bacterial-annotator 0.3.9 → 0.4.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/bacterial-annotator/remote-ncbi.rb +3 -2
- data/lib/bacterial-annotator.rb +1 -3
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: cd091580560639a95025ce9d6d188068ebd5518c
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data.tar.gz: 3c470334e7aff680a48fe4132236d2bb646dedc5
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 3ed95c575eb03b791c5f848a1417f4690f0141720992f2832ede949c1e81a7d8d74d3528d0951105affc3abcb2f4418ab89948c3cd4512cad1afeb7f3570d8d3
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7
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data.tar.gz: 90a71c6d106aef5fd570d7a3b497e5426bde5f72aad1eba533dde1b55530bb0c9e6282ceb54f174c80a68291b45161a5661d56ffd1dc0105456c57909f504095
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@@ -176,9 +176,10 @@ class RemoteNCBI
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split("; Flags:")[0].
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split(" ; Short=")[0].strip
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gi = hit.hit_id.to_s.split("|")[1]
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accession = hit.hit_accession.to_s
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organism = ""
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definition_clean = hit.definition.split(">")[0]
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if ! definition_clean[/\[.*\]/].nil?
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if ! definition_clean[/\[.*\]/].nil?
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organism = definition_clean[/\[.*\]/].gsub("[","").gsub("]","")
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end
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@aln_hits[prot_id] = {
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@@ -186,7 +187,7 @@ class RemoteNCBI
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length: hit.target_len.to_i,
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evalue: hit.evalue,
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score: hit.bit_score.to_f,
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hits: [{gi: gi, product: product, org: organism}]
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hits: [{gi: gi, accession: accession, product: product, org: organism}]
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}
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end
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end
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data/lib/bacterial-annotator.rb
CHANGED
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@@ -118,9 +118,7 @@ class BacterialAnnotator
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@rna_synteny.extract_hits_dna :rna
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@contig_annotations_rna = {}
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@fasta.prodigal_files[:contigs].each_with_index do |contig, contig_index|
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puts "adding rna_annotation for contig #{contig}"
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@contig_annotations_rna[contig] = @rna_synteny.get_annotation_for_contig contig
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p @contig_annotations_rna[contig]
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end
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else # no reference genome
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@@ -250,7 +248,7 @@ class BacterialAnnotator
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gbk_to_annotate.add_annotations contig_prot_annotations, "inplace", reference_locus
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if @contig_annotations_rna.has_key? contig
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puts "
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# puts "RNA annotation"
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gbk_to_annotate.add_annotations @contig_annotations_rna[contig], "new"
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end
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: bacterial-annotator
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version: !ruby/object:Gem::Version
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version: 0.
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version: 0.4.0
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platform: ruby
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authors:
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- Maxime Deraspe
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2017-02-
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date: 2017-02-14 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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