Class: InterMine::PathQuery::Query

Inherits:
Object
  • Object
show all
Defined in:
lib/intermine/bio.rb

Overview

Biologically specific Extensions to the Query class.

These methods provide mechanisms for accessing results in Biologically appropriate formats, being at present GFF3, FASTA, and UCSC-BED.

The methods provided here can be used to both return the data as a string, and to iterate over the data in logical chunks, approriate to the format in question.

:include:contact_header.rdoc

Instance Method Summary collapse

Instance Method Details

#bed(ucscCompatible = true) ⇒ Object

Return the results from this query as BED

If a block is given, each line of the BED results will be yielded in turn, and the header will be returned, otherwise the content of the BED results will be returned as one string.

If the optional parameter is set to false, then the “chr” prefix on the chromosome id will be omitted.

header = query.bed do |line|
   process line
end

puts query.bed(false)



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# File 'lib/intermine/bio.rb', line 141

def bed(ucscCompatible=true)
    if block_given?
        header = ""
        results_reader.each_bed(ucscCompatible) do |bed|
            if bed =~ /^\s*(#|track)/
                header << bed
            else
                yield bed
            end
        end
        return header
    else
        buffer = ""
        results_reader.each_bed(ucscCompatible) do |bed|
            buffer.concat(bed)
        end
        return buffer
    end
end

#fasta ⇒ Object

Return the results from this query as FASTA

If a block is given, each FASTA record will be yielded in turn, and the query will be returned, otherwise the content of the FASTA results will be returned as one string.

query.fasta do |record|
   process record
end

puts query.fasta



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# File 'lib/intermine/bio.rb', line 103

def fasta # :yields: record
    if block_given?
        buffer = nil
        results_reader.each_fasta do |line|
            if line.start_with? ">"
                yield buffer unless buffer.nil?
                buffer = line
            else
                raise BioError, "Incorrect fasta - no header line" if buffer.nil?
                buffer << line
            end
        end
        yield buffer unless buffer.nil?
        return self
    else
        buffer = ""
        results_reader.each_fasta do |line|
            buffer.concat(line)
        end
        return buffer
    end
end

#gff3 ⇒ Object

Return the results from this query as GFF3

If a block is given, each line of the GFF3 will be yielded in turn, omitting any header lines, which are returned at the end of the iteration, otherwise the content of the GFF3 results will be returned as one string.

header = query.gff3 do |line|
   process line
end

puts query.gff3



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# File 'lib/intermine/bio.rb', line 71

def gff3
    if block_given?
        header = ""
        results_reader.each_gff3 do |gff3|
            if gff3.start_with? "#"
                header << gff3
            else
                yield gff3
            end
        end
        return header
    else
        buffer = ""
        results_reader.each_gff3 do |gff3|
            buffer.concat(gff3)
        end
        return buffer
    end
end