ef96676b48 |
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1 package CPT::Bio::GFF_Parsing; | |
2 use Moose; | |
3 use autodie; | |
4 | |
5 my $tags = 'allele anticodon artificial_location | |
6 bio_material bound_moiety cell_line cell_type chromosome citation | |
7 clone clone_lib codon_start collected_by collection_date compare | |
8 country cultivar culture_collection db_xref dev_stage direction | |
9 EC_number ecotype environmental_sample estimated_length exception | |
10 experiment focus frequency function gap_type gene gene_synonym | |
11 germline haplogroup haplotype host identified_by inference isolate | |
12 isolation_source lab_host lat_lon linkage_evidence locus_tag | |
13 macronuclear map mating_type mobile_element_type mod_base mol_type | |
14 ncRNA_class note number old_locus_tag operon organelle organism | |
15 partial PCR_conditions PCR_primers phenotype plasmid pop_variant | |
16 product protein_id proviral pseudo rearranged replace | |
17 ribosomal_slippage rpt_family rpt_type rpt_unit_range rpt_unit_seq | |
18 satellite segment serotype serovar sex specimen_voucher | |
19 standard_name strain sub_clone sub_species sub_strain tag_peptide | |
20 tissue_lib tissue_type transgenic translation transl_except | |
21 transl_table trans_splicing variety'; | |
22 my %valid_tags = map { $_ => 1 } split( /\s+/, $tags ); | |
23 | |
24 my $keys = "-10_signal -35_signal 3'UTR 5'UTR | |
25 CAAT_signal CDS C_region D-loop D_segment GC_signal J_segment LTR | |
26 N_region RBS STS S_region TATA_signal V_region V_segment | |
27 assembly_gap attenuator enhancer exon gap gene iDNA intron mRNA | |
28 mat_peptide misc_RNA misc_binding misc_difference misc_feature | |
29 misc_recomb misc_signal misc_structure mobile_element | |
30 modified_base ncRNA old_sequence operon oriT polyA_signal | |
31 polyA_site precursor_RNA prim_transcript primer_bind promoter | |
32 protein_bind rRNA rep_origin repeat_region sig_peptide source | |
33 stem_loop tRNA terminator tmRNA transit_peptide unsure variation"; | |
34 my %valid_keys = map { $_ => 1 } split( /\s+/, $keys ); | |
35 | |
36 has 'tag_conv' => ( is => 'ro', isa => 'HashRef', default => sub { return { | |
37 #tags | |
38 'dbxref' => 'db_xref', | |
39 'parent' => 'note', | |
40 'name' => 'label', | |
41 'Name' => 'label', | |
42 'old-name' => 'obsolete_name', | |
43 'id' => 'note', | |
44 'nat-host' => 'host', | |
45 'genome' => 'note', | |
46 'region' => 'source', | |
47 }; }); | |
48 | |
49 | |
50 sub fix_gff_tag { | |
51 my ($self, $tag) = @_; | |
52 # Lowercase it | |
53 if(defined $tag && defined(${$self->tag_conv()}{lc($tag)})){ | |
54 return ${$self->tag_conv()}{lc($tag)}; | |
55 } | |
56 return $tag; | |
57 } | |
58 | |
59 | |
60 no Moose; | |
61 1; | |
62 | |
63 __END__ | |
64 | |
65 =pod | |
66 | |
67 =encoding UTF-8 | |
68 | |
69 =head1 NAME | |
70 | |
71 CPT::Bio::GFF_Parsing | |
72 | |
73 =head1 VERSION | |
74 | |
75 version 1.99.4 | |
76 | |
77 =head1 AUTHOR | |
78 | |
79 Eric Rasche <rasche.eric@yandex.ru> | |
80 | |
81 =head1 COPYRIGHT AND LICENSE | |
82 | |
83 This software is Copyright (c) 2014 by Eric Rasche. | |
84 | |
85 This is free software, licensed under: | |
86 | |
87 The GNU General Public License, Version 3, June 2007 | |
88 | |
89 =cut |