Class: SequenceServer::Doctor

Inherits:
Object
  • Object
show all
Extended by:
Forwardable
Defined in:
lib/sequenceserver/doctor.rb

Overview

Doctor detects inconsistencies likely to cause problems with Sequenceserver operation.

Constant Summary collapse

ERROR_PARSE_SEQIDS = 
1
ERROR_NUMERIC_IDS = 
2
ERROR_PROBLEMATIC_IDS = 
3
AVOID_ID_REGEX = 
/^(?!gi|bbs)\w+\|\w*\|?/

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Doctor

Returns a new instance of Doctor.



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# File 'lib/sequenceserver/doctor.rb', line 98

def initialize
  @ignore     = []
  @all_seqids = Doctor.all_sequence_ids(@ignore)
end

Instance Attribute Details

#all_seqids ⇒ Object (readonly)

Returns the value of attribute all_seqids.



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# File 'lib/sequenceserver/doctor.rb', line 103

def all_seqids
  @all_seqids
end

#invalids ⇒ Object (readonly)

Returns the value of attribute invalids.



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# File 'lib/sequenceserver/doctor.rb', line 103

def invalids
  @invalids
end

Class Method Details

.all_sequence_ids(ignore) ⇒ Object

Retrieve sequence ids (specified by %i) from all databases. Using accession number is problematic because of several reasons.



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# File 'lib/sequenceserver/doctor.rb', line 31

def all_sequence_ids(ignore)
  Database.map do |db|
    next if ignore.include? db

    out = `blastdbcmd -entry all -db #{db.name} -outfmt "%i" 2> /dev/null`
    {
      db:     db,
      seqids: out.to_s.split
    }
  end.compact
end

.bullet_list(values) ⇒ Object

Pretty print database list.



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# File 'lib/sequenceserver/doctor.rb', line 54

def bullet_list(values)
  list = ''
  values.each do |value|
    list << "      - #{value}\n"
  end
  list
end

.inspect_parse_seqids(seqids) ⇒ Object

FASTA files formatted without -parse_seqids option won’t support the blastdbcmd command of fetching sequence ids using ‘%i’ identifier. In such cases, an array of ‘N/A’ values are returned which is checked in this case.



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# File 'lib/sequenceserver/doctor.rb', line 47

def inspect_parse_seqids(seqids)
  seqids.map do |sq|
    sq[:db] if sq[:seqids].include? 'N/A'
  end.compact
end

.inspect_seqids(seqids, &block) ⇒ Object

Returns an array of database objects in which each of the object has an array of sequence_ids satisfying the block passed to the method.



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# File 'lib/sequenceserver/doctor.rb', line 23

def inspect_seqids(seqids, &block)
  seqids.map do |sq|
    sq[:db] unless sq[:seqids].select(&block).empty?
  end.compact
end

.show_message(error, values) ⇒ Object

Print diagnostic error messages according to the type of error. rubocop:disable Metrics/MethodLength



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# File 'lib/sequenceserver/doctor.rb', line 64

def show_message(error, values)
  return if values.empty?

  case error
  when ERROR_PARSE_SEQIDS
    puts <<~MSG
      *** Doctor has found improperly formatted database:
      #{bullet_list(values)}
      Please reformat your databases with -parse_seqids switch (or use
      sequenceserver -m) for using SequenceServer as the current format
      may cause problems.

      These databases are ignored in further checks.
    MSG

  when ERROR_NUMERIC_IDS
    puts <<~MSG
      *** Doctor has found databases with numeric sequence ids:
      #{bullet_list(values)}
      Note that this may cause problems with sequence retrieval.
    MSG

  when ERROR_PROBLEMATIC_IDS
    puts <<~MSG
      *** Doctor has found databases with problematic sequence ids:
      #{bullet_list(values)}
      This causes some sequence to contain extraneous words like `gnl|`
      appended to their id string.
    MSG
  end
end

Instance Method Details

#check_id_format ⇒ Object

Warn users about sequence identifiers of format abc|def because then BLAST+ appends a gnl (for general) infront of the database identifiers. There are only two identifiers that we need to avoid when searching for this format. bbs|number, gi|number Note that while sequence ids could have been arbitrary, using parse_seqids reduces our search space substantially.



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# File 'lib/sequenceserver/doctor.rb', line 147

def check_id_format
  selector = proc { |id| id.match(AVOID_ID_REGEX) }

  Doctor.show_message(ERROR_PROBLEMATIC_IDS,
                      Doctor.inspect_seqids(@all_seqids, &selector))
end

#check_numeric_ids ⇒ Object

Check for the presence of numeric sequence ids within a database.



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# File 'lib/sequenceserver/doctor.rb', line 133

def check_numeric_ids
  selector = proc { |id| !id.to_i.zero? }

  Doctor.show_message(ERROR_NUMERIC_IDS,
                      Doctor.inspect_seqids(@all_seqids, &selector))
end

#check_parse_seqids ⇒ Object

Obtain files which aren’t formatted with -parse_seqids and add them to ignore list.



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# File 'lib/sequenceserver/doctor.rb', line 125

def check_parse_seqids
  without_parse_seqids = Doctor.inspect_parse_seqids(@all_seqids)
  Doctor.show_message(ERROR_PARSE_SEQIDS, without_parse_seqids)

  @ignore.concat(without_parse_seqids)
end

#diagnose ⇒ Object 



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# File 'lib/sequenceserver/doctor.rb', line 105

def diagnose
  puts "\n1/3 Inspecting databases for proper -parse_seqids formatting.."
  check_parse_seqids
  remove_invalid_databases

  puts "\n2/3 Inspecting databases for numeric sequence ids.."
  check_numeric_ids

  puts "\n3/3 Inspecting databases for problematic sequence ids.."
  check_id_format
end

#remove_invalid_databases ⇒ Object

Remove entried which are in ignore list or not formatted with -parse_seqids option.



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# File 'lib/sequenceserver/doctor.rb', line 119

def remove_invalid_databases
  @all_seqids.delete_if { |sq| @ignore.include? sq[:db] }
end