Top Level Namespace

Defined Under Namespace

Modules: BioPangenome Classes: GFF3, MrnaStats, MultipleGFFs, String

Constant Summary collapse

USAGE =

BioRuby bio-pangenome Plugin BioPangenome

Author

homonecloco

Copyright

2019

"pangenome_gene_bed_files.rb [options]"
VERSION_FILENAME = 
File.join(gempath,'VERSION')

Instance Method Summary collapse

Instance Method Details

#bedAroundToRegions(lines: [], distance: 1000, prefix: "../flanking/filtered/", suffix: ".RefSeqv1.1.reg", suffix_in: ".RefSeqv1.1.bed") ⇒ Object 



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# File 'bin/pangenome_gene_bed_files.rb', line 80

def bedAroundToRegions(lines:[], distance: 1000, prefix: "../flanking/filtered/", suffix: ".RefSeqv1.1.reg" , suffix_in: ".RefSeqv1.1.bed" )
    lines.each do |k|
        path="#{prefix}#{k}_#{distance}bp_#{suffix_in}"
        path2="#{prefix}#{k}_#{distance}bp_#{suffix}"
        path3="#{prefix}#{k}_#{distance}bp_#{suffix}.map"
        puts path
        out=File.open(path2, "w")
        out2=File.open(path3, "w")
        File.foreach(path) do |line|
           # puts line
            arr = line.chomp!.split "\t"
            first=arr[1]
            last=arr[2]
            name=arr[0]
            #if(arr[5] == "-")
            #    first=arr[2]
            #    last=arr[1]
            #end
          
            reg =  "#{name}:#{first}-#{last}"
            out.puts reg
            out2.puts [reg,arr[3]].join "\t"
            #puts reg
            #v.bedAroundGene(distance:distance, out:out)
            #break
        end
        out.close
        out2.close
    end
end