Class: Bio::GFFbrowser::Helpers::LinkedRecs

Inherits:
Hash
  • Object
show all
Includes:
Logger
Defined in:
lib/bio/db/gff/gffvalidate.rb

Overview

Helper class for storing linked records based on a shared ID

Instance Method Summary collapse

Methods included from Logger

#debug, #error, #info, #log_sys_info, #warn

Instance Method Details

#add(id, rec) ⇒ Object 



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# File 'lib/bio/db/gff/gffvalidate.rb', line 37

def add id, rec
  info "Adding #{rec.feature_type} (validate)",id
  raise "ID should not be empty" if id == nil or id == ""
  self[id] = [] if self[id] == nil
  self[id] << rec
end

#validate_nonoverlapping ⇒ Object

walk all (CDS) lists for every container/component and validate they do not overlap



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# File 'lib/bio/db/gff/gffvalidate.rb', line 77

def validate_nonoverlapping
  each do | id, rec |
    sections = Sections::sort(rec)
    sections.each_with_index do | check, i |
      neighbour = sections[i+1]
      if neighbour and check.intersection(neighbour)
        warn "Overlapping sections for ",id
      end
    end
  end
end

#validate_seqname ⇒ Object

Validate all lists belong to the same container/component



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# File 'lib/bio/db/gff/gffvalidate.rb', line 45

def validate_seqname
  each do | id, rec |
    seqname = rec.first.seqname
    rec.each do | section |
      raise "Non-matching seqname #{section.seqname} in #{seqname}" if section.seqname != seqname
    end
  end
end

#validate_shared_parent ⇒ Object

Validate all lists share the same parent (if available). First checks for Parent attribute, next for mRNA attribute



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# File 'lib/bio/db/gff/gffvalidate.rb', line 56

def validate_shared_parent
  each do | id, rec |
    parent = rec.first.get_attribute('Parent')
    if parent
      rec.each do | section |
        _parent = section.get_attribute('Parent')
        raise "Non-matching parent #{_parent} and #{parent} in #{id}" if _parent != parent
      end
    end
    parent = rec.first.get_attribute('mRNA')
    if parent
      rec.each do | section |
        _parent = section.get_attribute('mRNA')
        raise "Non-matching parent #{_parent} and #{parent} in #{id}" if _parent != parent
      end
    end
  end
end